EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis

Arabidopsis RTE1 is essential to ethylene receptor ETR1 amino-terminal signaling independent of CTR1

The Arabidopsis (Arabidopsis thaliana) ethylene receptor Ethylene Response1 (ETR1) can mediate the receptor signal output via its carboxyl terminus interacting with the amino (N) terminus of Constitutive Triple Response1 (CTR1) or via its N terminus (etr1¹⁻³⁴⁹ or the dominant ethylene-insensitive etr1-1¹⁻³⁴⁹) by an unknown mechanism. Given that CTR1 is essential to ethylene receptor signaling and that overexpression of Reversion To Ethylene Sensitivity1 (RTE1) promotes ETR1 N-terminal signaling, we evaluated the roles of CTR1 and RTE1 in ETR1 N-terminal signaling. The mutant phenotype of ctr1-1 and ctr1-2 was suppressed in part by the transgenes etr1¹⁻³⁴⁹ and etr1-1¹⁻³⁴⁹, with etr1-1 conferring ethylene insensitivity. Coexpression of 35S:RTE1 and etr1¹⁻³⁴⁹ conferred ethylene insensitivity in ctr1-1, whereas suppression of the ctr1-1 phenotype by etr1¹⁻³⁴⁹ was prevented by rte1-2. Thus, RTE1 was essential to ETR1 N-terminal signaling independent of the CTR1 pathway. An excess amount of the CTR1 N terminus CTR1⁷⁻⁵⁶⁰ prevented ethylene receptor signaling, and the CTR1⁷⁻⁵⁶⁰ overexpressor CTR1-Nox showed a constitutive ethylene response phenotype. Expression of the ETR1 N terminus suppressed the CTR1-Nox phenotype. etr1¹⁻³⁴⁹ restored the ethylene insensitivity conferred by dominant receptor mutant alleles in the ctr1-1 background. Therefore, ETR1 N-terminal signaling was not mediated by full-length ethylene receptors; rather, full-length ethylene receptors acted cooperatively with the ETR1 N terminus to mediate the receptor signal independent of CTR1. ETR1 N-terminal signaling may involve RTE1, receptor cooperation, and negative regulation by the ETR1 carboxyl terminus.

Ethylene signaling negatively regulates freezing tolerance by repressing expression of CBF and type-A ARR genes in Arabidopsis

The phytohormone ethylene regulates multiple aspects of plant growth and development and responses to environmental stress. However, the exact role of ethylene in freezing stress remains unclear. Here, we report that ethylene negatively regulates plant responses to freezing stress in Arabidopsis thaliana. Freezing tolerance was decreased in ethylene overproducer1 and by the application of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid but increased by the addition of the ethylene biosynthesis inhibitor aminoethoxyvinyl glycine or the perception antagonist Ag+. Furthermore, ethylene-insensitive mutants, including etr1-1, ein4-1, ein2-5, ein3-1, and ein3 eil1, displayed enhanced freezing tolerance. By contrast, the constitutive ethylene response mutant ctr1-1 and EIN3-overexpressing plants exhibited reduced freezing tolerance. Genetic and biochemical analyses revealed that EIN3 negatively regulates the expression of CBFs and type-A Arabidopsis response regulator5 (ARR5), ARR7, and ARR15 by binding to specific elements in their promoters. Overexpression of these ARR genes enhanced the freezing tolerance of plants. Thus, our study demonstrates that ethylene negatively regulates cold signaling at least partially through the direct transcriptional control of cold-regulated CBFs and type-A ARR genes by EIN3. Our study also provides evidence that type-A ARRs function as key nodes to integrate ethylene and cytokinin signaling in regulation of plant responses to environmental stress.

Cyanide is an adequate agonist of the plant hormone ethylene for studying signalling of sensor kinase ETR1 at the molecular level

The plant hormone ethylene is involved in many developmental processes and responses to environmental stresses in plants. Although the elements of the signalling cascade and the receptors operating the ethylene pathway have been identified, a detailed understanding of the molecular processes related to signal perception and transfer is still lacking. Analysis of these processes using purified proteins in physical, structural and functional studies is complicated by the gaseous character of the plant hormone. In the present study, we show that cyanide, a π-acceptor compound and structural analogue of ethylene, is a suitable substitute for the plant hormone for in vitro studies with purified proteins. Recombinant ethylene receptor protein ETR1 (ethylene-resistant 1) showed high level and selective binding of [14C]cyanide in the presence of copper, a known cofactor in ethylene binding. Replacement of Cys65 in the ethylene-binding domain by serine dramatically reduced binding of radiolabelled cyanide. In contrast with wild-type ETR1, autokinase activity of the receptor is not reduced in the ETR1-C65S mutant upon addition of cyanide. Additionally, protein–protein interaction with the ethylene signalling protein EIN2 (ethylene-insensitive 2) is considerably sustained by cyanide in wild-type ETR1, but is not affected in the mutant. Further evidence for the structural and functional equivalence of ethylene and cyanide is given by the fact that the ethylene-responsive antagonist silver, which is known to allow ligand binding but prevent intrinsic signal transduction, also allows specific binding of cyanide, but shows no effect on autokinase activity and ETR1–EIN2 interaction.

Four alleles of AtCESA3 form an allelic series with respect to root phenotype in Arabidopsis thaliana

Plant cell shape is determined by the orientation of cellulose microfibrils in the primary cell wall. Consequently, mutations that affect genes encoding the enzymes responsible for the synthesis of cellulose, namely, the cellulose synthase catalytic subunits, can alter cell shape substantially, particularly in the roots of affected plants. The multiple response expansion1 (mre1) mutant of Arabidopsis thaliana results from a point mutation in the AtCESA3 gene, which encodes one of the three isoforms of the cellulose synthase catalytic subunit required for synthesis of cellulose in the primary cell wall. Phenotypic comparison of the mre1 mutant with three other alleles (ectopic lignification1-1, ectopic lignification1-2 and constitutive expression of vsp1) showed that these four alleles form an allelic series with respect to their root phenotypes, with mre1 being the weakest allele identified to date. These analyses demonstrated that sucrose affects a significant alteration of cell shape in the roots of these mutants and likely suppresses root cell division in them as well, and that the chemical aminoisobutyric acid can suppress these effects of sucrose. Interestingly, the cell walls in the roots of these four AtCESA3 alleles contain different percentages of cellulose, and these percentages correlate with the lengths of the roots and cortex cells in these roots when grown on media containing high levels of sucrose.

A loss-of-function mutation in the nucleoporin AtNUP160 indicates that normal auxin signalling is required for a proper ethylene response in Arabidopsis

As part of a continuing effort to elucidate mechanisms that regulate the magnitude of ethylene signalling, an Arabidopsis mutant with an enhanced ethylene response was identified. Subsequent characterization of this loss-of-function mutant revealed severe hypocotyl shortening in the presence of saturating ethylene along with increased expression in leaves of a subset of ethylene-responsive genes. It was subsequently determined by map-based cloning that the mutant (sar1-7) represents a loss-of-function mutation in the previously described nucleoporin AtNUP160 (At1g33410, SAR1). In support of previously reported results, the sar1-7 mutant partially restored auxin responsiveness to roots of an rce1 loss-of-function mutant, indicating that AtNUP160/SAR1 is required for proper expression of factors responsible for the repression of auxin signalling. Analysis of arf7-1/sar1-7 and arf19-1/sar1-7 double mutants revealed that mutations affecting either ARF7 or ARF19 function almost fully blocked manifestation of the sar1-7-dependent ethylene hypersensitivity phenotype, suggesting that ARF7- and ARF19-mediated auxin signalling is responsible for regulating the magnitude of and/or competence for the ethylene response in Arabidopsis etiolated hypocotyls. Consistent with this, addition of auxin to ethylene-treated seedlings resulted in severe hypocotyl shortening, reminiscent of that seen for other eer (enhanced ethylene response) mutants, suggesting that auxin functions in part synergistically with ethylene to control hypocotyl elongation and other ethylene-dependent phenomena.

Arabidopsis ETR1 and ERS1 differentially repress the ethylene response in combination with other ethylene receptor genes

The ethylene response is negatively regulated by a family of five ethylene receptor genes in Arabidopsis (Arabidopsis thaliana). The five members of the ethylene receptor family can physically interact and form complexes, which implies that cooperativity for signaling may exist among the receptors. The ethylene receptor gene mutations etr1-1((C65Y))(for ethylene response1-1), ers1-1((I62P)) (for ethylene response sensor1-1), and ers1(C65Y) are dominant, and each confers ethylene insensitivity. In this study, the repression of the ethylene response by these dominant mutant receptor genes was examined in receptor-defective mutants to investigate the functional significance of receptor cooperativity in ethylene signaling. We showed that etr1-1((C65Y)), but not ers1-1((I62P)), substantially repressed various ethylene responses independent of other receptor genes. In contrast, wild-type receptor genes differentially supported the repression of ethylene responses by ers1-1((I62P)); ETR1 and ETHYLENE INSENSITIVE4 (EIN4) supported ers1-1((I62P)) functions to a greater extent than did ERS2, ETR2, and ERS1. The lack of both ETR1 and EIN4 almost abolished the repression of ethylene responses by ers1(C65Y), which implied that ETR1 and EIN4 have synergistic effects on ers1(C65Y) functions. Our data indicated that a dominant ethylene-insensitive receptor differentially repressed ethylene responses when coupled with a wild-type ethylene receptor, which supported the hypothesis that the formation of a variety of receptor complexes may facilitate differential receptor signal output, by which ethylene responses can be repressed to different extents. We hypothesize that plants can respond to a broad ethylene concentration range and exhibit tissue-specific ethylene responsiveness with differential cooperation of the multiple ethylene receptors.

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

The root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. Elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (Oryza sativa). As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray approach. The crown root was divided into eight developmental stages along the longitudinal axis and three radial tissue types at two different developmental stages, namely: epidermis, exodermis and sclerenchyma; cortex; and endodermis, pericycle and stele. We analyzed a total of 38 microarray data and identified 22,297 genes corresponding to 17,010 loci that showed sufficient signal intensity as well as developmental- and tissue type-specific transcriptome signatures. Moreover, we clarified gene networks associated with root cap function and lateral root formation, and further revealed antagonistic and synergistic interactions of phytohormones such as auxin, cytokinin, brassinosteroids and ethylene, based on the expression pattern of genes related to phytohormone biosynthesis and signaling. Expression profiling of transporter genes defined not only major sites for uptake and transport of water and nutrients, but also distinct signatures of the radial transport system from the rhizosphere to the xylem vessel for each nutrient. All data can be accessed from our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp), thereby providing useful information for understanding the molecular mechanisms involved in root system development of crop plants.

Protein kinase domain of CTR1 from Arabidopsis thaliana promotes ethylene receptor cross talk

Ethylene controls many aspects of plant growth and development. Signaling by the gaseous phytohormone is initiated by disulfide-linked membrane-bound receptors, and the formation of heteromeric receptor clusters contributes to the broad range of ethylene responsiveness. In Arabidopsis thaliana, the TCS-like ethylene receptors interact with the cytosolic serine/threonine kinase constitutive triple response 1 (CTR1), a proposed mitogen-activated protein kinase kinase kinase. In the absence of the hormone, the receptor and therefore CTR1 are active. Hence, ethylene acts as an inverse agonist of its signaling pathway. The three-dimensional structures of the active, triphosphorylated and the unphosphorylated, inactive kinase domain of CTR1 in complex with staurosporine illustrate the conformational rearrangements that form the basis of activity regulation. Additionally, in analytical ultracentrifugation experiments, active kinase domains form back-to-back dimers, while inactive and activation loop variants are monomers. Together with a front-to-front activation interface, the active protein kinase dimers thereby engage in interactions that promote CTR1-mediated cross talk between ethylene receptor clusters. This model provides a structural foundation for the observed high sensitivity of plants to ethylene.

Ethylene inhibits lateral root development, increases IAA transport and expression of PIN3 and PIN7 auxin efflux carriers

We used genetic and molecular approaches to identify mechanisms by which the gaseous plant hormone ethylene reduces lateral root formation and enhances polar transport of the hormone auxin. Arabidopsis thaliana mutants, aux1, lax3, pin3 and pin7, which are defective in auxin influx and efflux proteins, were less sensitive to the inhibition of lateral root formation and stimulation of auxin transport following treatment with the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). By contrast, pin2 and abcb19 mutants exhibited wild-type ACC responses. ACC and indole-3-acetic acid (IAA) increased the abundance of transcripts encoding auxin transport proteins in an ETR1 and EIN2 (ethylene signaling)-dependent and TIR1 (auxin receptor)-dependent fashion, respectively. The effects of ACC on these transcripts and on lateral root development were still present in the tir1 mutant, suggesting independent signaling networks. ACC increased auxin-induced gene expression in the root apex, but decreased expression in regions where lateral roots form and reduced free IAA in whole roots. The ethylene synthesis inhibitor aminoethoxyvinylglycine (AVG) had opposite effects on auxin-dependent gene expression. These results suggest that ACC affects root development by altering auxin distribution. PIN3- and PIN7-GFP fluorescence was increased or decreased after ACC or AVG treatment, respectively, consistent with the role of PIN3 and PIN7 in ACC-elevated transport. ACC treatment abolished a localized depletion of fluorescence of PIN3- and PIN7-GFP, normally found below the site of primordia formation. These results suggest that ACC treatment increased PIN3 and PIN7 expression, resulting in elevated auxin transport, which prevented the localized accumulation of auxin needed to drive lateral root formation.

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

Plants feature a particularly diverse population of short (s)RNAs, the central component of all RNA silencing pathways. Next generation sequencing techniques enable deeper insights into this complex and highly conserved mechanism and allow identification and quantification of sRNAs. We employed deep sequencing to monitor the sRNAome of developing tomato fruits covering the period between closed flowers and ripened fruits by profiling sRNAs at 10 time-points. It is known that microRNAs (miRNAs) play an important role in development but very little information is available about the majority of sRNAs that are not miRNAs. Here we show distinctive patterns of sRNA expression that often coincide with stages of the developmental process such as flowering, early and late fruit maturation. Moreover, thousands of non-miRNA sRNAs are differentially expressed during fruit development and ripening. Some of these differentially expressed sRNAs derived from transposons but many derive from protein coding genes or regions that show homology to protein coding genes, several of which are known to play a role in flower and fruit development. These findings raise the possibility of a regulative role of these sRNAs during fruit onset and maturation in a crop species. We also identified six new miRNAs and experimentally validated two target mRNAs. These two mRNAs are targeted by the same miRNA but do not belong to the same gene family, which is rare for plant miRNAs. Expression pattern and putative function of these targets indicate a possible role in glutamate accumulation, which contributes to establishing the taste of the fruit.

The role of the pod in seed development: strategies for manipulating yield

Pods play a key role in encapsulating the developing seeds and protecting them from pests and pathogens. In addition to this protective function, it has been shown that the photosynthetically active pod wall contributes assimilates and nutrients to fuel seed growth. Recent work has revealed that signals originating from the pod may also act to coordinate grain filling and regulate the reallocation of reserves from damaged seeds to those that have retained viability. In this review we consider the evidence that pods can regulate seed growth and maturation, particularly in members of the Brassicaceae family, and explore how the timing and duration of pod development might be manipulated to enhance either the quantity of crop yield or its nutritional properties.

Ethylene receptor ETHYLENE RECEPTOR1 domain requirements for ethylene responses in Arabidopsis seedlings

Ethylene influences many processes in Arabidopsis (Arabidopsis thaliana) through the action of five receptor isoforms. We used high-resolution, time-lapse imaging of dark-grown Arabidopsis seedlings to better understand the roles of each isoform in the regulation of growth in air, ethylene-stimulated nutations, and growth recovery after ethylene removal. We found that ETHYLENE RECEPTOR1 (ETR1) is both necessary and sufficient for nutations. Transgene constructs in which the ETR1 promoter was used to drive expression of cDNAs for each of the five receptor isoforms were transferred into etr1-6;etr2-3;ein4-4 triple loss-of-function mutants that have constitutive growth inhibition in air, fail to nutate in ethylene, and take longer to recover a normal growth rate when ethylene is removed. The patterns of rescue show that ETR1, ETR2, and ETHYLENE INSENSITIVE4 (EIN4) have the prominent roles in rapid growth recovery after removal of ethylene whereas ETR1 was the sole isoform that rescued nutations. ETR1 histidine kinase activity and phosphotransfer through the receiver domain are not required to rescue nutations. However, REVERSION TO SENSITIVITY1 modulates ethylene-stimulated nutations but does not modulate the rate of growth recovery after ethylene removal. Several chimeric receptor transgene constructs where domains of EIN4 were swapped into ETR1 were also introduced into the triple mutant. The pattern of phenotype rescue by the chimeric receptors used in this study supports a model where a receptor with a receiver domain is required for normal growth recovery and that nutations specifically require the full-length ETR1 receptor.

Molecular association of the Arabidopsis ETR1 ethylene receptor and a regulator of ethylene signaling, RTE1

The plant hormone ethylene plays important roles in growth and development. Ethylene is perceived by a family of membrane-bound receptors that actively repress ethylene responses. When the receptors bind ethylene, their signaling is shut off, activating responses. REVERSION-TO-ETHYLENE SENSITIVITY (RTE1) encodes a novel membrane protein conserved in plants and metazoans. Genetic analyses in Arabidopsis thaliana suggest that RTE1 promotes the signaling state of the ethylene receptor ETR1 through the ETR1 N-terminal domain. RTE1 and ETR1 have been shown to co-localize to the endoplasmic reticulum (ER) and Golgi apparatus in Arabidopsis. Here, we demonstrate a physical association of RTE1 and ETR1 using in vivo and in vitro methods. Interaction of RTE1 and ETR1 was revealed in vivo by bimolecular fluorescence complementation (BiFC) in a tobacco cell transient assay and in stably transformed Arabidopsis. The association was also observed using a truncated version of ETR1 comprising the N terminus (amino acids 1-349). Interaction of RTE1 and ETR1 was confirmed by co-immunoprecipitation from Arabidopsis. The interaction occurs with high affinity (K(d), 117 nM) based on tryptophan fluorescence spectroscopy using purified recombinant RTE1 and a tryptophan-less version of purified recombinant ETR1. An amino acid substitution (C161Y) in RTE1 that is known to confer an ETR1 loss-of-function phenotype correspondingly gives a nearly 12-fold increase in the dissociation constant (K(d), 1.38 μM). These findings indicate that a high affinity association of RTE1 and ETR1 is important in the regulation of ETR1.

Illuminating COI1: a component of the Arabidopsis jasomonate receptor complex also interacts with ethylene signaling

A significant portion of developmental and environmental responses in plants is mediated through phytohormone signaling, often if not always integrated with outputs from other signals. We have recently shown that CORONATINE INSENSITIVE1 (COI1), a component of a jasmonate receptor complex, is involved in ethylene-induced root growth inhibition of Arabidopsis, in the light. This response is neither due to elevated levels of jasmonates in response to ethylene treatment nor dependent on the known jasmonate signal-transduction cascade, except that it requires COI1. Further, we have shown that the ethylene-induced COI1-mediated pathway functions in parallel with, and additively to, the conventional ethylene signaling pathway, and that the light requirement is primarily for long photoperiods. This unexpected interaction of COI1 with ethylene signaling has also been extended to other developmental processes including germination and fertility. This addendum summarizes the earlier findings with some new insights, and describes and speculates on the mechanisms by which these processes are regulated, in the context of the interaction between COI1 and ethylene signaling.

Analysis of the functional conservation of ethylene receptors between maize and Arabidopsis

Ethylene, a regulator of plant growth and development, is perceived by specific receptors that act as negative regulators of the ethylene response. Five ethylene receptors, i.e., ETR1, ERS1, EIN4, ETR2, and ERS2, are present in Arabidopsis and dominant negative mutants of each that confer ethylene insensitivity have been reported. In contrast, maize contains just two types of ethylene receptors: ZmERS1, encoded by ZmERS1a and ZmERS1b, and ZmETR2, encoded by ZmETR2a and ZmETR2b. In this study, we introduced a Cys to Tyr mutation in the transmembrane domain of ZmERS1b and ZmETR2b that is present in the etr1-1 dominant negative mutant and expressed each protein in Arabidopsis. Mutant Zmers1b and Zmetr2b receptors conferred ethylene insensitivity and Arabidopsis expressing Zmers1b or Zmetr2b were larger and exhibited a delay in leaf senescence characteristic of ethylene insensitive Arabidopsis mutants. Zmers1b and Zmetr2b were dominant and functioned equally well in a hemizygous or homozygous state. Expression of the Zmers1b N-terminal transmembrane domain was sufficient to exert dominance over endogenous Arabidopsis ethylene receptors whereas the Zmetr2b N-terminal domain failed to do so. Neither Zmers1b nor Zmetr2b functioned in the absence of subfamily 1 ethylene receptors, i.e., ETR1 and ERS1. These results suggest that Cys65 in maize ZmERS1b and ZmETR2b plays the same role that it does in Arabidopsis receptors. Moreover, the results demonstrate that the mutant maize ethylene receptors are functionally dependent on subfamily 1 ethylene receptors in Arabidopsis, indicating substantial functional conservation between maize and Arabidopsis ethylene receptors despite their sequence divergence.

COI1, a jasmonate receptor, is involved in ethylene-induced inhibition of Arabidopsis root growth in the light

Plant response to stress is orchestrated by hormone signalling pathways including those activated by jasmonates (JAs) and by ethylene, both of which stunt root growth. COI1 is a JA receptor and is required for the known responses to this hormone. It was observed that the coi1 mutant, which is largely unresponsive to growth inhibition by JAs, was also partially unresponsive to growth inhibition by ethylene and by its immediate precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), in the light but not in the dark. Although COI1 was required for this response to ACC, other components of the JA signal perception pathway were not. Mutants selected for insensitivity to ethylene, including etr1, ein2, and ein3, showed greater ACC-induced root growth inhibition in the light than in the dark. However, the double mutants etr1;coi1, ein2;coi1, and ein3;coi1, and coi1 seedlings treated with silver ions to block the ethylene receptors showed almost complete unresponsiveness to ACC-induced root growth inhibition in the light. The light requirement for the COI1-mediated growth inhibition by ACC was for long photoperiods, and the ACC response was not abolished by mutations in the known photoreceptors. The complementation assay indicated that SCF complex assembly was not required for COI1 function in the ACC response, in contrast to the JA response. It is concluded that COI1 is required for the light-dependent, JA-independent, root growth inhibition by ethylene.

The copper transporter RAN1 is essential for biogenesis of ethylene receptors in Arabidopsis

Plants utilize ethylene as a hormone to regulate multiple developmental processes and to coordinate responses to biotic and abiotic stress. In Arabidopsis thaliana, a small family of five receptor proteins typified by ETR1 mediates ethylene perception. Our previous work suggested that copper ions likely play a role in ethylene binding. An independent study indicated that the ran1 mutants, which display ethylene-like responses to the ethylene antagonist trans-cyclooctene, have mutations in the RAN1 copper-transporting P-type ATPase, once again linking copper ions to the ethylene-response pathway. The results presented herein indicate that genetically engineered Saccharomyces cerevisiae expressing ETR1 but lacking the RAN1 homolog Ccc2p (Δccc2) lacks ethylene-binding activity. Ethylene-binding activity was restored when copper ions were added to the Δccc2 mutants, showing that it is the delivery of copper that is important. Additionally, transformation of the Δccc2 mutant yeast with RAN1 rescued ethylene-binding activity. Analysis of plants carrying loss-of-function mutations in ran1 showed that they lacked ethylene-binding activity, whereas seedlings carrying weak alleles of ran1 had normal ethylene-binding activity but were hypersensitive to copper-chelating agents. Altogether, the results show an essential role for RAN1 in the biogenesis of the ethylene receptors and copper homeostasis in Arabidopsis seedlings. Furthermore, the results indicate cross-talk between the ethylene-response pathway and copper homeostasis in Arabidopsis seedling development.

New insight in ethylene signaling: autokinase activity of ETR1 modulates the interaction of receptors and EIN2

Ethylene insensitive 2 (EIN2), an integral membrane protein of the ER network, has been identified as the central regulator of the ethylene signaling pathway. Still, the mechanism by which the ethylene signal is transferred from the receptors to EIN2 has not been solved yet. Here, we show that protein phosphorylation is a key mechanism to control the interaction of EIN2 and the receptors. In vivo and in vitro fluorescence studies reveal that the kinase domain of the receptors is essential for the interaction. Cyanide, an ethylene agonist, which is known to reduce auto-phosphorylation of the ethylene receptor ethylene resistant 1 (ETR1) or a mutation in the kinase domain of ETR1 that prevents auto-phosphorylation (H353A), increases the affinity of the receptors for EIN2. On the other hand, mimicking permanent auto-phosphorylation of ETR1 as in the mutant H353E releases the EIN2-ETR1 interaction from the control by the plant hormone. Based on our data, we propose a novel model on the integration of EIN2 in the ethylene signaling cascade.

Relationship between Rh-RTH1 and ethylene receptor gene expression in response to ethylene in cut rose

A cDNA clone encoding a putative RTE1-like protein (Rh-RTH1) was obtained from total RNA isolated from senescing rose (Rosa hybrida cv. Tineke) petals using RT-PCR and RACE techniques. The cDNA (1,061 bp) contained an open reading frame of 684 bp corresponding to 227 amino acids. The amino acid sequence had 60.0, 49.6, 61.2, 42.5 and 39.8% identity with that of Arabidopsis RTH, RTE1, tomato GRL2, GRL1 and GR, respectively. Northern hybridization indicated that Rh-RTH1 expression is enhanced by endogenous and exogenous ethylene and inhibited by 1-MCP in petals and gynoecia. Rh-RTH1 expression partly correlated with sites of the ethylene receptor gene Rh-ETR1 and Rh-ETR3 expression, such as the petals, gynoecia, roots, and buds. The induction of Rh-RTH1 and Rh-ETR3 expression was substantially suppressed by 1-MCP treatment, while Rh-ETR1 expression was not reduced by 1-MCP treatment. Following treatment of flowers with sucrose, the level of Rh-RTH1 and Rh-ETR3 mRNA was only slightly decreased in petals and gynoecia. Upon wounding treatment, Rh-RTH1, Rh-ETR1 and Rh-ETR3 showed a quick increase in mRNA accumulation which was positively correlated with the increase in ethylene production. The expression of Rh-RTH1 showed partial correlation with that of Rh-ETR1 and Rh-ETR3.

Ethylene-induced stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 is mediated by proteasomal degradation of EIN3 binding F-box 1 and 2 that requires EIN2 in Arabidopsis

Plant responses to ethylene are mediated by regulation of EBF1/2-dependent degradation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Here, we report that the level of EIL1 protein is upregulated by ethylene through an EBF1/2-dependent pathway. Genetic analysis revealed that EIL1 and EIN3 cooperatively but differentially regulate a wide array of ethylene responses, with EIL1 mainly inhibiting leaf expansion and stem elongation in adult plants and EIN3 largely regulating a multitude of ethylene responses in seedlings. When EBF1 and EBF2 are disrupted, EIL1 and EIN3 constitutively accumulate in the nucleus and remain unresponsive to exogenous ethylene application. Further study revealed that the levels of EBF1 and EBF2 proteins are downregulated by ethylene and upregulated by silver ion and MG132, suggesting that ethylene stabilizes EIN3/EIL1 by promoting EBF1 and EBF2 proteasomal degradation. Also, we found that EIN2 is indispensable for mediating ethylene-induced EIN3/EIL1 accumulation and EBF1/2 degradation, whereas MKK9 is not required for ethylene signal transduction, contrary to a previous report. Together, our studies demonstrate that ethylene similarly regulates EIN3 and EIL1, the two master transcription factors coordinating myriad ethylene responses, and clarify that EIN2 but not MKK9 is required for ethylene-induced EIN3/EIL1 stabilization. Our results also reveal that EBF1 and EBF2 act as essential ethylene signal transducers that by themselves are subject to proteasomal degradation.

Genetic and transformation studies reveal negative regulation of ERS1 ethylene receptor signaling in Arabidopsis

BACKGROUND

Ethylene receptor single mutants of Arabidopsis do not display a visibly prominent phenotype, but mutants defective in multiple ethylene receptors exhibit a constitutive ethylene response phenotype. It is inferred that ethylene responses in Arabidopsis are negatively regulated by five functionally redundant ethylene receptors. However, genetic redundancy limits further study of individual receptors and possible receptor interactions. Here, we examined the ethylene response phenotype in two quadruple receptor knockout mutants, (ETR1) ers1 etr2 ein4 ers2 and (ERS1) etr1 etr2 ein4 ers2, to unravel the functions of ETR1 and ERS1. Their functions were also reciprocally inferred from phenotypes of mutants lacking ETR1 or ERS1. Receptor protein levels are correlated with receptor gene expression. Expression levels of the remaining wild-type receptor genes were examined to estimate the receptor amount in each receptor mutant, and to evaluate if effects of ers1 mutations on the ethylene response phenotype were due to receptor functional compensation. As ers1 and ers2 are in the Wassilewskija (Ws) ecotype and etr1, etr2, and ein4 are in the Columbia (Col-0) ecotype, possible effects of ecotype mixture on ethylene responses were also investigated.

RESULTS

Ethylene responses were scored based on seedling hypocotyl measurement, seedling and rosette growth, and relative Chitinase B (CHIB) expression. Addition of ers1 loss-of-function mutations to any ETR1-containing receptor mutants alleviated ethylene growth inhibition. Growth recovery by ers1 mutation was reversed when the ers1 mutation was complemented by ERS1p:ERS1. The addition of the ers2-3 mutation to receptor mutants did not reverse the growth inhibition. Overexpressing ERS1 receptor protein in (ETR1 ERS1)etr2 ein4 ers2 substantially elevated growth inhibition and CHIB expression. Receptor gene expression analyses did not favor receptor functional compensation upon the loss of ERS1.

CONCLUSIONS

Our results suggest that ERS1 has dual functions in the regulation of ethylene responses. In addition to repressing ethylene responses, ERS1 also promotes ethylene responses in an ETR1-dependent manner. Several lines of evidence support the argument that ecotype mixture does not reverse ethylene responses. Loss of ERS1 did not lead to an increase in total receptor gene expression, and functional compensation was not observed. The inhibitory effects of ERS1 on the ethylene signaling pathway imply negative receptor collaboration.

Regulated ethylene insensitivity through the inducible expression of the Arabidopsis etr1-1 mutant ethylene receptor in tomato

Ethylene serves as an important hormone controlling several aspects of plant growth and development, including fruit ripening and leaf and petal senescence. Ethylene is perceived following its binding to membrane-localized receptors, resulting in their inactivation and the induction of ethylene responses. Five distinct types of receptors are expressed in Arabidopsis (Arabidopsis thaliana), and mutant receptors have been described that repress ethylene signaling in a dominant negative manner. One such mutant, ethylene resistant1-1 (etr1-1), results in a strong ethylene-insensitive phenotype in Arabidopsis. In this study, regulated expression of the Arabidopsis etr1-1 in tomato (Solanum lycopersicum) was achieved using an inducible promoter. In the absence of the inducer, transgenic seedlings remained sensitive to ethylene, but in its presence, a state of ethylene insensitivity was induced, resulting in the elongation of the hypocotyl and root in dark-grown seedlings in the presence of ethylene, a reduction or absence of an apical hook, and repression of ethylene-inducible E4 expression. The level of ethylene sensitivity could be controlled by the amount of inducer used, demonstrating a linear relationship between the degree of insensitivity and etr1-1 expression. Induction of etr1-1 expression also repressed the epinastic response to ethylene as well as delayed fruit ripening. Restoration of ethylene sensitivity was achieved following the cessation of the induction. These results demonstrate the ability to control ethylene responses temporally and in amount through the control of mutant receptor expression.

Silencing Sl-EBF1 and Sl-EBF2 expression causes constitutive ethylene response phenotype, accelerated plant senescence, and fruit ripening in tomato

The hormone ethylene regulates a wide range of plant developmental processes and EBF (EIN3-binding F-box) proteins were shown to negatively regulate the ethylene signalling pathway via mediating the degradation of EIN3/EIL proteins. The present study reports on the identification of two tomato F-box genes, Sl-EBF1 and Sl-EBF2 from the EBF subfamily. The two genes display contrasting expression patterns in reproductive and vegetative tissues and in response to ethylene and auxin treatment. Sl-EBF1 and Sl-EBF2 genes are actively regulated at crucial stages in the development of the reproductive organs. Their dynamic expression in flowers during bud-to-anthesis and anthesis-to-post-anthesis transitions, and at the onset of fruit ripening, suggests their role in situations where ethylene is required for stimulating flower opening and triggering fruit ripening. VIGS-mediated silencing of a single tomato EBF gene uncovered a compensation mechanism that tends to maintain a threshold level of Sl-EBF expression via enhancing the expression of the second Sl-EBF gene. In line with this compensation, tomato plants silenced for either of the Sl-EBF genes were indistinguishable from control plants, indicating functional redundancy among Sl-EBF genes. By contrast, co-silencing of both Sl-EBFs resulted in ethylene-associated phenotypes. While reports on EBF genes to date have focused on their role in modulating ethylene responses in Arabidopsis, the present study uncovered their role in regulating crucial stages of flower and fruit development in tomato. The data support the hypothesis that protein degradation via the ubiquitin/26S proteasome pathway is a control point of fruit ripening and open new leads for engineering fruit quality.

Ethylene signalling and ethylene-targeted transcription factors are required to balance beneficial and nonbeneficial traits in the symbiosis between the endophytic fungus Piriformospora indica and Arabidopsis thaliana

*The endophytic fungus Piriformospora indica colonizes the roots of the model plant Arabidopsis thaliana and promotes its growth and seed production. The fungus can be cultivated in axenic culture without a host, and therefore this is an excellent system to investigate plant-fungus symbiosis. *The growth of etr1, ein2 and ein3/eil1 mutant plants was not promoted or even inhibited by the fungus; the plants produced less seeds and the roots were more colonized compared with the wild-type. This correlates with a mild activation of defence responses. The overexpression of ETHYLENE RESPONSE FACTOR1 constitutively activated defence responses, strongly reduced root colonization and abolished the benefits for the plants. *Piriformospora indica-mediated stimulation of growth and seed yield was not affected by jasmonic acid, and jasmonic acid-responsive promoter beta-glucuronidase gene constructs did not respond to the fungus in Arabidopsis roots. *We propose that ethylene signalling components and ethylene-targeted transcription factors are required to balance beneficial and nonbeneficial traits in the symbiosis. The results show that the restriction of fungal growth by ethylene signalling components is required for the beneficial interaction between the two symbionts.

Ethylene perception is involved in female cucumber flower development

It is well established that ethylene promotes female flower development in cucumber. However, little is known about how the gaseous hormone selectively affects female flowers, and what mechanism it uses. Previously, we found organ-specific DNA damage in the primordial anther of female cucumber flowers. This finding led to a hypothesis that ethylene might promote female flower development via the organ-specific induction of DNA damage in primordial anthers. In this study, we tested this hypothesis first by demonstrating ethylene induction of DNA damage via the ethylene signaling pathway using cucumber protoplasts. Then, using representative component genes of the ethylene signaling pathway as probes, we found that one of the ethylene receptors, CsETR1, was temporally and spatially downregulated in the stamens of stage-6 female cucumber flowers, especially along with the increase of the nodes. Furthermore, by constructing transgenic Arabidopsis plants with organ-specific expression of antisense CsETR1 under the control of an AP3 promoter to downregulate ETR1 expression in the stamens, we generated Arabidopsis 'female flowers', in which the abnormal stamens mimic those of female cucumber flowers. Our data suggest that ethylene perception is involved in the arrest of stamen development in female cucumber flowers through the induction of DNA damage. This opens up a novel perspective and approach to solve the half-century-long puzzle of how gaseous ethylene selectively promotes female flowers in the monoecious cucumber plant.

Ethylene-induced hyponastic growth in Arabidopsis thaliana is controlled by ERECTA

Plants can respond quickly and profoundly to detrimental changes in their environment. For example, Arabidopsis thaliana can induce an upward leaf movement response through differential petiole growth (hyponastic growth) to outgrow complete submergence. This response is induced by accumulation of the phytohormone ethylene in the plant. Currently, only limited information is available on how this response is molecularly controlled. In this study, we utilized quantitative trait loci (QTL) analysis of natural genetic variation among Arabidopsis accessions to isolate novel factors controlling constitutive petiole angles and ethylene-induced hyponastic growth. Analysis of mutants in various backgrounds and complementation analysis of naturally occurring mutant accessions provided evidence that the leucin-rich repeat receptor-like Ser/Thr kinase gene, ERECTA, controls ethylene-induced hyponastic growth. Moreover, ERECTA controls leaf positioning in the absence of ethylene treatment. Our data demonstrate that this is not due to altered ethylene production or sensitivity.

Postembryonic seedling lethality in the sterol-deficient Arabidopsis cyp51A2 mutant is partially mediated by the composite action of ethylene and reactive oxygen species

Seedling-lethal phenotypes of Arabidopsis (Arabidopsis thaliana) mutants that are defective in early steps in the sterol biosynthetic pathway are not rescued by the exogenous application of brassinosteroids. The detailed molecular and physiological mechanisms of seedling lethality have yet to be understood. Thus, to elucidate the underlying mechanism of lethality, we analyzed transcriptome and proteome profiles of the cyp51A2 mutant that is defective in sterol 14alpha-demethylation. Results revealed that the expression levels of genes involved in ethylene biosynthesis/signaling and detoxification of reactive oxygen species (ROS) increased in the mutant compared with the wild type and, thereby, that the endogenous ethylene level also increased in the mutant. Consistently, the seedling-lethal phenotype of the cyp51A2 mutant was partly attenuated by the inhibition of ethylene biosynthesis or signaling. However, photosynthesis-related genes including Rubisco large subunit, chlorophyll a/b-binding protein, and components of photosystems were transcriptionally and/or translationally down-regulated in the mutant, accompanied by the transformation of chloroplasts into gerontoplasts and a reduction in both chlorophyll contents and photosynthetic activity. These characteristics observed in the cyp51A2 mutant resemble those of leaf senescence. Nitroblue tetrazolium staining data revealed that the mutant was under oxidative stress due to the accumulation of ROS, a key factor controlling both programmed cell death and ethylene production. Our results suggest that changes in membrane sterol contents and composition in the cyp51A2 mutant trigger the generation of ROS and ethylene and eventually induce premature seedling senescence.

Genetic dissection of the role of ethylene in regulating auxin-dependent lateral and adventitious root formation in tomato

In this study we investigated the role of ethylene in the formation of lateral and adventitious roots in tomato (Solanum lycopersicum) using mutants isolated for altered ethylene signaling and fruit ripening. Mutations that block ethylene responses and delay ripening -Nr (Never ripe), gr (green ripe), nor (non ripening), and rin (ripening inhibitor) - have enhanced lateral root formation. In contrast, the epi (epinastic) mutant, which has elevated ethylene and constitutive ethylene signaling in some tissues, or treatment with the ethylene precursor 1-aminocyclopropane carboxylic acid (ACC), reduces lateral root formation. Treatment with ACC inhibits the initiation and elongation of lateral roots, except in the Nr genotype. Root basipetal and acropetal indole-3-acetic acid (IAA) transport increase with ACC treatments or in the epi mutant, while in the Nr mutant there is less auxin transport than in the wild type and transport is insensitive to ACC. In contrast, the process of adventitious root formation shows the opposite response to ethylene, with ACC treatment and the epi mutation increasing adventitious root formation and the Nr mutation reducing the number of adventitious roots. In hypocotyls, ACC treatment negatively regulated IAA transport while the Nr mutant showed increased IAA transport in hypocotyls. Ethylene significantly reduces free IAA content in roots, but only subtly changes free IAA content in tomato hypocotyls. These results indicate a negative role for ethylene in lateral root formation and a positive role in adventitious root formation with modulation of auxin transport as a central point of ethylene-auxin crosstalk.

EIN2, the central regulator of ethylene signalling, is localized at the ER membrane where it interacts with the ethylene receptor ETR1

Genetic studies have identified the membrane protein EIN2 (ethylene insensitive 2) as a central component of ethylene signalling in Arabidopsis. In addition, EIN2 might take part in multiple hormone signalling pathways and in response to pathogens as demonstrated by recent genetic and biochemical studies. Here we show, by an integrated approach using in vivo and in vitro fluorescence techniques, that EIN2 is localized at the ER (endoplasmic reticulum) membrane where it shows specific interaction with the ethylene receptor protein ETR1.

Ethylene signaling and response: where different regulatory modules meet

The structural simplicity of the gaseous hormone ethylene stands in contrast with the complexity of the physiological processes ethylene regulates. Initial studies suggested a simple linear arrangement of signaling molecules leading from the ethylene receptors to the EIN3 family of transcription factors. Recent discoveries have substantially changed this view. Current models suggest existence of a complex signaling pathway composed of several phosphorylation cascades, feedback-regulated transcriptional networks, and protein and mRNA turnover regulatory modules. Interactions between ethylene and other signals determine which of the ethylene-mediated responses get activated in a particular cell at a particular time. Tissue-specific regulation of auxin biosynthesis, transport, and response by ethylene is emerging as a key element in this signal integration process.

Effects of tobacco ethylene receptor mutations on receptor kinase activity, plant growth and stress responses

Ethylene receptor is the first component of ethylene signaling that regulates plant growth, development and stress responses. Previously, we have demonstrated that tobacco subfamily 2 ethylene receptor NTHK1 had Ser/Thr kinase activity, and overexpression of NTHK1 caused large rosette, reduced ethylene sensitivity, and increased salt sensitivity in transgenic Arabidopsis plants. Here we found that N-box mutation in the NTHK1 kinase domain abolished the kinase activity and led to disruption of NTHK1 roles in conferring reduced ethylene sensitivity and salt sensitive response in transgenic Arabidopsis plants. However, N-box mutation had partial effects on NTHK1 regulation of rosette growth and expression of salt- and ethylene-responsive genes AtNAC2, AtERF1 and AtCor6.6. Mutation of conserved residues in the H box did not affect kinase activity, seedling growth, ethylene sensitivity or salt-induced epinasty in transgenic plants but did influence NTHK1 function in control of specific salt- and ethylene-responsive gene expression. Compared with NTHK1, the tobacco subfamily 1 ethylene receptor NtETR1 had His kinase activity and played a weak role in regulation of rosette growth, triple response and salt response. Mutation of the conserved His residue in the NtETR1 H box eliminated phosphorylation and altered the effect of Ntetr1-1 on reporter gene activity. These results imply that the Ser/Thr kinase activity of NTHK1 is differentially required for various responses, and NTHK1 plays a larger role than NtETR1.

Antagonism between abscisic acid and ethylene in Arabidopsis acts in parallel with the reciprocal regulation of their metabolism and signaling pathways

Although abscisic acid (ABA) and ethylene have antagonistic functions in the control of plant growth and development, including seed germination and early seedling development, it remains unknown whether a convergent point exists between these two signaling pathways or whether they operate in parallel in Arabidopsis thaliana. To elucidate this issue, four ethylene mutants, ctr1, ein2, ein3, and ein6, were crossed with aba2 (also known as gin1-3) to generate double mutants. Genetic epistasis analysis revealed that all of the resulting double mutants displayed aba2 mutant phenotypes with a small plant size and wiltiness when grown in soil or on agar plates. Further ethylene sensitivity or triple response analyses demonstrated that these double mutants also retained the ctr1 or ein mutant phenotypes, showing ethylene constitutive triple and insensitive responses, respectively. Our current data therefore demonstrate that ABA and ethylene act in parallel, at least in primary signal transduction pathways. Moreover, by microarray analysis we found that an ACC oxidase (ACO) was significantly upregulated in the aba2 mutant, whereas the 9-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) gene in ein2 was upregulated, and both the ABSCISIC ACID INSENSITIVE1 (ABI1) and cytochrome P450, family 707, subfamily A, polypeptide 2 (CYP707A2) genes in etr1-1 were downregulated. These data further suggest that ABA and ethylene may control the hormonal biosynthesis, catabolism, or signaling of each other to enhance their antagonistic effects upon seed germination and early seedling growth.

Apple ethylene receptor protein concentrations are affected by ethylene, and differ in cultivars that have different storage life

Ethylene plays a crucial role in apple fruit ripening. Ethylene receptors have been identified and are known to be negative regulators of ethylene signalling. We examined ethylene receptors MdERS1 and MdERS2 in 1-MCP-treated and untreated fruit and leaves of cultivar 'Orin' and 'Fuji' apples. MdERS1 and MdERS2 transcription increased rapidly after harvest in control fruit, but in 1-MCP-treated fruit, increases were delayed for 30 days. However, MdERS1 and MdERS2 protein levels behaved differently. MdERS1 decreased gradually in both the control and 1-MCP treatments. MdERS2, however, increased gradually in control 'Fuji' and remained steady in 1-MCP-treated 'Fuji' but remained low in 'Orin'. Exogenous ethylene treatment of fruit increased MdERS1 and MdERS2 expression with slightly decreased protein levels. The ratios of proteins to mRNAs were much lower in 'Orin' fruit, and they decreased with ethylene treatment in both cultivars. However, protein to transcript ratio was higher in 'Fuji' ethylene treated fruit than in air- and ethylene-treated 'Orin' fruit. MdERS1 and MdERS2 transcript levels were increased by exogenous ethylene treatment in air pre-treated leaves, but MdERS1 and MdERS2 protein levels did not change or decrease with ethylene treatment, and the ratio of protein to mRNA was lower in ethylene-treated leaves. Differences between transcription and protein levels may be due to receptor turnover differences in the presence or absence of ethylene. Furthermore, MdERS1 and MdERS2 protein stabilities in the presence of ethylene were different in the two cvs. 'Orin' and 'Fuji'.

The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice

Ethylene regulates multiple aspects of plant growth and development in dicotyledonous plants; however, its roles in monocotyledonous plants are poorly known. Here, we characterized a subfamily II ethylene receptor, ETHYLENE RESPONSE2 (ETR2), in rice (Oryza sativa). The ETR2 receptor with a diverged His kinase domain is a Ser/Thr kinase, but not a His kinase, and can phosphorylate its receiver domain. Mutation of the N box of the kinase domain abolished the kinase activity of ETR2. Overexpression of ETR2 in transgenic rice plants reduced ethylene sensitivity and delayed floral transition. Conversely, RNA interference (RNAi) plants exhibited early flowering and the ETR2 T-DNA insertion mutant etr2 showed enhanced ethylene sensitivity and early flowering. The effective panicles and seed-setting rate were reduced in the ETR2-overexpressing plants, while thousand-seed weight was substantially enhanced in both the ETR2-RNAi plants and the etr2 mutant compared with controls. Starch granules accumulated in the internodes of the ETR2-overexpressing plants, but not in the etr2 mutant. The GIGANTEA and TERMINAL FLOWER1/CENTRORADIALIS homolog (RCN1) that cause delayed flowering were upregulated in ETR2-overexpressing plants but downregulated in the etr2 mutant. Conversely, the alpha-amylase gene RAmy3D was suppressed in ETR2-overexpressing plants but enhanced in the etr2 mutant. Thus, ETR2 may delay flowering and cause starch accumulation in stems by regulating downstream genes.

Emerging connections in the ethylene signaling network

The gaseous plant hormone ethylene acts as a pivotal mediator to respond to and coordinate internal and external cues in modulating plant growth dynamics and developmental programs. Genetic analysis of Arabidopsis thaliana has been used to identify key components and to build a linear ethylene-signaling pathway from the receptors through to the nuclear transcription factors. Studies applying integrative approaches have revealed new regulators, molecular connections and mechanisms in ethylene signaling and unexpected links to other plant hormones. Here, we review and discuss recent discoveries about the functional mode of ethylene receptor complexes, dual mitogen-activated protein kinase cascade signaling, stability control of the master nuclear transcription activator ETHYLENE INSENSITIVE 3 (EIN3), and the contextual relationships between ethylene and other plant hormones, such as auxin and gibberellins, in organ-specific growth regulation.

Ethylene modulates the role of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 in cross talk between salicylate and jasmonate signaling

The plant hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) play crucial roles in the signaling network that regulates induced defense responses against biotic stresses. Antagonism between SA and JA operates as a mechanism to fine-tune defenses that are activated in response to multiple attackers. In Arabidopsis (Arabidopsis thaliana), NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) was demonstrated to be required for SA-mediated suppression of JA-dependent defenses. Because ET is known to enhance SA/NPR1-dependent defense responses, we investigated the role of ET in the SA-JA signal interaction. Pharmacological experiments with gaseous ET and the ET precursor 1-aminocyclopropane-1-carboxylic acid showed that ET potentiated SA/NPR1-dependent PATHOGENESIS-RELATED1 transcription, while it rendered the antagonistic effect of SA on methyl jasmonate-induced PDF1.2 and VSP2 expression NPR1 independent. This overriding effect of ET on NPR1 function in SA-JA cross talk was absent in the npr1-1/ein2-1 double mutant, demonstrating that it is mediated via ET signaling. Abiotic and biotic induction of the ET response similarly abolished the NPR1 dependency of the SA-JA signal interaction. Furthermore, JA-dependent resistance against biotic attackers was antagonized by SA in an NPR1-dependent fashion only when the plant-attacker combination did not result in the production of high levels of endogenous ET. Hence, the interaction between ET and NPR1 plays an important modulating role in the fine tuning of the defense signaling network that is activated upon pathogen and insect attack. Our results suggest a model in which ET modulates the NPR1 dependency of SA-JA antagonism, possibly to compensate for enhanced allocation of NPR1 to function in SA-dependent activation of PR genes.

Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis

The gaseous plant hormone ethylene can trigger myriad physiological and morphological responses in plants. While many ethylene signaling pathway components have been identified and characterized, little is known about the function of the integral membrane protein ETHYLENE-INSENSITIVE2 (EIN2), a central regulator of all ethylene responses. Here, we demonstrate that Arabidopsis thaliana EIN2 is a protein with a short half-life that undergoes rapid proteasome-mediated protein turnover. Moreover, EIN2 protein accumulation is positively regulated by ethylene. We identified two F-box proteins, EIN2 TARGETING PROTEIN1 (ETP1) and EIN2 TARGETING PROTEIN2 (ETP2), that interact with the EIN2 C-terminal domain (EIN2-CEND), which is highly conserved and sufficient to activate most ethylene responses. Overexpression of ETP1 or ETP2 disrupts EIN2 protein accumulation, and these plants manifest a strong ethylene-insensitive phenotype. Furthermore, knocking down the levels of both ETP1 and ETP2 mRNAs using an artificial microRNA (amiRNA) leads to accumulation of EIN2 protein, resulting in plants that display constitutive ethylene response phenotypes. Finally, ethylene down-regulates ETP1 and ETP2 proteins, impairing their ability to interact with EIN2. Thus, these studies reveal that a complex interplay between ethylene, the regulation of ETP1/ETP2 F-box proteins, and subsequent targeting and degradation of EIN2 is essential for triggering ethylene responses in plants.

Ethylene response factor TERF1 enhances glucose sensitivity in tobacco through activating the expression of sugar-related genes

Ethylene response factor (ERF) proteins are important plant-specific transcription factors. Increasing evidence shows that ERF proteins regulate plant pathogen resistance, abiotic stress response and plant development through interaction with different stress responsive pathways. Previously, we revealed that overexpression of TERF1 in tobacco activates a cluster gene expression through interacting with GCC box and dehydration responsive element (DRE), resulting in enhanced sensitivity to abscisic acid (ABA) and tolerance to drought, and dark green leaves of mature plants, indicating that TERF1 participates in the integration of ethylene and osmotic responses. Here we further report that overexpression of TERF1 confers sugar response in tobacco. Analysis of the novel isolated tomato TERF1 promoter provides information indicating that there are many cis-acting elements, including sugar responsive elements (SURE) and W box, suggesting that TERF1 might be sugar inducible. This prediction is confirmed by results of reverse transcription-polymerase chain reaction amplification, indicating that transcripts of TERF1 are accumulated in tomato seedlings after application of glucose. Further investigation indicates that the expression of TERF1 in tobacco enhances sensitivity to glucose during seed germination, root and seedling development, showing a decrease of the fresh weight and root elongation under glucose treatment. Detailed investigations provide evidence that TERF1 interacts with the sugar responsive cis-acting element SURE and activates the expression of sugar response genes, establishing the transcriptional regulation of TERF1 in sugar response. Therefore, our results deepen our understanding of the glucose response mediated by the ERF protein TERF1 in tobacco.

Differential petiole growth in Arabidopsis thaliana: photocontrol and hormonal regulation

Environmental challenges such as low light intensity induce differential growth-driven upward leaf movement (hyponastic growth) in Arabidopsis thaliana. However, little is known about the physiological regulation of this response. Here, we studied how low light intensity is perceived and translated into a differential growth response in Arabidopsis. We used mutants defective in light, ethylene and auxin signaling, and in polar auxin transport, as well as chemical inhibitors, to analyze the mechanisms of low light intensity-induced differential growth. Our data indicate that photosynthesis-derived signals and blue light wavelengths affect petiole movements and that rapid induction of hyponasty by low light intensity involves functional cryptochromes 1 and 2, phytochrome-A and phytochrome-B photoreceptor proteins. The response is independent of ethylene signaling. Auxin and polar auxin transport, by contrast, play a role in low light intensity-induced differential petiole growth. We conclude that low light intensity-induced differential petiole growth requires blue light, auxin signaling and polar auxin transport and is, at least in part, genetically separate from well-characterized ethylene-induced differential growth.

The BTB ubiquitin ligases ETO1, EOL1 and EOL2 act collectively to regulate ethylene biosynthesis in Arabidopsis by controlling type-2 ACC synthase levels

Ethylene biosynthesis is directed by a family of 1-aminocyclopropane-1-carboxylic acid (ACC) synthases (ACS) that convert S-adenosyl-l-methionine to the immediate precursor ACC. Members of the type-2 ACS subfamily are strongly regulated by proteolysis with various signals stabilizing the proteins to increase ethylene production. In Arabidopsis, this turnover is mediated by the ubiquitin/26 S proteasome system, using a broad complex/tramtrack/bric-a-brac (BTB) E3 assembled with the ETHYLENE OVERPRODUCER 1 (ETO1) BTB protein for target recognition. Here, we show that two Arabidopsis BTB proteins closely related to ETO1, designated ETO1-like (EOL1) and EOL2, also negatively regulate ethylene synthesis via their ability to target ACSs for breakdown. Like ETO1, EOL1 interacts with type-2 ACSs (ACS4, ACS5 and ACS9), but not with type-1 or type-3 ACSs, or with type-2 ACS mutants that stabilize the corresponding proteins in planta. Whereas single and double mutants affecting EOL1 and EOL2 do not show an ethylene-related phenotype, they exaggerate the effects caused by inactivation of ETO1, and further increase ethylene production and the accumulation of ACS5 in eto1 plants. The triple eto1 eol1 eol2 mutant phenotype can be effectively rescued by the ACS inhibitor aminoethoxyvinylglycine, and by silver, which antagonizes ethylene perception. Together with hypocotyl growth assays showing that the sensitivity and response kinetics to ethylene are normal, it appears that ethylene synthesis, but not signaling, is compromised in the triple mutant. Collectively, the data indicate that the Arabidopsis BTB E3s assembled with ETO1, EOL1 and EOL2 work together to negatively regulate ethylene synthesis by directing the degradation of type-2 ACS proteins.

Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures

The research that aims at furthering our understanding of plant primary metabolism has intensified during the last decade. The presented study validated a systems biology methodological framework for the analysis of stress-induced molecular interaction networks in the context of plant primary metabolism, as these are expressed during the first hours of the stress treatment. The framework involves the application of time-series integrated full-genome transcriptomic and polar metabolomic analyses on plant liquid cultures. The latter were selected as the model system for this type of analysis, because they provide a well-controlled growth environment, ensuring that the observed plant response is due only to the applied perturbation. An enhanced gas chromatography-mass spectrometry (GC-MS) metabolomic data correction strategy and a new algorithm for the significance analysis of time-series "omic" data are used to extract information about the plant's transcriptional and metabolic response to the applied stress from the acquired datasets; in this article, it is the first time that these are applied for the analysis of a large biological dataset from a complex eukaryotic system. The case-study involved Arabidopsis thaliana liquid cultures subjected for 30 h to elevated (1%) CO2 stress. The advantages and validity of the methodological framework are discussed in the context of the known A. thaliana or plant, in general, physiology under the particular stress. Of note, the ability of the methodology to capture dynamic aspects of the observed molecular response allowed for 9 and 24 h of treatment to be indicated as corresponding to shifts in both the transcriptional and metabolic activity; analysis of the pathways through which these activity changes are manifested provides insight to regulatory processes.

The interconversion of ACC deaminase and D-cysteine desulfhydrase by directed mutagenesis

Progress in DNA sequencing of plant genomes has revealed that, in addition to microorganisms, a number of plants contain genes which share similarity to microbial 1-aminocyclopropane-1-carboxylate (ACC) deaminases. These enzymes cleave ACC, the immediate precursor of ethylene in plants, into ammonia and alpha-ketobutyrate. We therefore sought to isolate putative ACC deaminase cDNAs from tomato plants with the objective of establishing whether the product of this gene is a functional ACC deaminase. In the work reported here, it was demonstrated that the enzyme encoded by the putative ACC deaminase cDNA does not have the ability to break the cyclopropane ring of ACC, but rather it utilizes D: -cysteine as a substrate, and in fact encodes a D: -cysteine desulfhydrase. Kinetic characterization of the tomato enzyme indicates that it is similar to other, previously characterized, D: -cysteine desulfhydrases. Using site-directed mutagenesis, it was shown that altering only two amino acid residues within the predicted active site served to change the enzyme from D: -cysteine desulfhydrase to ACC deaminase. Conversely, by altering two amino acid residues at the same positions within the active site of ACC deaminase from Pseudomonas putida UW4 the enzyme was converted into D: -cysteine desulfhydrase. Therefore, it is possible that a change in these two residues may have occurred in an ancestral protein to result in two different enzymatic activities.

Involvement of RTE1 in conformational changes promoting ETR1 ethylene receptor signaling in Arabidopsis

Ethylene is an important regulator of plant growth, development and responses to environmental stresses. Arabidopsis perceives ethylene through five homologous receptors that negatively regulate ethylene responses. RTE1, a novel gene conserved in plants, animals and some protists, was recently identified as a positive regulator of the ETR1 ethylene receptor. Here, we genetically analyze the dependence of ETR1 on RTE1 in order to obtain further insight into RTE1 function. The function of RTE1 was found to be independent and distinct from that of RAN1, which encodes a copper transporter required for ethylene receptor function. We tested the ability of an rte1 loss-of-function mutation to suppress 11 etr1 ethylene-binding domain mis-sense mutations, all of which result in dominant ethylene insensitivity due to constitutive signaling. This suppression test uncovered two classes of etr1 mutations -RTE1-dependent and RTE1-independent. The nature of these mutations suggests that the ethylene-binding domain is a possible target of RTE1 action. Based on these findings, we propose that RTE1 promotes ETR1 signaling through a conformational effect on the ethylene-binding domain.

MAPK signaling in plant hormone ethylene signal transduction

The signal transduction pathway of the plant stress and defense hormone, ethylene, has been extensively elucidated using the plant genetic model Arabidopsis over the last two decades. Among others, a MAPKKK CTR1 was identified as a negative regulator that has led to the speculation of MAPK involvement in ethylene signaling. However, it remained unclear how the MAPK modules acting downstream of the receptors to mediate ethylene signaling. We have recently presented new evidence that the MKK9-MPK3/6 modules identified by combined functional genomic and genetic screens mediate ethylene signaling, which is negatively regulated by the genetically identified CTR1-dependent cascades. Our genetic studies show consistently that the MKK9-MPK3/MPK6 modules act downstream of the ethylene receptors. Biochemical and transgenic analyses further demonstrated that the positive-acting and negative-acting MAPK activities are integrated and act simultaneously to control the key transcription factor EIN3 through dual phosphorylations to regulate the EIN3 protein stability and downstream transcription cascades. This study has revealed a novel molecular mechanism that defines the specificity of complex MAPK signaling. Comprehensive elucidation of MAPK cascades and the underlying molecular mechanisms would provide more precise explanations for how plant cells utilize MAPK cascades to control specific downstream outputs in response to distinct stimuli.

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access

We analyzed global gene expression in Arabidopsis in response to various hormones and in related experiments as part of the AtGenExpress project. The experimental agents included seven basic phytohormones (auxin, cytokinin, gibberellin, brassinosteroid, abscisic acid, jasmonate and ethylene) and their inhibitors. In addition, gene expression was investigated in hormone-related mutants and during seed germination and sulfate starvation. Hormone-inducible genes were identified from the hormone response data. The effects of each hormone and the relevance of the gene lists were verified by comparing expression profiles for the hormone treatments and related experiments using Pearson's correlation coefficient. This approach was also used to analyze the relationships among expression profiles for hormone responses and those included in the AtGenExpress stress-response data set. The expected correlations were observed, indicating that this approach is useful to monitor the hormonal status in the stress-related samples. Global interactions among hormones-inducible genes were analyzed in a pairwise fashion, and several known and novel hormone interactions were detected. Genome-wide transcriptional gene-to-gene correlations, analyzed by hierarchical cluster analysis (HCA), indicated that our data set is useful for identification of clusters of co-expressed genes, and to predict the functions of unknown genes, even if a gene's function is not directly related to the experiments included in AtGenExpress. Our data are available online from AtGenExpressJapan; the results of genome-wide HCA are available from PRIMe. The data set presented here will be a versatile resource for future hormone studies, and constitutes a reference for genome-wide gene expression in Arabidopsis.

Two-component signaling elements and histidyl-aspartyl phosphorelays

Two-component systems are an evolutionarily ancient means for signal transduction. These systems are comprised of a number of distinct elements, namely histidine kinases, response regulators, and in the case of multi-step phosphorelays, histidine-containing phosphotransfer proteins (HPts). Arabidopsis makes use of a two-component signaling system to mediate the response to the plant hormone cytokinin. Two-component signaling elements have also been implicated in plant responses to ethylene, abiotic stresses, and red light, and in regulating various aspects of plant growth and development. Here we present an overview of the two-component signaling elements found in Arabidopsis, including functional and phylogenetic information on both bona-fide and divergent elements.

Global identification of DELLA target genes during Arabidopsis flower development

Gibberellin (GA) plays important roles in regulating many aspects of plant development. GA derepresses its signaling pathway by promoting the degradation of DELLA proteins, a family of nuclear growth repressors. Although the floral organ identity is established in flowers of the GA-deficient mutant ga1-3, the growth of all floral organs is severely retarded. In particular, abortive anther development in ga1-3 results in male sterility. Genetic analysis has revealed that various combinations of null mutants of DELLA proteins could gradually rescue floral organ defects in ga1-3 and that RGA is the most important DELLA protein involved in floral organ development. To elucidate the early molecular events controlled by RGA during flower development, we performed whole-genome microarray analysis to identify genes in response to the steroid-inducible activation of RGA in ga1-3 rgl2 rga 35S:RGA-GR. Although DELLA proteins were suggested as transcriptional repressors, similar numbers of genes were down-regulated or up-regulated by RGA during floral organ development. More than one-third of RGA down-regulated genes were specifically or predominantly expressed in stamens. A significant number of RGA-regulated genes are involved in phytohormone signaling or stress response. Further expression analysis through activation of RGA by steroid induction combined with cycloheximide identified eight genes as immediate targets of RGA. In situ hybridization and transgenic studies further showed that the expression pattern and function of several selected genes were consistent with the predictions from microarray analysis. These results suggest that DELLA regulation of floral organ development is modulated by multiple phytohormones and stress signaling pathways.

Global identification of DELLA target genes during Arabidopsis flower development

Gibberellin (GA) plays important roles in regulating many aspects of plant development. GA derepresses its signaling pathway by promoting the degradation of DELLA proteins, a family of nuclear growth repressors. Although the floral organ identity is established in flowers of the GA-deficient mutant ga1-3, the growth of all floral organs is severely retarded. In particular, abortive anther development in ga1-3 results in male sterility. Genetic analysis has revealed that various combinations of null mutants of DELLA proteins could gradually rescue floral organ defects in ga1-3 and that RGA is the most important DELLA protein involved in floral organ development. To elucidate the early molecular events controlled by RGA during flower development, we performed whole-genome microarray analysis to identify genes in response to the steroid-inducible activation of RGA in ga1-3 rgl2 rga 35S:RGA-GR. Although DELLA proteins were suggested as transcriptional repressors, similar numbers of genes were down-regulated or up-regulated by RGA during floral organ development. More than one-third of RGA down-regulated genes were specifically or predominantly expressed in stamens. A significant number of RGA-regulated genes are involved in phytohormone signaling or stress response. Further expression analysis through activation of RGA by steroid induction combined with cycloheximide identified eight genes as immediate targets of RGA. In situ hybridization and transgenic studies further showed that the expression pattern and function of several selected genes were consistent with the predictions from microarray analysis. These results suggest that DELLA regulation of floral organ development is modulated by multiple phytohormones and stress signaling pathways.