A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis

Identification and deletion analysis of the promoter of the pepper SAR8.2 gene activated by bacterial infection and abiotic stresses

The pepper SAR8.2 gene, CASAR82A, was locally and systemically induced in pepper plants which had been infected by Xanthomonas campestris pv. vesicatoria or by Pseudomonas fluorescens. The DNA 1,283 bp sequence upstream of the CASAR82A gene was assessed with regard to the activity of the CASAR82A promoter fused to the beta-glucuronidase (GUS) reporter gene, via an Agrobacterium-mediated transient expression assay. In tobacco leaves which transiently expressed the -831 bp CASAR82A promoter, GUS activity was locally and systemically induced by Pseudomonas syringae pv. tabaci. GUS activity, which was driven by the -831 promoter, was also differentially activated in the leaves as the result of treatment with salicylic acid, ethylene, methyl jasmonate, abscisic acid, NaCl, and low temperatures. The -831 bp sequence upstream of the CASAR82A gene elicited full promoter activity in response to pathogen infection, abiotic elicitors, and environmental stresses. The expression of the pepper transcription factor, CARAV1, was shown to activate the CASAR82A promoter. Analyses of a series of 5'-deletions of the CASAR82A promoter revealed that novel cis-acting elements necessary for the induction of gene expression as the result of exposure to pathogen and abiotic elicitors appear to be localized in the promoter region between -831 and -759 bp.

Factors modulating the levels of the allelochemical sorgoleone in Sorghum bicolor

Sorgoleone is the major component of the hydrophobic root exudate of sorghum [Sorghum bicolor (L.) Moench]. The presence of this allelochemical is intrinsically linked to root growth and the development of mature root hairs. However, factors modulating root formation and the biosynthesis of sorgoleone are not well known. Sorgoleone production was independent of early stages of plant development. The optimum temperature for root growth and sorgoleone production was 30 degrees C. Seedling development and sorgoleone levels were greatly reduced at temperatures below 25 degrees C and above 35 degrees C. The level of sorgoleone was also sensitive to light, being reduced by nearly 50% upon exposure to blue light (470 nm) and by 23% with red light (670 nm). Applying mechanical pressure over developing seedlings stimulated root formation but did not affect the biosynthesis of this lipid benzoquinone. Sorgoleone production did not change in seedlings exposed to plant defense elicitors. On the other hand, sorgoleone levels increased in plants treated with a crude extract of velvetleaf (Abutilon theophrasti Medik.) root. This stimulation was not associated with increased osmotic stress, since decreases in water potential (Psi(w)) by increasing solute concentrations with sorbitol reduces sorgoleone production. Sorgoleone production appears to be constitutively expressed in young developing sorghum plants. Other than with temperature, changes in the environmental factors had either no effect or caused a reduction in sorgoleone levels. However, the stimulation observed with velvetleaf root crude extract suggests that sorghum seedlings may respond to the presence of other plants by releasing more of this allelochemical.

The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens

The pathogen Agrobacterium tumefaciens infects a broad range of plants, introducing the T-DNA into their genome. Contrary to all known bacterial phytopathogens, A. tumefaciens lacks the hypersensitive response-inducing hrp genes, although it introduces numerous proteins into the plant cell through a type IV secretion system. To understand the timing and extent of the plant transcriptional response to this unusual pathogen, we used an Arabidopsis 26,000-gene oligonucleotide microarray. We inoculated Arabidopsis cell cultures with an oncogenic Agrobacterium strain and analyzed four biological replicates to identify two robust sets of regulated genes, one induced and the other suppressed. In both cases, the response was distinct at 48 h after infection, but not at 24 h or earlier. The induced set includes genes encoding known defense proteins, and the repressed set is enriched with genes characteristic of cell proliferation even though a growth arrest was not visible in the inoculated cultures. The analysis of the repressed genes revealed that the conserved upstream regulatory elements Frankiebox (also known as "site II") and Telobox are associated with the suppression of gene expression. The regulated gene sets should be useful in dissecting the signaling pathways in this plant-pathogen interaction.

A model of the ethylene signaling pathway and its gene response in Arabidopsis thaliana: pathway cross-talk and noise-filtering properties

Dynamic models of molecular networks and pathways enable in silico evaluations of the consistency of proposed interactions and the outcomes of perturbations as well as of hypotheses on system-level structure and function. We postulate a continuous model of the activation dynamics of the ethylene response factor 1 (ERF1) gene in response to ethylene signaling. This activation elicits the response of the plant defensin 1 (PDF1) gene, which also responds to jasmonic acid, and the inhibition of the putative auxin responsive factor 2 (ARF2) gene, that also responds to auxin. Our model allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated and seems to consider key components of the ethylene pathway because the ERF1 dose-response curve that we predict has the same qualitative form as the phenotypic dose-response curves obtained experimentally. Therefore, our model suggests that the phenotypic dose-response curves obtained experimentally could be due, at least in part, to ERF1 changes to different ethylene concentrations. Stability analyses show that the model's results are robust to parameter estimates. Of interest is that our model predicts that the ethylene pathway may filter stochastic and rapid chaotic fluctuations in ethylene availability. This novel approach may be applied to any cellular signaling and response pathway in plants and animals.

A second member of the Nicotiana glauca lipid transfer protein gene family, NgLTP2, encodes a divergent and differentially expressed protein

Multiple, highly similar members of the lipid transfer protein (LTP) family have been identified in Nicotiana glauca L. Here we describe four new members of the NgLTP gene family and further characterise one member. Three genes were isolated from a guard cell cDNA library and one (NgLTP2) was isolated from a genomic library. These four NgLTPs, as well as one described previously, NgLTP1, share >83% amino acid similarity, but the deduced protein sequence of NgLTP2 lacks the last five residues compared with other LTPs. Since the DNA sequences of the five genes are nearly identical, techniques based on nucleic acid hybridisation or PCR amplification were not sufficient to resolve the expression of the individual genes with confidence. Therefore, we characterised the expression pattern of NgLTP2, the only NgLTP gene that was not found in the guard cell cDNA library, using an NgLTP2 promoter-GUS reporter assay. GUS activity driven by the NgLTP2 promoter was assayed in three species of transgenic plants as an indicator of the endogenous pattern of expression of this gene. GUS was strongly induced upon wounding, whereas NgLTP1 was induced by drought stress. Sequence analysis of the NgLTP2 promoter revealed cis-acting motifs associated with induction by wounding. Differential expression of the NgLTP gene family, revealed by the different expression patterns of NgLTP1 and NgLTP2, is further evidence that these genes have multiple functions in N. glauca.

The role of ethylene in host-pathogen interactions

The phytohormone ethylene is a principal modulator in many aspects of plant life, including various mechanisms by which plants react to pathogen attack. Induced ethylene biosynthesis and subsequent intracellular signaling through a single conserved pathway have been well characterized. This leads to a cascade of transcription factors consisting of primary EIN3-like regulators and downstream ERF-like transcription factors. The latter control the expression of various effector genes involved in various aspects of systemic induced defense responses. Moreover, at this level significant cross-talk occurs with other defense response pathways controlled by salicylic acid and jasmonate, eventually resulting in a differentiated disease response.

An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family

AP2/EREBP transcription factors (TFs) play functionally important roles in plant growth and development, especially in hormonal regulation and in response to environmental stress. Here we reported verification and correction of annotation through an exhaustive cDNA cloning and sequence analysis performed on 145 of 147 gene family members. A RACE analysis performed on genes with potential in-frame up-stream ATG codon resulted in identification of At2g28520 as an authentic AP2/EREBP member and corrected ORF annotations for three other members. A further phylogenetic analysis of this updated and likely complete family divided it into three major subfamilies. The expression patterns of the AP2/EREBP family members among the 11 organ or tissue types were examined using an oligo microarray and their hormonal and environmental responsiveness were further characterized using cDNA custom macroarrays. These detailed expression profile results provide strong support for a role for AP2/EREBP family members in development and in response to environmental stimuli, and a foundation for future functional analysis of this gene family.

The SEN1 gene of Arabidopsis is regulated by signals that link plant defence responses and senescence

Plant defence and senescence share many similarities as evidenced by extensive co-regulation of many genes during these responses. To better understand the nature of signals that are common to plant defence and senescence, we studied the regulation of SEN1 encoding a senescence-associated protein during plant defence responses in Arabidopsis. Pathogen inoculations and treatments with defence-related chemical signals, salicylic acid and methyl jasmonate induced changes in SEN1 transcript levels. Analysis of transgenic plants expressing the SEN1 promoter fused to uidA reporter gene confirmed the responsiveness of the SEN1 promoter to defence- and senescence-associated signals. Expression analysis of SEN1 in a number of defence signalling mutants indicated that activation of this gene by pathogen occurs predominantly via the salicylic and jasmonic acid signalling pathways, involving the functions of EDS5, NPR1 and JAR1. In addition, in the absence of pathogen challenge, the cpr5/hys1 mutant showed elevated SEN1 expression and displayed an accelerated senescence response following inoculation with the necrotrophic fungal pathogen Fusarium oxysporum. Although the analysis of the sen1-1 knock-out mutant did not reveal any obvious role for this gene in defence or senescence-associated events, our results presented here show that SEN1 is regulated by signals that link plant defence and senescence responses and thus represents a useful marker gene to study the overlap between these two important physiological events.

Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression

To identify transcription factors (TFs) involved in jasmonate (JA) signaling and plant defense, we screened 1,534 Arabidopsis (Arabidopsis thaliana) TFs by real-time quantitative reverse transcription-PCR for their altered transcript at 6 h following either methyl JA treatment or inoculation with the incompatible pathogen Alternaria brassicicola. We identified 134 TFs that showed a significant change in expression, including many APETALA2/ethylene response factor (AP2/ERF), MYB, WRKY, and NAC TF genes with unknown functions. Twenty TF genes were induced by both the pathogen and methyl JA and these included 10 members of the AP2/ERF TF family, primarily from the B1a and B3 subclusters. Functional analysis of the B1a TF AtERF4 revealed that AtERF4 acts as a novel negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. In contrast, functional analysis of the B3 TF AtERF2 showed that AtERF2 is a positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. Our results suggest that plants coordinately express multiple repressor- and activator-type AP2/ERFs during pathogen challenge to modulate defense gene expression and disease resistance.

Repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of Arabidopsis transcription factor gene expression

To identify transcription factors (TFs) involved in jasmonate (JA) signaling and plant defense, we screened 1,534 Arabidopsis (Arabidopsis thaliana) TFs by real-time quantitative reverse transcription-PCR for their altered transcript at 6 h following either methyl JA treatment or inoculation with the incompatible pathogen Alternaria brassicicola. We identified 134 TFs that showed a significant change in expression, including many APETALA2/ethylene response factor (AP2/ERF), MYB, WRKY, and NAC TF genes with unknown functions. Twenty TF genes were induced by both the pathogen and methyl JA and these included 10 members of the AP2/ERF TF family, primarily from the B1a and B3 subclusters. Functional analysis of the B1a TF AtERF4 revealed that AtERF4 acts as a novel negative regulator of JA-responsive defense gene expression and resistance to the necrotrophic fungal pathogen Fusarium oxysporum and antagonizes JA inhibition of root elongation. In contrast, functional analysis of the B3 TF AtERF2 showed that AtERF2 is a positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation. Our results suggest that plants coordinately express multiple repressor- and activator-type AP2/ERFs during pathogen challenge to modulate defense gene expression and disease resistance.

Molecular players regulating the jasmonate signalling network

Many plant developmental and stress responses require the coordinated interaction of the jasmonate and other signalling pathways, such as those for ethylene, salicylic acid and abscisic acid. Recent research in Arabidopsis has uncovered several key players that regulate crosstalk between these signalling pathways and that shed light on the molecular mechanisms modulating this coordinated interaction. Genes that are involved in the regulation of protein stability through the ubiquitin-proteasome pathway (COI1, AXR1 and SGT1b), signalling proteins (MPK4) and transcription factors (AtMYC2, ERF1, NPR1 and WRKY70) form a regulatory network that allows the plant to fine-tune specific responses to different stimuli.

Microarray Analysis Reveals Vegetative Molecular Phenotypes of Arabidopsis Flowering-time Mutants

The transition to flowering occurs at the shoot apex; however, most of the characterized genes that affect the timing of floral induction are expressed throughout the plant. To further our understanding of these genes and the flowering process, the vegetative molecular phenotypes of 16 Arabidopsis mutants associated with the major flowering initiation pathways were assayed using a 13,000 clone microarray under two different conditions that affect flowering. All mutants showed at least one change in gene expression other than the mutant flowering gene. Metabolism- and defence-related pathways were the areas with the most frequent gene expression changes detected in the mutants. Several genes such as EARLI1 were differentially expressed in a number of flowering mutants from different flowering pathways. Analysis of the promoter regions of genes differentially expressed identified common promoter elements, indicating some form of common regulation.

Elicitor signal transduction leading to production of plant secondary metabolites

Plant secondary metabolites are unique sources for pharmaceuticals, food additives, flavors, and other industrial materials. Accumulation of such metabolites often occurs in plants subjected to stresses including various elicitors or signal molecules. Understanding signal transduction paths underlying elicitor-induced production of secondary metabolites is important for optimizing their commercial production. This paper summarizes progress made on several aspects of elicitor signal transduction leading to production of plant secondary metabolites, including: elicitor signal perception by various receptors of plants; avirulence determinants and corresponding plant R proteins; heterotrimeric and small GTP binding proteins; ion fluxes, especially Ca2+ influx, and Ca2+ signaling; medium alkalinization and cytoplasmic acidification; oxidative burst and reactive oxygen species; inositol trisphosphates and cyclic nucleotides (cAMP and cGMP); salicylic acid and nitric oxide; jasmonate, ethylene, and abscisic acid signaling; oxylipin signals such as allene oxide synthase-dependent jasmonate and hydroperoxide lyase-dependent C12 and C6 volatiles; as well as other lipid messengers such as lysophosphatidylcholine, phosphatidic acid, and diacylglycerol. All these signal components are employed directly or indirectly by elicitors for induction of plant secondary metabolite accumulation. Cross-talk between different signaling pathways is very common in plant defense response, thus the cross-talk amongst these signaling pathways, such as elicitor and jasmonate, jasmonate and ethylene, and each of these with reactive oxygen species, is discussed separately. This review also highlights the integration of multiple signaling pathways into or by transcription factors, as well as the linkage of the above signal components in elicitor signaling network through protein phosphorylation and dephosphorylation. Some perspectives on elicitor signal transduction and plant secondary metabolism at the transcriptome and metabolome levels are also presented.

Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses

The phytohormone abscisic acid (ABA) modulates the expression of many genes important to plant growth and development and to stress adaptation. In this study, we found that an APETALA2/EREBP-type transcription factor, AtERF7, plays an important role in ABA responses. AtERF7 interacts with the protein kinase PKS3, which has been shown to be a global regulator of ABA responses. AtERF7 binds to the GCC box and acts as a repressor of gene transcription. AtERF7 interacts with the Arabidopsis thaliana homolog of a human global corepressor of transcription, AtSin3, which in turn may interact with HDA19, a histone deacetylase. The transcriptional repression activity of AtERF7 is enhanced by HDA19 and AtSin3. Arabidopsis plants overexpressing AtERF7 show reduced sensitivity of guard cells to ABA and increased transpirational water loss. By contrast, AtERF7 and AtSin3 RNA interference lines show increased sensitivity to ABA during germination. Together, our results suggest that AtERF7 plays an important role in ABA responses and may be part of a transcriptional repressor complex and be regulated by PKS3.

Functional analysis of Arabidopsis ethylene-responsive element binding protein conferring resistance to Bax and abiotic stress-induced plant cell death

Arabidopsis (Arabidopsis thaliana) ethylene-responsive element binding protein (AtEBP) gene was isolated as a suppressor of Bax-induced cell death by functional screening in yeast (Saccharomyces cerevisiae). To further examine the cell death suppressive action of AtEBP in plant cells, we established transgenic tobacco (Nicotiana tabacum) plants overexpressing AtEBP as well as transgenic tobacco plants ectopically expressing mouse Bax protein under a dexamethasone-inducible promoter. We prepared the crosses of the selective lines of each transgenic plant, which were evaluated in terms of cell death suppression activity. Results indicate that AtEBP suppressed Bax-induced cell death in tobacco plants, an action also associated with a lowered level of ion leakage. Furthermore, tobacco Bright Yellow-2 cells overexpressing AtEBP conferred resistance to hydrogen peroxide (H(2)O(2)) and heat treatments. AtEBP protein localized in the nucleus and functioned as an in vivo transcription activator as confirmed in transient assays and experiments using stable transgenic system. Up-regulation of defense genes was observed in transgenic Arabidopsis plants overexpressing AtEBP. Based on the analysis of mRNA accumulation in ethylene-related mutants, the position of AtEBP in signaling pathway is presented.

Arabidopsis ERF4 is a transcriptional repressor capable of modulating ethylene and abscisic acid responses

ERFs (ethylene-responsive element binding factors) belong to a large family of plant transcription factors that are found exclusively in plants. A small subfamily of ERF proteins can act as transcriptional repressors. The Arabidopsis genome contains eight ERF repressors, namely AtERF3, AtERF4, and AtERF7 to AtERF12. Members of ERF repressors show differential expression, suggesting that they may have different function. Using a transient expression system, we demonstrated that AtERF4, AtERF7, AtERF10, AtERF11 and AtERF12 can function as transcriptional repressors. The expression of AtERF4 can be induced by ethylene, jasmonic acid, and abscisic acid (ABA). By using green fluorescent protein fusion, we demonstrated that AtEFR4 accumulated in the nuclear bodies of Arabidopsis cells. Expression of 35S:AtERF4-GFP in transgenic Arabidopsis plants conferred an ethylene-insensitive phenotype and repressed the expression of Basic Chitinase and beta-1,3-Glucanase, the GCC-box-containing genes. In comparison with wild-type plants, 35S:AtERF4-GFP transgenic plants had decreased sensitivity to ABA and were hypersensitive to sodium chloride. The expression of the ABA responsive genes, ABI2, rd29B and rab18, was decreased in the 35S:AtERF4-GFP transgenic plants. Our study provides evidence that AtERF4 is a negative regulator capable of modulating ethylene and abscisic acid responses.

Herbivore-induced, indirect plant defences

Indirect responses are defensive strategies by which plants attract natural enemies of their herbivores that act as plant defending agents. Such defences can be either constitutively expressed or induced by the combined action of mechanical damage and low- or high-molecular-weight elicitors from the attacking herbivore. Here, we focus on two induced indirect defences, namely the de novo production of volatiles and the secretion of extrafloral nectar, which both mediate interactions with organisms from higher trophic levels (i.e., parasitoids or carnivores). We give an overview on elicitors, early signals, and signal transduction resulting in a complex regulation of indirect defences and discuss effects of cross-talks between the signalling pathways (synergistic and antagonistic effects). In the light of recent findings, we review molecular and genetic aspects of the biosynthesis of herbivore-induced plant volatiles comprising terpenoids, aromatic compounds, and metabolites of fatty acids which act as infochemicals for animals and some of which even induce defence genes in neighbouring plants. Finally, ecological aspects of these two indirect defences such as their variability, specificity, evolution as well as their ecological relevance in nature are discussed.

Plant defence responses: conservation between models and crops

Diseases of plants are a major problem for agriculture world wide. Understanding the mechanisms employed by plants to defend themselves against pathogens may lead to novel strategies to enhance disease resistance in crop plants. Much of the research in this area has been conducted with Arabidopsis as a model system, and this review focuses on how relevant the knowledge generated from this model system will be for increasing resistance in crop plants. In addition, the progress made using other model plant species is discussed. While there appears to be substantial similarity between the defence responses of Arabidopsis and other plants, there are also areas where significant differences are evident. For this reason it is also necessary to increase our understanding of the specific aspects of the defence response that cannot be studied using Arabidopsis as a model.

Concurrent activation of cell death-regulating signaling pathways by singlet oxygen in Arabidopsis thaliana

Upon a dark/light shift the conditional flu mutant of Arabidopsis starts to generate singlet oxygen ((1)O(2)), a non-radical reactive oxygen species that is restricted to the plastid compartment. Immediately after the shift, plants stop growing and develop necrotic lesions. We have established a protoplast system, which allows detection and characterization of the death response in flu induced by the release of (1)O(2). Vitamin B6 that quenches (1)O(2) in fungi was able to protect flu protoplasts from cell death. Blocking ethylene production was sufficient to partially inhibit the death reaction. Similarly, flu mutant seedlings expressing transgenic NahG were partially protected from the death provoked by the release of (1)O(2), indicating a requirement for salicylic acid (SA) in this process, whereas in cells depleted of both, ethylene and SA, the extent of cell death was reduced to the wild-type level. The flu mutant was also crossed with the jasmonic acid (JA)-depleted mutant opr3, and with the JA, OPDA and dinor OPDA (dnOPDA)-depleted dde2-2 mutant. Analysis of the resulting double mutants revealed that in contrast to the JA-induced suppression of H(2)O(2)/superoxide-dependent cell death reported earlier, JA promotes singlet oxygen-mediated cell death in flu, whereas other oxylipins such as OPDA and dnOPDA antagonize this death-inducing activity of JA.

Evaluation of natural and synthetic stimulants of plant immunity by microarray technology

Induction of local defence, as well as systemic resistance, of plants is associated with transcriptional reprogramming. Here we report on defence gene induction by natural and synthetic stimulants of plant immunity. Gene expression changes in Arabidopsis thaliana were monitored in response to several plant immunity stimulants (plant activators) using Northern blotting and an application-based array representing c. 750 genes involved in several aspects of plant defence and/or plant stress. The commercial plant activators Bio-S, Neudo-Vital and PRORADIX have been shown to induce systemic resistance. Here, Neudo-Vital, PRORADIX and Bio-S treatment induced different patterns of salicylic acid (SA) and jasmonic acid (JA) accumulation. Gene induction by these plant activators proved to be very complex. Rather than simply mimicking one of the known defence pathways induced by SA or JA, the response to the plant activators showed aspects of both major defence systems. A general feature was the transient activation of JA biosynthesis genes, combined with a much more sustained SA-associated defence gene induction. Our results demonstrate that plant immunity stimulants activate systemic immunity at the transcriptional level, and they provide insight into the coordinated transcriptional regulation of several classes of plant defence genes.

Antagonistic interaction between abscisic acid and jasmonate-ethylene signaling pathways modulates defense gene expression and disease resistance in Arabidopsis

The plant hormones abscisic acid (ABA), jasmonic acid (JA), and ethylene are involved in diverse plant processes, including the regulation of gene expression during adaptive responses to abiotic and biotic stresses. Previously, ABA has been implicated in enhancing disease susceptibility in various plant species, but currently very little is known about the molecular mechanisms underlying this phenomenon. In this study, we obtained evidence that a complex interplay between ABA and JA-ethylene signaling pathways regulate plant defense gene expression and disease resistance. First, we showed that exogenous ABA suppressed both basal and JA-ethylene-activated transcription from defense genes. By contrast, ABA deficiency as conditioned by the mutations in the ABA1 and ABA2 genes, which encode enzymes involved in ABA biosynthesis, resulted in upregulation of basal and induced transcription from JA-ethylene responsive defense genes. Second, we found that disruption of AtMYC2 (allelic to JASMONATE INSENSITIVE1 [JIN1]), encoding a basic helix-loop-helix Leu zipper transcription factor, which is a positive regulator of ABA signaling, results in elevated levels of basal and activated transcription from JA-ethylene responsive defense genes. Furthermore, the jin1/myc2 and aba2-1 mutants showed increased resistance to the necrotrophic fungal pathogen Fusarium oxysporum. Finally, using ethylene and ABA signaling mutants, we showed that interaction between ABA and ethylene signaling is mutually antagonistic in vegetative tissues. Collectively, our results indicate that the antagonistic interactions between multiple components of ABA and the JA-ethylene signaling pathways modulate defense and stress responsive gene expression in response to biotic and abiotic stresses.

The ethylene-, jasmonate-, abscisic acid- and NaCl-responsive tomato transcription factor JERF1 modulates expression of GCC box-containing genes and salt tolerance in tobacco

Ethylene responsive factors (ERFs) are important plant-specific transcription factors, some of which have been demonstrated to interact with the ethylene-responsive GCC box and the dehydration-responsive element (DRE); however, data on the roles of ERF proteins in connection with various signaling pathways are limited. In this research, we used the GCC box, an essential cis-acting element responsive to ethylene and methyl jasmonate (MeJA), as bait in a yeast one-hybrid system to isolate transcription factors from tomato (Lycopersicon esculentum Mill.). One of the cDNAs, which was designated Jasmonate and Ethylene Response Factor 1 (JERF1), encodes an ERF protein, containing a conserved ERF DNA-binding motif and functioning as a transcriptional activator in yeast through targeting to the nucleus in onion (Allium cepa L.) epidermal cells. Biochemical analysis revealed that JERF1 bound not only to the GCC box but also to the DRE sequence. Expression of the JERF1 gene in tomato was induced by ethylene, MeJA, abscisic acid (ABA) and salt treatment, indicating that JERF1 might act as a connector among different signal transduction pathways. Further research with transgenic JERF1 tobacco (Nicotiana tabacum L.) plants indicated that overexpressing JERF1 activated expression of GCC box-containing genes such as osmotin, GLA, Prb-1b and CHN50 under normal growth conditions, and subsequently resulted in enhanced tolerance to salt stress, suggesting that JERF1 modulates osmotic tolerance by activation of downstream gene expression through interaction with the GCC box or DRE.

Phylogenetic analysis of 5'-noncoding regions from the ABA-responsive rab16/17 gene family of sorghum, maize and rice provides insight into the composition, organization and function of cis-regulatory modules

Phylogenetic analysis of sequences from gene families and homologous genes from species of varying divergence can be used to identify conserved noncoding regulatory elements. In this study, phylogenetic analysis of 5'-noncoding sequences was optimized using rab17, a well-characterized ABA-responsive gene from maize, and five additional rab16/17 homologs from sorghum and rice. Conserved 5'-noncoding sequences among the maize, sorghum, and rice rab16/17 homologs were identified with the aid of the software program FootPrinter and by screening for known transcription-factor-binding sites. Searches for 7 of 8 (7/8)bp sequence matches within aligned 5'-noncoding segments of the rab genes identified many of the cis-elements previously characterized by biochemical analysis in maize rab17 plus several additional putative regulatory elements. Differences in the composition of conserved noncoding sequences among rab16/17 genes were related to variation in rab gene mRNA levels in different tissues and to response to ABA treatment using qRT-PCR. Absence of a GRA-like element in the promoter of sorghum dhn2 relative to maize rab17 was correlated with an approximately 85-fold reduction of dhn2 RNA in sorghum shoots. Overall, we conclude that phylogenetic analysis of gene families among rice, sorghum, and maize will help identify regulatory sequences in the noncoding regions of genes and contribute to our understanding of grass gene regulatory networks.

Tomato TERF1 modulates ethylene response and enhances osmotic stress tolerance by activating expression of downstream genes

The interaction between ethylene and osmotic stress pathways modulates the expression of the genes relating to stress adaptation; however, the mechanism is not well understood. In this paper, we report a novel ethylene responsive factor, tomato ethylene responsive factor 1 (TERF1), that integrates ethylene and osmotic stress pathways. Biochemical analysis indicated that TERF1 binds to the GCC box (an element responsive to ethylene) and to the dehydration responsive element, which is responsive to the osmoticum. Expression of TERF1 was induced by ethylene and NaCl treatment. Under normal growth conditions, overexpression of TERF1 in tobacco activated the expression of GCC box-containing pathogen related genes and also caused the typical ethylene triple response. Further investigation indicated that transgenic TERF1 tobacco exhibited salt tolerance, suggesting that TERF1 might function as a linker between the ethylene and osmotic stress pathways.

Analysis of transcripts that are differentially expressed in three sectors of the rice root system under water deficit

Short periods of water deprivation can stimulate the growth of seminal and lateral roots in rice, and inhibit the emergence of adventitious roots. Identification of genes in the different tissues that respond to a water deficit may help us to understand the mechanism underlying root growth under conditions when water is scarce. cDNA-amplified fragment length polymorphism (AFLP) analysis was used to profile gene expression upon imposition of water deficit in three types of root tissue from the upland rice variety Azucena: seminal root tips, lateral root zones and adventitious root primordial zones. In all, 121 unique transcript-derived fragments (TDFs) were cloned, and Northern analysis was carried out for 30 TDFs to confirm their expression patterns. Sixty-six TDFs were differentially expressed in all three root samples. Four (AC2, D6, L22 and T23) were up-regulated by water deficit in seminal root tips and lateral root zones, and down-regulated in adventitious root primordial zones, an expression pattern which reflects the phenotypic changes observed in the different root sectors. In contrast, T17 and T37 showed the opposite expression pattern in Azucena: up-regulation in adventitious roots and repression in the other two zones. Functions could be assigned to five of these six TDFs on the basis of homology: they encode an expansin (T37), a fruit-ripening protein similar to ASR (T23), submergence-induced protein 2A (T17), a dehydrin (D6) and a 9- cis -epoxycarotenoid dioxygenase1 (L22), respectively. AC2 did not show a significant match to any known gene. Northern analysis showed that these six clones exhibited expression patterns that differed between the two cultivars tested (Azucena and the lowland variety IR1552) with respect to regulation by water limitation. Furthermore, T17, T37, D6 and T23 mapped within intervals known to contain QTLs (quantitative trait loci) for root growth in rice under water deficit. These genes may regulate or co-regulate the growth and development of the three root zones in a tissue-specific manner, and may play a role in the processes that underlie the early changes in root architecture under conditions of water deprivation.

Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis

Jasmonates (JA) are important regulators of plant defense responses that activate expression of many wound-induced genes including the tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes. Elements required for JA induction of the LAP gene are all present in the -317 to -78 proximal promoter region. Using yeast one-hybrid screening, we have identified the bHLH-leu zipper JAMYC2 and JAMYC10 proteins, specifically recognizing a T/G-box AACGTG motif in this promoter fragment. Mutation of the G-box element decreases JA-responsive LAP promoter expression. Expression of JAMYC2 and JAMYC10 is induced by JA, with a kinetics that precedes that of the LAP or pin2 transcripts. JAMYC overexpression enhanced JA-induced expression of these defense genes in potato, but did not result in constitutive transcript accumulation. Using footprinting assays, an additional protected element was identified, located directly adjacent to the T/G-box motif. Mutation of this element abolishes JA response, showing that recognition of this duplicated element is also required for gene expression. Knockout mutants in the AtMYC2 homolog gene of Arabidopsis are insensitive to JA and exhibit a decreased activation of the JA-responsive genes AtVSP and JR1. Activation of the PDF1.2 and b-CHI, ethylene/JA-responsive genes, is, however, increased in these mutants. These results show that the JAMYC/AtMYC2 transcription factors function as members of a MYC-based regulatory system conserved in dicotyledonous plants with a key role in JA-induced defense gene activation.

Regulation of disease resistance pathways by AP2/ERF transcription factors

The AP2 transcription factor family, found only in plants, includes several genes that encode proteins involved in the regulation of disease resistance pathways. These genes are members of the ethylene response factor (ERF) subfamily of AP2 transcription factor genes, which have only a single DNA-binding domain and are distinct from members of the dehydration-responsive element binding (DREB) subfamily. Some ERF subgroups are enriched in such genes, suggesting that they have conserved functions that are required for the regulation of disease resistance pathways. The expression of several ERF genes is regulated by plant hormones, such as jasmonic acid, salicylic acid and ethylene, as well as by pathogen challenge. A phylogenetic overview of these genes, with a focus on Arabidopsis, rice and tomato, suggests that despite broad conservation of their function in monocots and dicots, some structural elements are specialized within each of these two lineages.

Plant growth-promoting rhizobacteria systemically protect Arabidopsis thaliana against Cucumber mosaic virus by a salicylic acid and NPR1-independent and jasmonic acid-dependent signaling pathway

Arabidopsis thaliana ecotype Columbia plants (Col-0) treated with plant growth-promoting rhizobacteria (PGPR) Serattia marcescens strain 90-166 and Bacillus pumilus strain SE34 had significantly reduced symptom severity by Cucumber mosaic virus (CMV). In some cases, CMV accumulation was also significantly reduced in systemically infected leaves. The signal transduction pathway(s) associated with induced resistance against CMV by strain 90-166 was determined using mutant strains and transgenic and mutant Arabidopsis lines. NahG plants treated with strains 90-166 and SE34 had reduced symptom severity indicating that the resistance did not require salicylic acid (SA). Strain 90-166 naturally produces SA under iron-limited conditions. Col-0 and NahG plants treated with the SA-deficient mutant, 90-166-1441, had significantly reduced CMV symptom severity with reduced virus accumulation in Col-0 plants. Another PGPR mutant, 90-166-2882, caused reduced disease severity in Col-0 and NahG plants. In a time course study, strain 90-166 reduced virus accumulation at 7 but not at 14 and 21 days post-inoculation (dpi) on the non-inoculated leaves of Col-0 plants. NahG and npr1-1 plants treated with strain 90-166 had reduced amounts of virus at 7 and 14 dpi but not at 21 dpi. In contrast, no decrease in CMV accumulation occurred in strain 90-166-treated fad3-2 fad7-2 fad8 plants. These data indicate that the protection of Arabidopsis against CMV by strain 90-166 follows a signaling pathway for virus protection that is independent of SA and NPR1, but dependent on jasmonic acid.

JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis

In spite of the importance of jasmonates (JAs) as plant growth and stress regulators, the molecular components of their signaling pathway remain largely unknown. By means of a genetic screen that exploits the cross talk between ethylene (ET) and JAs, we describe the identification of several new loci involved in JA signaling and the characterization and positional cloning of one of them, JASMONATE-INSENSITIVE1 (JAI1/JIN1). JIN1 encodes AtMYC2, a nuclear-localized basic helix-loop-helix-leucine zipper transcription factor, whose expression is rapidly upregulated by JA, in a CORONATINE INSENSITIVE1-dependent manner. Gain-of-function experiments confirmed the relevance of AtMYC2 in the activation of JA signaling. AtMYC2 differentially regulates the expression of two groups of JA-induced genes. The first group includes genes involved in defense responses against pathogens and is repressed by AtMYC2. Consistently, jin1 mutants show increased resistance to necrotrophic pathogens. The second group, integrated by genes involved in JA-mediated systemic responses to wounding, is activated by AtMYC2. Conversely, Ethylene-Response-Factor1 (ERF1) positively regulates the expression of the first group of genes and represses the second. These results highlight the existence of two branches in the JA signaling pathway, antagonistically regulated by AtMYC2 and ERF1, that are coincident with the alternative responses activated by JA and ET to two different sets of stresses, namely pathogen attack and wounding.

JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis

In spite of the importance of jasmonates (JAs) as plant growth and stress regulators, the molecular components of their signaling pathway remain largely unknown. By means of a genetic screen that exploits the cross talk between ethylene (ET) and JAs, we describe the identification of several new loci involved in JA signaling and the characterization and positional cloning of one of them, JASMONATE-INSENSITIVE1 (JAI1/JIN1). JIN1 encodes AtMYC2, a nuclear-localized basic helix-loop-helix-leucine zipper transcription factor, whose expression is rapidly upregulated by JA, in a CORONATINE INSENSITIVE1-dependent manner. Gain-of-function experiments confirmed the relevance of AtMYC2 in the activation of JA signaling. AtMYC2 differentially regulates the expression of two groups of JA-induced genes. The first group includes genes involved in defense responses against pathogens and is repressed by AtMYC2. Consistently, jin1 mutants show increased resistance to necrotrophic pathogens. The second group, integrated by genes involved in JA-mediated systemic responses to wounding, is activated by AtMYC2. Conversely, Ethylene-Response-Factor1 (ERF1) positively regulates the expression of the first group of genes and represses the second. These results highlight the existence of two branches in the JA signaling pathway, antagonistically regulated by AtMYC2 and ERF1, that are coincident with the alternative responses activated by JA and ET to two different sets of stresses, namely pathogen attack and wounding.

Real-time PCR: what relevance to plant studies?

The appearance of genetically modified organisms on the food market a few years ago, and the demand for more precise and reliable techniques to detect foreign (transgenic or pathogenic) DNA in edible plants, have been the driving force for the introduction of real-time PCR techniques in plant research. This was followed by numerous fundamental research applications aiming to study the expression profiles of endogenous genes and multigene families. Since then, the interest in this technique in the plant scientist community has increased exponentially. This review describes the technical features of quantitative real-time PCR that are especially relevant to plant research, and summarizes its present and future applications.

Ectopic overexpression of tomato JERF3 in tobacco activates downstream gene expression and enhances salt tolerance

The ethylene, jasmonic acid and osmotic signaling pathways respond to environmental stimuli and in order to understand how plants adapt to biotic and abiotic stresses it is important to understand how these pathways interact each other. In this paper, we report a novel ERF protein--jasmonate and ethylene-responsive factor 3 (JERF3)--that unites these pathways. JERF3, which functions as an in vivo transcription activator in yeast, binds to the GCC box, an element responsive to ethylene/JA signaling, as well as to DRE, a dehydration-responsive element that responds to dehydration, high salt and low-temperature. Expression of JERF3 in tomato is mainly induced by ethylene, JA, cold, salt or ABA. Constitutive expression of JERF3 in transgenic tobacco significantly activated expression of pathogenesis-related genes that contained the GCC box, resulting in enhanced tolerance to salt. These results indicate that JERF3 functions as a linker in ethylene- and osmotic stress-signaling pathways.

An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro

To analyze transcription factor-promoter interactions in Arabidopsis, a general strategy for generating a promoter microarray has been established. This includes an integrated platform for promoter sequence extraction and the design of primers for the PCR amplification of the promoter regions of annotated genes in the Arabidopsis genome. A web-interfaced primer-retrieval program was used to obtain up to 10 primer pairs with a suitability ranking given to each gene. We selected primer pairs for the promoters of about 3800 genes, and greater than 95% of the promoter fragments from the total genomic DNA were successfully amplified by PCR. These PCR products were purified and used to print an Arabidopsis promoter microarray. This initial promoter microarray was used to study the in vitro binding of the transcription factor HY5 to its promoter targets. A set of promoter fragments exhibited consistent and strong interaction with the HY5 protein in vitro, and computational analysis revealed that they were enriched with the HY5 consensus binding G-box motif. Thus, a promoter microarray can be a useful tool for identifying transcription factor binding sites at the genomic scale in higher plants.

The ethylene signaling pathway: new insights

During the past decade, molecular genetic studies on the reference plant Arabidopsis have established a largely linear signal transduction pathway for the response to ethylene gas. The biochemical modes of action of many of the signaling components are still unresolved. During the past year, however, progress in several areas has been made on several fronts. The different approaches used have included a functional study of the activity of the receptor His kinase, the determination of the ethylene receptor signaling complex at the endoplasmic reticulum and of the regulation of CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) activity by these receptors, the identification of a unique MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) cascade, the cloning and characterization of numerous ETHYLENE INSENSITIVE3 (EIN3)/EIN3-like (EIL) transcription factors from many plant species, and the integration of the ethylene and jasmonate response pathways via the ETHYLENE RESPONSE FACTOR (ERF) family of transcription factors. The elucidation of the biochemical mechanisms of ethylene signal transduction and the identification of new components in the ethylene response pathway in Arabidopsis are providing a framework for understanding how all plants sense and respond to ethylene.

Pathogen-responsive expression of a putative ATP-binding cassette transporter gene conferring resistance to the diterpenoid sclareol is regulated by multiple defense signaling pathways in Arabidopsis

The ATP-binding cassette (ABC) transporters are encoded by large gene families in plants. Although these proteins are potentially involved in a number of diverse plant processes, currently, very little is known about their actual functions. In this paper, through a cDNA microarray screening of anonymous cDNA clones from a subtractive library, we identified an Arabidopsis gene (AtPDR12) putatively encoding a member of the pleiotropic drug resistance (PDR) subfamily of ABC transporters. AtPDR12 displayed distinct induction profiles after inoculation of plants with compatible and incompatible fungal pathogens and treatments with salicylic acid, ethylene, or methyl jasmonate. Analysis of AtPDR12 expression in a number of Arabidopsis defense signaling mutants further revealed that salicylic acid accumulation, NPR1 function, and sensitivity to jasmonates and ethylene were all required for pathogen-responsive expression of AtPDR12. Germination assays using seeds from an AtPDR12 insertion line in the presence of sclareol resulted in lower germination rates and much stronger inhibition of root elongation in the AtPDR12 insertion line than in wild-type plants. These results suggest that AtPDR12 may be functionally related to the previously identified ABC transporters SpTUR2 and NpABC1, which transport sclareol. Our data also point to a potential role for terpenoids in the Arabidopsis defensive armory.