Ethylene Regulates Levels of Ethylene Receptor/CTR1 Signaling Complexes in Arabidopsis thaliana

Heavy metals and ethylene: shaping plant responses through signaling

Heavy metal (HM) contamination is an escalating global issue, significantly affecting crop quality and productivity, and this problem is further exacerbated by rapid population growth. HMs impact plant productivity by interfering with a range of morphologic, biochemical, physiologic, and molecular functions, as documented in numerous studies. Upon entry into plant cells, these metals compromise cell membrane integrity, induce reactive oxygen species production in excess, disrupt enzymatic activities, damage photosynthetic pigments and photosystems, and disturb water and nutrient uptake mechanisms. Within the cellular environment, several signaling pathways are either activated or repressed, adjusting cellular responses in accordance with their genetic potential. Phytohormones are key regulators in these processes, utilizing signaling cascades such as mitogen-activated-protein-kinase and calcium dependent pathways. Among them, ethylene, traditionally known for its role in exhibiting critical role in modulating plant responses to HM stress. This review focuses on ethylene's interaction under HM stress, examining its crosstalk with other plant hormones. In addition, it explores HM sources, bioavailability, implications for human health, plant responses to HM exposure, and the influence of ethylene biosynthesis and signaling pathways in the regulation of HM-induced stress responses.

Modulation of plant growth and development through altered ethylene binding affinity of the ethylene receptor ETR1

Arabidopsis senses ethylene through a five-member family of ethylene receptors, of which the ethylene receptor ETR1 plays the major role. We examined how changes in ethylene binding affinity of ETR1 can regulate physiological and molecular responses to ethylene, taking advantage of an Asp25Asn mutation that still produces a functional ETR1 receptor (ETR1D25N) but one with 100-fold reduced ethylene binding affinity compared to wild-type ETR1 (ETR1wt). Analysis was performed in a genetic background that lacks the five native members of the receptor family so that the specific role of ETR1 in plant growth and development could be assessed. From this analysis, we determined that changes in ethylene binding affinity of ETR1 are reflected in plant growth and responses to ethylene. Differences in plant growth and ethylene responses for the ETR1wt and ETR1D25N lines were uncovered in seedlings grown under light or dark conditions, and when assayed for short- or long-term responses to ethylene. Dose response analysis revealed that differences in the ethylene responses for ETR1wt and ETR1D25N lines are proportional to the binding affinity of the corresponding receptor variants. Results from the characterization of the ETR1wt line and an etr1 etr2 ein4 triple mutant demonstrate that plants have greater sensitivity to ethylene than previously recognized.

The RNA helicase LOS4 regulates pre-mRNA splicing of key genes (EIN2, ERS2, CTR1) in the ethylene signaling pathway

KEY MESSAGE

The Arabidopsis RNA helicase LOS4 plays a key role in regulating pre-mRNA splicing of the genes EIN2, CTR1, and ERS2 in ethylene signaling pathway. The plant hormone ethylene plays diverse roles in plant growth, development, and responses to stress. Ethylene is perceived by the membrane-bound ethylene receptors complex, and then triggers downstream components, such as EIN2, to initiate signal transduction into the nucleus, leading to the activation of ethylene-responsive genes. Over the past decades, substantial information has been accumulated regarding gene cloning, protein-protein interactions, and downstream gene expressions in the ethylene pathway. However, our understanding of mRNA post-transcriptional processing and modification of key genes in the ethylene signaling pathway remains limited. This study aims to provide evidence demonstrating the involvement of the Arabidopsis RNA helicase LOS4 in pre-mRNA splicing of the genes EIN2, CTR1, and ERS2 in ethylene signaling pathway. Various genetic approaches including RNAi gene silencing, CRISPR-Cas9 gene editing, and amino acid mutations were employed in this study. When LOS4 was silenced or knocked down, the ethylene sensitivity of etiolated seedlings was significantly enhanced. Further investigation revealed errors in the EIN2 pre-mRNA splicing when LOS4 was knocked down. In addition, aberrant pre-mRNA splicing was observed in the ERS2 and CTR1 genes in the pathway. Biochemical assays indicated that the los4-2 (E94K) mutant protein exhibited increased ATP binding and enhanced ATP hydrolytic activity. Conversely, the los4-1 (G364R) mutant had reduced substrate RNA binding and lower ATP binding activities. These findings significantly advanced our comprehension of the regulatory functions and molecular mechanisms of RNA helicase in ethylene signaling.

Interactions between Brassinosteroids and Strigolactones in Alleviating Salt Stress in Maize

Exogenous brassinolide (BR) and strigolactones (SLs) play an important role in alleviating salt stress in maize. We studied the morphological and physiological responses of the salt-sensitive genotype PH4CV and salt-tolerant genotype Zheng58 to BR (1.65 nM), SL (1 µM), and BS (1.65 nM BR + 1 µM SL) under salt stress. Phenotypic analysis showed that salt stress significantly inhibited the growth of maize seedlings and significantly increased the content of Na+ in the roots. Exogenous hormones increased oxidase activity and decreased Na+ content in the roots and mitigated salt stress. Transcriptome analysis showed that the interaction of BR and SL is involved in photosynthesis-antenna proteins, the TCA cycle, and plant hormone signal transduction pathways. This interaction influences the expression of chlorophyll a/b-binding protein and glucose-6-phosphate isomerase 1 chloroplastic, and aconitase genes are affected. Furthermore, the application of exogenous hormones regulates the expression of genes associated with the signaling pathways of cytokinin (CK), gibberellins (GA), auxin (IAA), brassinosteroid (BR), abscisic acid (ABA), and jasmonic acid (JA). Additionally, exogenous hormones inhibit the expression of the AKT2/3 genes, which are responsible for regulating ion transduction and potassium ion influx. Four candidate genes that may regulate the seedling length of maize were screened out through WGCNA. Respective KOG notes concerned inorganic ion transport and metabolism, signal transduction mechanisms, energy production and conversion, and amino acid transport and metabolism. The findings of this study provide a foundation for the proposition that BR and SL can be employed to regulate salt stress alleviation in maize.

Transcriptomic analysis unveils alterations in the genetic expression profile of tree peony (Paeonia suffruticosa Andrews) infected by Alternaria alternata

BACKGROUND

Black spot disease in tree peony caused by the fungal necrotroph A. alternata, is a primary limiting factor in the production of the tree peony. The intricate molecular mechanisms underlying the tree peony resistance to A. alternata have not been thoroughly investigated.

RESULTS

The present study utilized high-throughput RNA sequencing (RNA-seq) technology to conduct global expression profiling, revealing an intricate network of genes implicated in the interaction between tree peony and A. alternata. RNA-Seq libraries were constructed from leaf samples and high-throughput sequenced using the BGISEQ-500 sequencing platform. Six distinct libraries were characterized. M1, M2 and M3 were derived from leaves that had undergone mock inoculation, while I1, I2 and I3 originated from leaves that had been inoculated with the pathogen. A range of 10.22-11.80 gigabases (Gb) of clean bases were generated, comprising 68,131,232 - 78,633,602 clean bases and 56,677 - 68,996 Unigenes. A grand total of 99,721 Unigenes were acquired, boasting a mean length of 1,266 base pairs. All these 99,721 Unigenes were annotated in various databases, including NR (Non-Redundant, 61.99%), NT (Nucleotide, 45.50%), SwissProt (46.32%), KEGG (Kyoto Encyclopedia of Genes and Genomes, 49.33%), KOG (clusters of euKaryotic Orthologous Groups, 50.18%), Pfam (Protein family, 47.16%), and GO (Gene Ontology, 34.86%). In total, 66,641 (66.83%) Unigenes had matches in at least one database. By conducting a comparative transcriptome analysis of the mock- and A. alternata-infected sample libraries, we found differentially expressed genes (DEGs) that are related to phytohormone signalling, pathogen recognition, active oxygen generation, and circadian rhythm regulation. Furthermore, multiple different kinds of transcription factors were identified. The expression levels of 10 selected genes were validated employing qRT-PCR (quantitative real-time PCR) to confirm RNA-Seq data.

CONCLUSIONS

A multitude of transcriptome sequences have been generated, thus offering a valuable genetic repository for further scholarly exploration on the immune mechanisms underlying the tree peony infected by A. alternata. While the expression of most DEGs increased, a few DEGs showed decreased expression.

Discovery of candidate genes involved in ethylene biosynthesis and signal transduction pathways related to peach bud cold resistance

Background: Low temperature pose significant challenges to peach cultivation, causing severe damage to peach buds and restricting production and distribution. Ethylene, an important phytohormone, plays a critical role in enhancing plant cold resistance. Structural genes and transcription factors involved in ethylene biosynthesis and signal transduction pathways are associated with cold resistance. However, no research has specifically addressed their roles in peach cold resistance. Methods: In this study, we aimed for cold-resistance gene discovery in cold-sensitive peach cultivar "21Shiji" (21SJ) and cold-resistance cultivar "Shijizhixing" (SJZX) using RNA-seq and gas chromatography. Results: The findings revealed that under cold stress conditions, ethylene biosynthesis in "SJZX" was significantly induced. Subsequently, a structural gene, PpACO1-1, involved in ethylene biosynthesis in peach buds was significantly upregulated and showed a higher correlation with ethylene release rate. To identify potential transcription factors associated with PpACO1-1 expression and ethylene signal transduction, weighted gene co-expression network analysis was conducted using RNA-seq data. Four transcription factors: PpERF2, PpNAC078, PpWRKY65 and PpbHLH112, were identified. Conclusion: These findings provide valuable theoretical insights for investigating the regulatory mechanisms of peach cold resistance and guiding breeding strategies.

Ethylene biosynthesis and signal transduction during ripening and softening in non-climacteric fruits: an overview

In recent years, the ethylene-mediated ripening and softening of non-climacteric fruits have been widely mentioned. In this paper, recent research into the ethylene-mediated ripening and softening of non-climacteric fruits is summarized, including the involvement of ethylene biosynthesis and signal transduction. In addition, detailed studies on how ethylene interacts with other hormones to regulate the ripening and softening of non-climacteric fruits are also reviewed. These findings reveal that many regulators of ethylene biosynthesis and signal transduction are linked with the ripening and softening of non-climacteric fruits. Meanwhile, the perspectives of future research on the regulation of ethylene in non-climacteric fruit are also proposed. The overview of the progress of ethylene on the ripening and softening of non-climacteric fruit will aid in the identification and characterization of key genes associated with ethylene perception and signal transduction during non-climacteric fruit ripening and softening.

Recent Advances in Dissecting the Function of Ethylene in Interaction between Host and Pathogen

Pathogens influence the growth and development of plants, resulting in detrimental damage to their yields and quality. Ethylene, a gaseous phytohormone, serves a pivotal function in modulating diverse physiological processes in plants, including defense mechanisms against pathogen invasion. Ethylene biosynthesis is involved in both plants and pathogens. Recent empirical research elucidates the intricate interactions and regulatory mechanisms between ethylene and pathogens across various plant species. In this review, we provide a comprehensive overview of the latest findings concerning ethylene's role and its regulatory networks in host-pathogen interactions. Additionally, we explore the crosstalk between ethylene and other phytohormones. Points regarding ethylene emission and its modulation by pathogens are also emphasized. Moreover, we also discuss potential unresolved issues in the field that warrant further investigation.

Defense signaling pathways in resistance to plant viruses: Crosstalk and finger pointing

Resistance to infection by plant viruses involves proteins encoded by plant resistance (R) genes, viz., nucleotide-binding leucine-rich repeats (NLRs), immune receptors. These sensor NLRs are activated either directly or indirectly by viral protein effectors, in effector-triggered immunity, leading to induction of defense signaling pathways, resulting in the synthesis of numerous downstream plant effector molecules that inhibit different stages of the infection cycle, as well as the induction of cell death responses mediated by helper NLRs. Early events in this process involve recognition of the activation of the R gene response by various chaperones and the transport of these complexes to the sites of subsequent events. These events include activation of several kinase cascade pathways, and the syntheses of two master transcriptional regulators, EDS1 and NPR1, as well as the phytohormones salicylic acid, jasmonic acid, and ethylene. The phytohormones, which transit from a primed, resting states to active states, regulate the remainder of the defense signaling pathways, both directly and by crosstalk with each other. This regulation results in the turnover of various suppressors of downstream events and the synthesis of various transcription factors that cooperate and/or compete to induce or suppress transcription of either other regulatory proteins, or plant effector molecules. This network of interactions results in the production of defense effectors acting alone or together with cell death in the infected region, with or without the further activation of non-specific, long-distance resistance. Here, we review the current state of knowledge regarding these processes and the components of the local responses, their interactions, regulation, and crosstalk.

GLABROUS INFLORESCENCE STEMS3 binds to and activates RHD2 and RHD4 genes to promote root hair elongation in Arabidopsis

Root hairs are crucial in the uptake of essential nutrients and water in plants. This study showed that a zinc finger protein, GIS3 is involved in root hair growth in Arabidopsis. The loss-of-function gis3 and GIS3 RNAi transgenic line exhibited a significant reduction in root hairs compared to the wild type. The application of 1-aminocyclopropane-1-carboxylic acid (ACC), an exogenous ethylene precursor, and 6-benzyl amino purine (BA), a synthetic cytokinin, significantly restored the percentage of hair cells in the epidermis in gis3 and induced GIS3 expression in the wild type. More importantly, molecular and genetic studies revealed that GIS3 acts upstream of ROOT HAIR DEFECTIVE 2 (RHD2) and RHD4 by binding to their promoters. Furthermore, exogenous ACC and BA application significantly induced the expression of RHD2 and RHD4, while root hair phenotype of rhd2-1, rhd4-1, and rhd4-3 was insensitive to ACC and BA treatment. We can therefore conclude that GIS3 modulates root hair development by directly regulating RHD2 and RHD4 expression through ethylene and cytokinin signals in Arabidopsis.

Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants

The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.

Are Histidine Kinases of Arbuscular Mycorrhizal Fungi Involved in the Response to Ethylene and Cytokinins?

Signals are exchanged at all stages of the arbuscular mycorrhizal (AM) symbiosis between fungi and their host plants. Root-exuded strigolactones are well-known early symbiotic cues, but the role of other phytohormones as interkingdom signals has seldom been investigated. Here we focus on ethylene and cytokinins, for which candidate receptors have been identified in the genome of the AM fungus Rhizophagus irregularis. Ethylene is known from the literature to affect asymbiotic development of AM fungi, and in the present study, we found that three cytokinin forms could stimulate spore germination in R. irregularis. Heterologous complementation of a Saccharomyces cerevisiae mutant strain with the candidate ethylene receptor RiHHK6 suggested that this protein can sense and transduce an ethylene signal. Accordingly, its N-terminal domain expressed in Pichia pastoris displayed saturable binding to radiolabeled ethylene. Thus, RiHHK6 displays the expected characteristics of an ethylene receptor. In contrast, the candidate cytokinin receptor RiHHK7 did not complement the S. cerevisiae mutant strain or Medicago truncatula cytokinin receptor mutants and seemed unable to bind cytokinins, suggesting that another receptor is involved in the perception of these phytohormones. Taken together, our results support the hypothesis that AM fungi respond to a range of phytohormones and that these compounds bear multiple functions in the rhizosphere beyond their known roles as internal plant developmental regulators. Our analysis of two phytohormone receptor candidates also sheds new light on the possible perception mechanisms in AM fungi. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Role of EIN2-mediated ethylene signaling in regulating petal senescence, abscission, reproductive development, and hormonal crosstalk in tobacco

Ethylene plays a pivotal role in a wide range of developmental, physiological, and defense processes in plants. EIN2 (ETHYLENE INSENSITIVE2) is a key player in the ethylene signaling pathway. To characterize the role of EIN2 in processes, such as petal senescence, where it has been found to play important roles along with various other developmental and physiological processes, the tobacco (Nicotiana tabacum) ortholog of EIN2 (NtEIN2) was isolated and NtEIN2 silenced transgenic lines were generated using RNA interference (RNAi). Silencing of NtEIN2 compromised plant defense against pathogens. NtEIN2 silenced lines displayed significant delays in petal senescence, and pod maturation, and adversely affected pod and seed development. This study further dissected the petal senescence in ethylene insensitive lines, that displayed alteration in the pattern of petal senescence and floral organ abscission. Delay in petal senescence was possibly because of delayed aging processes within petal tissues. Possible crosstalk between EIN2 and AUXIN RESPONSE FACTOR 2 (ARF2) in regulating the petal senescence process was also investigated. Overall, these experiments indicated a crucial role for NtEIN2 in controlling diverse developmental and physiological processes, especially in petal senescence.

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.

Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis

The gaseous hormone ethylene is perceived in plants by membrane-bound receptors, the best studied of these being ETR1 from Arabidopsis. Ethylene receptors can mediate a response to ethylene concentrations at less than one part per billion; however, the mechanistic basis for such high-affinity ligand binding has remained elusive. Here we identify an Asp residue within the ETR1 transmembrane domain that plays a critical role in ethylene binding. Site-directed mutation of the Asp to Asn results in a functional receptor that has a reduced affinity for ethylene, but still mediates ethylene responses in planta. The Asp residue is highly conserved among ethylene receptor-like proteins in plants and bacteria, but Asn variants exist, pointing to the physiological relevance of modulating ethylene-binding kinetics. Our results also support a bifunctional role for the Asp residue in forming a polar bridge to a conserved Lys residue in the receptor to mediate changes in signaling output. We propose a new structural model for the mechanism of ethylene binding and signal transduction, one with similarities to that found in a mammalian olfactory receptor.

A CsEIL3-CsARN6.1 module promotes waterlogging-triggered adventitious root formation in cucumber by activating the expression of CsPrx5

The formation of adventitious roots (ARs) derived from hypocotyl is the most important morphological adaptation to waterlogging stress in Cucumis sativus (cucumber). Our previous study showed that cucumbers with the gene CsARN6.1, encoding an AAA ATPase domain-containing protein, were more tolerant to waterlogging through increased AR formation. However, the apparent function of CsARN6.1 remained unknown. Here, we showed that the CsARN6.1 signal was predominantly observed throughout the cambium of hypocotyls, where de novo AR primordia are formed upon waterlogging treatment. The silencing of CsARN6.1 expression by virus-induced gene silencing and CRISPR/Cas9 technologies adversely affects the formation of ARs under conditions of waterlogging. Waterlogging treatment significantly induced ethylene production, thus upregulating CsEIL3 expression, which encodes a putative transcription factor involved in ethylene signaling. Furthermore, yeast one-hybrid, electrophoretic mobility assay and transient expression analyses showed that CsEIL3 binds directly to the CsARN6.1 promoter to initiate its expression. CsARN6.1 was found to interact with CsPrx5, a waterlogging-responsive class-III peroxidase that enhanced H₂ O₂ production and increased AR formation. These data provide insights into understanding the molecular mechanisms of AAA ATPase domain-containing protein and uncover a molecular mechanism that links ethylene signaling with the formation of ARs triggered by waterlogging.

Ethylene-triggered subcellular trafficking of CTR1 enhances the response to ethylene gas

The phytohormone ethylene controls plant growth and stress responses. Ethylene-exposed dark-grown Arabidopsis seedlings exhibit dramatic growth reduction, yet the seedlings rapidly return to the basal growth rate when ethylene gas is removed. However, the underlying mechanism governing this acclimation of dark-grown seedlings to ethylene remains enigmatic. Here, we report that ethylene triggers the translocation of the Raf-like protein kinase CONSTITUTIVE TRIPLE RESPONSE1 (CTR1), a negative regulator of ethylene signaling, from the endoplasmic reticulum to the nucleus. Nuclear-localized CTR1 stabilizes the ETHYLENE-INSENSITIVE3 (EIN3) transcription factor by interacting with and inhibiting EIN3-BINDING F-box (EBF) proteins, thus enhancing the ethylene response and delaying growth recovery. Furthermore, Arabidopsis plants with enhanced nuclear-localized CTR1 exhibited improved tolerance to drought and salinity stress. These findings uncover a mechanism of the ethylene signaling pathway that links the spatiotemporal dynamics of cellular signaling components to physiological responses.

Ethylene: A Master Regulator of Plant-Microbe Interactions under Abiotic Stresses

The plant phytohormone ethylene regulates numerous physiological processes and contributes to plant-microbe interactions. Plants induce ethylene production to ward off pathogens after recognition of conserved microbe-associated molecular patterns (MAMPs). However, plant immune responses against pathogens are essentially not different from those triggered by neutral and beneficial microbes. Recent studies indicate that ethylene is an important factor for beneficial plant-microbial association under abiotic stress such as salt and heat stress. The association of beneficial microbes with plants under abiotic stresses modulates ethylene levels which control the expression of ethylene-responsive genes (ERF), and ERFs further regulate the plant transcriptome, epi-transcriptome, Na⁺/K⁺ homeostasis and antioxidant defense mechanisms against reactive oxygen species (ROS). Understanding ethylene-dependent plant-microbe interactions is crucial for the development of new strategies aimed at enhancing plant tolerance to harsh environmental conditions. In this review, we underline the importance of ethylene in beneficial plant-microbe interaction under abiotic stresses.

Heteromeric interactions of ripening-related ethylene receptors in tomato fruit

Ripening of climacteric fruits is initiated when the gaseous plant hormone ethylene is perceived by the cell. Ethylene binding to membrane-associated ethylene receptors (ETRs) triggers a series of biochemical events through multiple components, resulting in the induction of numerous ripening-related genes. In tomato (Solanum lycopersicum L.), there are seven members of the ETR family, which each contribute to the regulation of fruit ripening. However, the relative contribution of each individual receptor to ethylene signaling remains unknown. Here, we demonstrated the formation of heteromeric receptor complexes across the two ETR subfamilies in tomato fruit. Immunoprecipitation of subfamily II SlETR4 resulted in co-purification of subfamily I (SlETR1, SlETR2, and SlETR3), but not subfamily II members (SlETR5, SlETR6, and SlETR7). Such biased interactions were verified in yeast two-hybrid assays, and in transgenic Arabidopsis plants, in which heterologous SlETR4 interacts with subfamily I ETRs. Our analysis also revealed that the receptor complexes engage the Raf-like protein kinases SlCTR1 and SlCTR3, which are potential regulators of signaling. Here, we suggest that tomato receptor members form heteromeric complexes to fine-tune signal output to the downstream pathway, which is similar to that of the Arabidopsis system but appears to be partially diverged.

Transcriptome Analysis of Soursop (Annona muricata L.) Fruit under Postharvest Storage Identifies Genes Families Involved in Ripening

Soursop (Annona muricata L.) is climacteric fruit with a short ripening period and postharvest shelf life, leading to a rapid softening. In this study, transcriptome analysis of soursop fruits was performed to identify key gene families involved in ripening under postharvest storage conditions (Day 0, Day 3 stored at 28 ± 2 °C, Day 6 at 28 ± 2 °C, Day 3 at 15 ± 2 °C, Day 6 at 15 ± 2 °C, Day 9 at 15 ± 2 °C). The transcriptome analysis showed 224,074 transcripts assembled clustering into 95, 832 unigenes, of which 21, 494 had ORF. RNA-seq analysis showed the highest number of differentially expressed genes on Day 9 at 15 ± 2 °C with 9291 genes (4772 up-regulated and 4519 down-regulated), recording the highest logarithmic fold change in pectin-related genes. Enrichment analysis presented significantly represented GO terms and KEGG pathways associated with molecular function, metabolic process, catalytic activity, biological process terms, as well as biosynthesis of secondary metabolites, plant hormone signal, starch, and sucrose metabolism, plant–pathogen interaction, plant–hormone signal transduction, and MAPK-signaling pathways, among others. Network analysis revealed that pectinesterase genes directly regulate the loss of firmness in fruits stored at 15 ± 2 °C.

Bacterial Modulation of the Plant Ethylene Signaling Pathway Improves Tolerance to Salt Stress in Lettuce (Lactuca sativa L.)

Salinity has extensive adverse effects on plant growth and the development of new agronomic strategies to improve crop salt tolerance is becoming necessary. Currently, the use of plant growth promoting rhizobacteria (PGPR) to mitigate abiotic stress in crops is of increasing interest. The most analyzed mechanism is based on ACC deaminase activity, an enzyme that decreases the ethylene synthesis, an important phytohormone in plant stress response. We aimed to identify other PGPR mediated mechanisms involved in the regulation of salt stress in plant. We used three PGPR strains (ESL001, ESL007, SH31), of which only ESL007 demonstrated ACC deaminase activity, to evaluate their effect on lettuce plants under salt stress (100 mM NaCl). We measured growth and biochemical parameters (e.g., proline content, lipid peroxidation and ROS degradation), as well as expression levels of genes involved in ethylene signaling (CTR1, EBF1) and transcription factors induced by ethylene (ERF5, ERF13). All bacterial strains enhanced growth on salt-stressed lettuce plants and modulated the proline levels. Strains ESL007 and SH31 triggered a higher catalase and ascorbate-peroxidase activity, compared to non-stressed plants. Differential expression of ethylene-related genes in inoculated plants subjected to salinity was observed. We gained consistent evidence for the existence of alternative mechanisms to ethylene modulation, which probably rely on bacterial IAA production and other chemical signals. These mechanisms modify the expression of genes associated with ethylene signaling and regulation, complementarily to the ACC deaminase model to diminish abiotic stress responses.

To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses

Plants often live in adverse environmental conditions and are exposed to various stresses, such as heat, cold, heavy metals, salt, radiation, poor lighting, nutrient deficiency, drought, or flooding. To adapt to unfavorable environments, plants have evolved specialized molecular mechanisms that serve to balance the trade-off between abiotic stress responses and growth. These mechanisms enable plants to continue to develop and reproduce even under adverse conditions. Ethylene, as a key growth regulator, is leveraged by plants to mitigate the negative effects of some of these stresses on plant development and growth. By cooperating with other hormones, such as jasmonic acid (JA), abscisic acid (ABA), brassinosteroids (BR), auxin, gibberellic acid (GA), salicylic acid (SA), and cytokinin (CK), ethylene triggers defense and survival mechanisms thereby coordinating plant growth and development in response to abiotic stresses. This review describes the crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses.

A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.)

Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.

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.

Plants Saline Environment in Perception with Rhizosphere Bacteria Containing 1-Aminocyclopropane-1-Carboxylate Deaminase

Soil salinity stress has become a serious roadblock for food production worldwide since it is one of the key factors affecting agricultural productivity. Salinity and drought are predicted to cause considerable loss of crops. To deal with this difficult situation, a variety of strategies have been developed, including plant breeding, plant genetic engineering, and a wide range of agricultural practices, including the use of plant growth-promoting rhizobacteria (PGPR) and seed biopriming techniques, to improve the plants' defenses against salinity stress, resulting in higher crop yields to meet future human food demand. In the present review, we updated and discussed the negative effects of salinity stress on plant morphological parameters and physio-biochemical attributes via various mechanisms and the beneficial roles of PGPR with 1-Aminocyclopropane-1-Carboxylate(ACC) deaminase activity as green bio-inoculants in reducing the impact of saline conditions. Furthermore, the applications of ACC deaminase-producing PGPR as a beneficial tool in seed biopriming techniques are updated and explored. This strategy shows promise in boosting quick seed germination, seedling vigor and plant growth uniformity. In addition, the contentious findings of the variation of antioxidants and osmolytes in ACC deaminase-producing PGPR treated plants are examined.

Varied Expression of Senescence-Associated and Ethylene-Related Genes during Postharvest Storage of Brassica Vegetables

The genus Brassica comprises a highly diverse range of vegetable crops varying in morphology, harvestable crop product, and postharvest shelf-life that has arisen through domestication, artificial selection and plant breeding. Previous postharvest studies on the shelf-life of Brassica species has mainly focused on the variable rates of physiological changes including respiration and transpiration. Therefore, further understanding of the molecular basis of postharvest senescence in Brassica vegetables is needed to understand its progression in improving their postharvest shelf-life. The aim of this study was to better understand the trajectory of molecular responses in senescence-associated genes but not induced by ethylene and ethylene-induced genes towards altered postharvest storage conditions. After storage at different temperatures, the expression levels of the key senescence-associated genes (SAGs) and the ethylene biosynthesis, perception, and signaling genes were quantitatively analyzed in cabbage, broccoli and kale. The expression levels of these genes were tightly linked to storage temperature and phase of senescence. Expression of ORE15, SAG12, and NAC29 were continuously increased during the twelve days of postharvest storage at room temperature. Prolonged exposure of these three vegetables to cold temperature reduced the variation in the expression levels of ORE15 and SAG12, observed as mostly decreased which resulted in limiting senescence. The transcript levels of the ethylene receptor were also decreased at lower temperature, further suggesting that decreased ethylene biosynthesis and signaling in cabbage during postharvest storage would delay the senescence mechanism. These results enhanced our understanding of the transcriptional changes in ethylene-independent SAGs and ethylene-related genes in postharvest senescence, as well as the timing and temperature sensitive molecular events associated with senescence in cabbage, broccoli and kale and this knowledge can potentially be used for the improvement of postharvest storage in Brassica vegetables.

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.

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.

Loss of function of CRT1a (calreticulin) reduces plant susceptibility to Verticillium longisporum in both Arabidopsis thaliana and oilseed rape (Brassica napus)

Brassica napus is highly susceptible towards Verticillium longisporum (Vl43) with no effective genetic resistance. It is believed that the fungus reprogrammes plant physiological processes by up-regulation of so-called susceptibility factors to establish a compatible interaction. By transcriptome analysis, we identified genes, which were activated/up-regulated in rapeseed after Vl43 infection. To test whether one of these genes is functionally involved in the infection process and loss of function would lead to decreased susceptibility, we firstly challenged KO lines of corresponding Arabidopsis orthologs with Vl43 and compared them with wild-type plants. Here, we report that the KO of AtCRT1a results in drastically reduced susceptibility of plants to Vl43. To prove crt1a mutation also decreases susceptibility in B. napus, we identified 10 mutations in a TILLING population. Three T3 mutants displayed increased resistance as compared to the wild type. To validate the results, we generated CRISPR/Cas-induced BnCRT1a mutants, challenged T2 plants with Vl43 and observed an overall reduced susceptibility in 3 out of 4 independent lines. Genotyping by allele-specific sequencing suggests a major effect of mutations in the CRT1a A-genome copy, while the C-genome copy appears to have no significant impact on plant susceptibility when challenged with Vl43. As revealed by transcript analysis, the loss of function of CRT1a results in activation of the ethylene signalling pathway, which may contribute to reduced susceptibility. Furthermore, this study demonstrates a novel strategy with great potential to improve plant disease resistance.

Receptor-Like Protein Kinases Function Upstream of MAPKs in Regulating Plant Development

Mitogen-activated protein kinases (MAPKs) are a group of protein kinase broadly involved in various signal pathways in eukaryotes. In plants, MAPK cascades regulate growth, development, stress responses and immunity by perceiving signals from the upstream regulators and transmitting the phosphorylation signals to the downstream signaling components. To reveal the interactions between MAPK cascades and their upstream regulators is important for understanding the functional mechanisms of MAPKs in the life span of higher plants. Typical receptor-like protein kinases (RLKs) are plasma membrane-located to perceive endogenous or exogenous signal molecules in regulating plant growth, development and immunity. MAPK cascades bridge the extracellular signals and intracellular transcription factors in many RLK-mediated signaling pathways. This review focuses on the current findings that RLKs regulate plant development through MAPK cascades and discusses questions that are worth investigating in the near future.

Transcriptome and phytohormone changes associated with ethylene-induced onion bulb dormancy

Control of dormancy and sprouting in onion bulbs is commercially important for postharvest management. Although ethylene application is sometimes used to extend dormancy, the underlying mechanisms regulating dormancy transition remain unclear. Since the sprout leaves emerge from the bulb baseplate, we used this tissue to assess the impact of ethylene treatment and storage time on the hormone profile and the transcriptome. Reads from 30 libraries were assembled and annotated, with 94,840 unigenes retained after filtering. The de novo transcriptome assembly was of high quality and continuity (N50: 1809 bp, GC content: 36.21 %), and was used to analyse differential expression and Gene Onotologies. Across two years, applied ethylene resulted in delayed dormancy break and reduced post-dormancy sprout vigour. Ethylene supplementation enhanced endogenous ethylene production and caused a transient climacteric-like increase in respiration. Significant changes in hormone and associated transcript profiles occurred through storage and in response to ethylene. In particular, abscisic acid (ABA) and its metabolite phaseic acid (PA) increased under ethylene during the longer dormancy period; however, cytokinin increases observed during storage appeared largely independent of ethylene treatment. Several hormone-related transcripts showed differential expression over time and/or in response to ethylene. Expression of ethylene biosynthesis (ACO), receptor (EIN4) and transcription factor (EIL3) genes were modified by ethylene, as were ABA biosynthesis genes such NCED, and cytokinin biosynthesis genes such as LOG and CKX. We conclude that ethylene substantially modifies expression of genes in several phytohormone pathways, and some of these changes may underlie the dormancy-extending effects of exogenous ethylene.

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.

Hormonal regulation of root hair growth and responses to the environment in Arabidopsis

The main functions of plant roots are water and nutrient uptake, soil anchorage, and interaction with soil-living biota. Root hairs, single cell tubular extensions of root epidermal cells, facilitate or enhance these functions by drastically enlarging the absorptive surface. Root hair development is constantly adapted to changes in the root's surroundings, allowing for optimization of root functionality in heterogeneous soil environments. The underlying molecular pathway is the result of a complex interplay between position-dependent signalling and feedback loops. Phytohormone signalling interconnects this root hair signalling cascade with biotic and abiotic changes in the rhizosphere, enabling dynamic hormone-driven changes in root hair growth, density, length, and morphology. This review critically discusses the influence of the major plant hormones on root hair development, and how changes in rhizosphere properties impact on the latter.

Different regulatory modules of two mango ERS1 promoters modulate specific gene expression in response to phytohormones in transgenic model plants

Ethylene is a key element of plant physiology, thus ethylene research is important for both, fundamental research and agriculture. Previous work on ethylene receptors focused on expression level and protein interaction, but knowledge on regulation of gene transcription is scarce. Promoters of mango ethylene receptor genes (pMiERS1a, pMiERS1b) were analysed particularly regarding responsiveness to hormones. The promoter sequences reveal some variation and they were characterized by identifying functional regulatory candidate modules via truncated-promoter approach. Based on ectopic gene expression studies in transgenic Arabidopsis and Nicotiana it is demonstrated that both promoters are positively responsive to ethylene. For pMiERS1a the AHBP/DOFF1 module is linked to ethylene responsiveness, while for pMiERS1b it is the module MYBL/OPAQ1. A negative gene regulation in response to abscisic acid (ABA) is linked to MYBL/DOFF2. A positive response to indole-3-acetic acid (IAA) was found for GTBX/MYCL1, containing the motifs IBOX/IDDF/TEFB, which are present in this combination only in pMiERS1b, but not in pMiERS1a. Conclusively, the general response of the ethylene receptor genes is conserved, but similar regulation can be linked to different modules. Further, a minor variation in a transcription factor binding site (TFBS) motif within an overall conserved module type can lead to a different expression.

New Insights in Transcriptional Regulation of the Ethylene Response in Arabidopsis

As any living organisms, plants must respond to a wide variety of environmental stimuli. Plant hormones regulate almost all aspects of plant growth and development. Among all the plant hormones, ethylene is the only gaseous plant hormone that plays pleiotropic roles in plant growth, plant development and stress responses. Transcription regulation is one main mechanism by which a cell orchestrates gene activity. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Here we review the progress of transcription regulation in the ethylene response.

A Functional Connection between the Circadian Clock and Hormonal Timing in Arabidopsis

The rotation of the Earth entails changes in environmental conditions that pervasively influence an organism's physiology and metabolism. An internal cellular mechanism known as the circadian clock acts as an internal timekeeper that is able to perceive the changes in environmental cues to generate 24-h rhythms in synchronization with daily and seasonal fluctuations. In plants, the circadian clock function is particularly important and regulates nearly every aspect of plant growth and development as well as proper responses to stresses. The circadian clock does not function in isolation but rather interconnects with an intricate network of different pathways, including those of phytohormones. Here, we describe the interplay of the circadian clock with a subset of hormones in Arabidopsis. The molecular components directly connecting the circadian and hormone pathways are described, highlighting the biological significance of such connections in the control of growth, development, fitness, and survival. We focus on the overlapping as well as contrasting circadian and hormonal functions that together provide a glimpse on how the Arabidopsis circadian system regulates hormone function in response to endogenous and exogenous cues. Examples of feedback regulation from hormone signaling to the clock are also discussed.

Phytohormones enhanced drought tolerance in plants: a coping strategy

Drought stress is a severe environmental constraint among the emerging problems. Plants are highly vulnerable to drought stress and a severe decrease in yield was recorded in the last few decades. So, it is highly desirable to understand the mechanism of drought tolerance in plants and consequently enhance the tolerance against drought stress. Phytohormones are known to play vital roles in regulating various phenomenons in plants to acclimatize to varying drought environment. Abscisic acid (ABA) is considered the main hormone which intensifies drought tolerance in plants through various morpho-physiological and molecular processes including stomata regulation, root development, and initiation of ABA-dependent pathway. In addition, jasmonic acid (JA), salicylic acid (SA) ethylene (ET), auxins (IAA), gibberellins (GAs), cytokinins (CKs), and brassinosteroids (BRs) are also very important phytohormones to congregate the challenges of drought stress. However, these hormones are usually cross talk with each other to increase the survival of plants in drought conditions. On the other hand, the transgenic approach is currently the most accepted technique to engineer the genes responsible for the synthesis of phytohormones in drought stress response. Our present review highlights the regulatory circuits of phytohormones in drought tolerance mechanism.

Plant Hormone Signaling Crosstalks between Biotic and Abiotic Stress Responses

In the natural environment, plants are often bombarded by a combination of abiotic (such as drought, salt, heat or cold) and biotic (necrotrophic and biotrophic pathogens) stresses simultaneously. It is critical to understand how the various response pathways to these stresses interact with one another within the plants, and where the points of crosstalk occur which switch the responses from one pathway to another. Calcium sensors are often regarded as the first line of response to external stimuli to trigger downstream signaling. Abscisic acid (ABA) is a major phytohormone regulating stress responses, and it interacts with the jasmonic acid (JA) and salicylic acid (SA) signaling pathways to channel resources into mitigating the effects of abiotic stresses versus defending against pathogens. The signal transduction in these pathways are often carried out via GTP-binding proteins (G-proteins) which comprise of a large group of proteins that are varied in structures and functions. Deciphering the combined actions of these different signaling pathways in plants would greatly enhance the ability of breeders to develop food crops that can thrive in deteriorating environmental conditions under climate change, and that can maintain or even increase crop yield.

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes

BACKGROUND

Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both reproducibility and reliability of RNA-seq results, there are still limitations and bias on the detectability for certain differentially expressed genes (DEGs). Whether the transcriptional dynamics of a gene can be captured accurately depends on experimental design/operation and the following data analysis processes. The workflow of subsequent data processing, such as reads alignment, transcript quantification, normalization, and statistical methods for ultimate identification of DEGs can influence the accuracy and sensitivity of DEGs analysis, producing a certain number of false-positivity or false-negativity. Machine learning (ML) is a multidisciplinary field that employs computer science, artificial intelligence, computational statistics and information theory to construct algorithms that can learn from existing data sets and to make predictions on new data set. ML-based differential network analysis has been applied to predict stress-responsive genes through learning the patterns of 32 expression characteristics of known stress-related genes. In addition, the epigenetic regulation plays critical roles in gene expression, therefore, DNA and histone methylation data has been shown to be powerful for ML-based model for prediction of gene expression in many systems, including lung cancer cells. Therefore, it is promising that ML-based methods could help to identify the DEGs that are not identified by traditional RNA-seq method.

RESULTS

We identified the top 23 most informative features through assessing the performance of three different feature selection algorithms combined with five different classification methods on training and testing data sets. By comprehensive comparison, we found that the model based on InfoGain feature selection and Logistic Regression classification is powerful for DEGs prediction. Moreover, the power and performance of ML-based prediction was validated by the prediction on ethylene regulated gene expression and the following qRT-PCR.

CONCLUSIONS

Our study shows that the combination of ML-based method with RNA-seq greatly improves the sensitivity of DEGs identification.

The Pivotal Role of Ethylene in Plant Growth

Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves.

The Pivotal Role of Ethylene in Plant Growth

Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves.

The effect of 1-methylcyclopropene (1-MCP) on expression of ethylene receptor genes in durian pulp during ripening

Rapid fruit ripening is a significant problem that limits the shelf life of durian, with ethylene having a major impact on the regulation of this event. Durian treated with ethephon ripened 3 d after treatment with increased pulp total soluble solids, ethylene production of the whole fruit and decreased pulp firmness compared to the control fruit. 1-MCP treatment delayed ripening by up to 9 d with inhibited accumulation of total soluble solids, color change, softening and ethylene production. Genes related to ethylene perception (DzETR1 and DzETR2) and the signaling pathway (DzCTR1, DzEIL1 and DzEIL2) in the pulp were investigated during this process, using qPCR to quantify changes in gene transcription. All candidate genes were significantly up-regulated in ripening durian pulp. Ethephon treatment increased the expression of DzETR1 and DzETR2 genes, while expression of DzCTR1, DzEIL1 and DzEIL2 were slightly affected. 1-MCP treatment significantly inhibited the expression of the DzETR2 and DzEIL1 genes. The promoters of DzETR2 genes were isolated and their activation by fruit transcription factors studied using transient expression in tobacco leaves. It was found that members of the kiwifruit and apple EIL1, EIL2 and EIL3 genes strongly activated the DzETR2 promoter. These results suggest that ethylene-induced ripening of durian is via the regulation of DzETR2 by EIL transcription factors.

Ethylene-Related Gene Expression Networks in Wood Formation

Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (Populus tremula) stems. ACC synthase expression suggests that the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is synthesized during xylem expansion and xylem cell maturation. Ethylene-mediated transcriptional reprogramming occurs during all stages of secondary growth, as deduced from AspWood expression profiles of ethylene-responsive genes. A network centrality analysis of the AspWood dataset identified EIN3D and 11 ERFs as hubs. No overlap was found between the co-expressed genes of the EIN3 and ERF hubs, suggesting target diversification and hence independent roles for these transcription factor families during normal wood formation. The EIN3D hub was part of a large co-expression gene module, which contained 16 transcription factors, among them several new candidates that have not been earlier connected to wood formation and a VND-INTERACTING 2 (VNI2) homolog. We experimentally demonstrated Populus EIN3D function in ethylene signaling in Arabidopsis thaliana. The ERF hubs ERF118 and ERF119 were connected on the basis of their expression pattern and gene co-expression module composition to xylem cell expansion and secondary cell wall formation, respectively. We hereby establish data resources for ethylene-responsive genes and potential targets for EIN3D and ERF transcription factors in Populus stem tissues, which can help to understand the range of ethylene targeted biological processes during secondary growth.

Histone Deacetylases SRT1 and SRT2 Interact with ENAP1 to Mediate Ethylene-Induced Transcriptional Repression

Ethylene plays pleiotropic roles in plant growth, plant development, and stress responses. Although the effects of ethylene on plants are well documented, little is known about molecular-level events that result in transcriptional repression during the ethylene response. In this study, we found that two histone deacetylases, SRT1 and SRT2, interact with ENAP1, which associates with EIN2 in the nucleus. Genetic and transcriptome analyses revealed that SRT1 and SRT2 are required for negative regulation of certain ethylene-responsive genes. The acetylation of HISTONE3 at K9 (H3K9Ac) is specifically regulated by SRT1 and SRT2 in ethylene-repressed genes. In addition, the srt1 srt2 double mutation in Arabidopsis thaliana suppresses both the ENAP1ox and the EIN3ox constitutive ethylene response phenotypes, and the ethylene-induced transcriptional repression observed in EIN3ox plants is derepressed in the EIN3ox/srt1 srt2 mutant. SRT2 and ENAP1 both bind to promoter regions of genes negatively regulated by ethylene, reducing H3K9Ac levels and resulting in transcriptional repression. This work establishes a mechanism by which histone deacetylases SRT1 and SRT2 interact with ENAP1 to mediate transcriptional repression by regulating the levels of H3K9 acetylation in the ethylene signaling.

Differentially localized rice ethylene receptors OsERS1 and OsETR2 and their potential role during submergence

Ethylene is gaseous plant hormone that controls a variety of physiologic activities. OsERS1 and OsETR2 are major ethylene receptors in rice that have been reported to have different regulatory functions. The GFP fused N-terminus of OsERS1 and OsETR2 showed differentially localization patterns when transiently expressed in onion epidermal cells. Base on these results, we suggested that OsERS1 could be localized to plasma membranes, whereas OsETR2 could be localized to the endoplasmic reticulum. Furthermore, instead of the constitutive expression profile of OsERS1, OsETR2 is differentially expressed in seedlings of light/dark-grown conditions, submergence or exogenous ethylene treatments. Our results and others support the notion that OsERS1 and OsETR2 could have different roles during rice plant submergence.

Analysis of Ethylene Receptor Interactions by Co-immunoprecipitation Assays

Ethylene receptors are predominantly localized to the endoplasmic reticulum (ER) membrane, and coordinate ethylene signal output through protein-protein interactions with each other and additional signaling components. Here, we describe a co-immunoprecipitation (Co-IP) assay based on the use of the Tandem Affinity Purification (TAP) tag to examine the interactions of ethylene receptors in plant extracts. Human IgG-agarose beads are used to pull down TAP-tagged versions of the protein of interest from detergent extracts of Arabidopsis membranes, and the precipitate then is analyzed immunologically for co-purification of the ethylene receptors. This method has been successfully used to examine interactions of the receptors with each other as well as with the Raf-like kinase CTR1.

Localization of the Ethylene-Receptor Signaling Complex to the Endoplasmic Reticulum: Analysis by Two-Phase Partitioning and Density-Gradient Centrifugation

Ethylene receptors and other elements of the ethylene-signal transduction pathway localize to membranes of the endoplasmic reticulum (ER). New players in the ethylene signaling pathway continue to be discovered and so it is important to have methods by which to diagnose their cellular localization. Two methods for microsome isolation and fractionation are described here that can assist in determining if a protein localizes to the ER: aqueous two-phase partitioning and equilibrium density-gradient centrifugation. Two-phase partitioning serves to purify plasma membrane away from other cellular membranes and can thus discriminate whether a protein is localized to the plasma membrane or not. Equilibrium density-gradient centrifugation is particularly useful for resolving if a protein is localized to the ER. Ribosomes are associated with the rough ER in the presence of Mg²⁺ but are stripped away when Mg²⁺is removed from the medium, resulting in a reduction in the ER membrane density and a diagnostic shift in migration when analyzed by equilibrium density-gradient centrifugation. A method for growing plants in liquid culture is also provided because these microsomal membranes exhibit consistent fractionation by both two-phase partitioning and density-gradient centrifugation.

Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing

BACKGROUND

Parthenocarpy is an important trait for yield and quality in many plants. But due to its complex interactions with genetic and physiological factors, it has not been adequately understood and applied to breeding and production. Finding novel and effective quantitative trait loci (QTLs) is a critical step towards understanding its genetic mechanism. Cucumber (Cucumis sativus L.) is a typical parthenocarpic plant but the QTLs controlling parthenocarpy in cucumber were not mapped on chromosomes, and the linked markers were neither user-friendly nor confirmed by previous studies. Hence, we conducted a two-season QTL study of parthenocarpy based on the cucumber genome with 145 F2:3 families derived from a cross between EC1 (a parthenocarpic inbred line) and 8419 s-1 (a non-parthenocarpic inbred line) in order to map novel QTLs. Whole genome re-sequencing was also performed both to develop effective linked markers and to predict candidate genes.

RESULTS

A genetic linkage map, employing 133 Simple Sequence Repeats (SSR) markers and nine Insertion/Deletion (InDel) markers spanning 808.1 cM on seven chromosomes, was constructed from an F2 population. Seven novel QTLs were identified on chromosomes 1, 2, 3, 5 and 7. Parthenocarpy 2.1 (Parth2.1), a QTL on chromosome 2, was a major-effect QTL with a logarithm of odds (LOD) score of 9.0 and phenotypic variance explained (PVE) of 17.0 % in the spring season and with a LOD score of 6.2 and PVE of 10.2 % in the fall season. We confirmed this QTL using a residual heterozygous line97-5 (RHL97-5). Effectiveness of linked markers of the Parth2.1 was validated in F3:4 population and in 21 inbred lines. Within this region, there were 57 genes with nonsynonymous SNPs/InDels in the coding sequence. Based on further combined analysis with transcriptome data between two parents, CsARF19, CsWD40, CsEIN1, CsPPR, CsHEXO3, CsMDL, CsDJC77 and CsSMAX1 were predicted as potential candidate genes controlling parthenocarpy.

CONCLUSIONS

A major-effect QTL Parth2.1 and six minor-effect QTLs mainly contribute to the genetic architecture of parthenocarpy in cucumber. SSR16226 and Indel-T-39 can be used in marker-assisted selection (MAS) of cucumber breeding. Whole genome re-sequencing enhances the efficiency of polymorphic marker development and prediction of candidate genes.