Regulation of ethylene-induced transcription of defense genes

Rapid and transient activation of transcription of the ERF3 gene by wounding in tobacco leaves: possible involvement of NtWRKYs and autorepression

This study investigated the regulatory mechanism of rapid and transient induction of a transcriptional repressor ERF3 gene by wounding in tobacco (Nicotiana tabacum) leaves. Deletion and mutation analysis of the promoter region have suggested that the proximal W boxes (TGAC(C/T)) and a GCC box, respectively, may be involved in the positive and negative regulation of wound-induced expression of the ERF3 gene. Electrophoretic mobility shift assays indicated that wounding enhanced the specific binding activity of nuclear factors to the W boxes. NtWRKY1, -2, and -4, which are tobacco group I WRKYs, interacted specifically with the W boxes and activated transcription via the W boxes. On the other hand, deletion of the GCC box from NsERF3 promoter-GUS reporter gene caused a delay in down-regulation of transcription after wound induction. In addition, ERF3 repressed transcription via the NsERF3 promoter activated by NtWRKYs. These results suggest the possible involvement of NtWRKYs and autorepression in the rapid and transient expression of the ERF3 gene by wounding.

Large-scale analysis of the barley transcriptome based on expressed sequence tags

To provide resources for barley genomics, 110,981 expressed sequence tags (ESTs) were generated from 22 cDNA libraries representing tissues at various developmental stages. This EST collection corresponds to approximately one-third of the 380,000 publicly available barley ESTs. Clustering and assembly resulted in 14,151 tentative consensi (TCs) and 11 073 singletons, altogether representing 25 224 putatively unique sequences. Of these, 17.5% showed no significant similarity to other barley ESTs present in dbEST. More than 41% of all barley genes are supposed to belong to multigene families and approximately 4% of the barley genes undergo alternative splicing. Based on the functional annotation of the set of unique sequences, the functional category 'Energy' was further analysed to reveal tissue- and stage-specific differences in gene expression. Hierarchical clustering of 362 differentially expressed TCs resulted in the identification of seven major clusters. The clusters reflect biochemical pathways predominantly activated in specific tissues and at various developmental stages. During seed germination glycolysis could be identified as the most predominant biochemical pathway. Germination-specific glycolysis is characterized by the coordinated expression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase, whose antagonistic actions possibly regulate the flux of amino acids into protein biosynthesis and gluconeogenesis respectively. The expression of defence-related and antioxidant genes during germination might be controlled by the ethylene-signalling pathway as concluded from the coordinated expression of those genes and the transcription factors (TF) EIN3 and EREBPG. Moreover, because of their predominant expression in germinating seeds, TF of the AP2 and MYB type are presumably major regulators of germination.

Overexpression of NtERF5, a new member of the tobacco ethylene response transcription factor family enhances resistance to tobacco mosaic virus

A new member of the tobacco (Nicotiana tabacum) AP2/ERF (ethylene response factor) transcription factor family, designated NtERF5, has been isolated by yeast one-hybrid screening. In vitro, recombinant NtERF5 protein weakly binds GCC box cis-elements, which mediate pathogen-regulated transcription of several PR (pathogenesis related) genes. NtERF5 transcription is transiently activated by wounding, by infection with the bacterial pathogen Pseudomonas syringae, as well as by inoculation with Tobacco mosaic virus (TMV). In contrast, NtERF5 transcription is not enhanced after application of salicylic acid, jasmonic acid, or ethylene. Constitutive overexpression of NtERF5 (ERF5-Oex) under control of the 35S promoter results in no visible alterations in plant growth or enhanced resistance to Pseudomonas infection. Furthermore, no constitutive expression of PR genes has been observed. In contrast, ERF5-Oex plants show enhanced resistance to TMV with reference to reduced size of local hypersensitive-response lesions and impaired systemic spread of the virus. Since, in TMV-infected ERF5-Oex plants, the viral RNA accumulates only up to 10 to 30% of the wild-type level, we suggest that NtERF5-regulated gene expression is controlling resistance to viral propagation. Previous research has demonstrated that overexpression of ERF genes enhances resistance to bacterial and fungal pathogens. Here, we provide further evidence that resistance to viral infection can be engineered by overexpression of ERF transcription factors.

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.

VOZ; Isolation and Characterization of Novel Vascular Plant Transcription Factors with a One-Zinc Finger from Arabidopsis thaliana

A 38-bp pollen-specific cis-acting region of the AVP1 gene is involved in the expression of the Arabidopsis thaliana V-PPase during pollen development. Here, we report the isolation and structural characterization of AtVOZ1 and AtVOZ2, novel transcription factors that bind to the 38-bp cis-acting region of A. thaliana V-PPase gene, AVP1. AtVOZ1 and AtVOZ2 show 53% amino acid sequence similarity. Homologs of AtVOZ1 and AtVOZ2 are found in various vascular plants as well as a moss, Physcomitrella patens. Promoter-β-glucuronidase reporter analysis shows that AtVOZ1 is specifically expressed in the phloem tissue and AtVOZ2 is strongly expressed in the root. In vivo transient effector-reporter analysis in A. thaliana suspension-cultured cells demonstrates that AtVOZ1 and AtVOZ2 function as transcriptional activators in the Arabidopsis cell. Two conserved regions termed Domain-A and Domain-B were identified from an alignment of AtVOZ proteins and their homologs of O. sativa and P. patens. AtVOZ2 binds as a dimer to the specific palindromic sequence, GCGTNx7ACGC, with Domain-B, which is comprised of a functional novel zinc coordinating motif and a conserved basic region. Domain-B is shown to function as both the DNA-binding and the dimerization domains of AtVOZ2. From highly the conservative nature among all identified VOZ proteins, we conclude that Domain-B is responsible for the DNA binding and dimerization of all VOZ-family proteins and designate it as the VOZ-domain.

Methyl jasmonate induced expression of the tobacco putrescine N -methyltransferase genes requires both G-box and GCC-motif elements

Putrescine N-methyltransferase (PMT) catalyzes the first committed step of nicotine biosynthesis, converting putrescine into N-methylputrescine. A variety of chemical, environmental, and developmental cues have been implicated in its regulation. Here we have examined the differential expression of beta-glucuronidase (GUS) transgenes under the control of the transcriptional regulatory sequences of four distinct members of the NtPMT gene family from tobacco (Nicotiana tabacum L.). BY-2 cell cultures expressing various NtPMT promoter-GUS constructs were examined for their response to treatment with various combinations of methyl jasmonate (MeJA), auxin (AUX), and ethylene (ETH). All four NtPMT gene promoters examined were inducible by MeJA, although the extent of the induction varied dramatically, with the NtPMT1a promoter being the most responsive. High AUX levels in the cell growth media repressed NtPMT::GUS transgene expression and inhibited their MeJA-induced transcription. Treatment of BY-2 cells with ETH alone did not result in a significant alteration in NtPMT::GUS expression. However, similar to AUX, ETH treatment led to the suppression of MeJA-induced transcription. Detailed deletion analysis of the NtPMT1a gene promoter showed that as little as 111 bp upstream of the transcriptional start site were sufficient to confer MeJA-responsiveness. Deletion of a conserved G-box element (GCACGTTG) at -103 to -96 bp completely abolished MeJA-responsiveness. Further mutagenesis studies revealed that in addition to a functional G-box, MeJA-responsiveness of the NtPMT1a promoter also required a TA-rich region and a GCC-motif (TGCGCCC) located at -80 to -69 bp and -62 to -56 bp relative to the start site, respectively. A synthetic G-box tetramer (4 X syn G-box) fused to a -83 bp fragment from the NtPMT1a promoter (containing the TA-rich region, GCC-box, and TATA-box) displayed a 30-fold induction by MeJA treatment, whereas when the 4 X syn G-box was fused to a minimal (-46 bp) promoter fragment derived from the CaMV 35S gene, no induction by MeJA treatment was detected. Our results indicate that multiple intersecting signal transduction pathways and different transcriptional regulatory factors are involved in mediating JA-responsiveness of NtPMT expression in tobacco.

Signal transduction systems regulating fruit ripening

Fruit ripening is a unique aspect of plant development with direct implications for a large component of the food supply and related areas of human health and nutrition. Recent advances in ripening research have given insights into the molecular basis of conserved developmental signals coordinating the ripening process and suggest that sequences related to floral development genes might be logical targets for additional discovery. Recent characterization of hormonal and environmental signal transduction components active in tomato fruit ripening (particularly ethylene and light) show conservation of signaling components yet novel gene family size and expression motifs that might facilitate complete and timely manifestation of ripening phenotypes. Emerging genomics tools and approaches are rapidly providing new clues and candidate genes that are expanding the known regulatory circuitry of ripening.

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.

Activation of a mitogen-activated protein kinase cascade induces WRKY family of transcription factors and defense genes in tobacco

Mitogen-activated protein kinase (MAPK) cascades are important signaling modules in eukaryotic cells that convert signals generated from the receptors/sensors to cellular responses. Upon activation, MAPKs can be translocated into nuclei where they phosphorylate transcription factors, which in turn activate gene expression. We recently identified NtMEK2, a tobacco MAPK kinase, as the upstream kinase of SIPK and WIPK, two well-characterized tobacco stress-responsive MAPKs. In the conditional gain-of-function NtMEK2DD transgenic tobacco plants, the activation of endogenous SIPK and WIPK by NtMEK2DD induces several groups of defense genes, including 3-hydroxy-3-methlyglutaryl CoA reductase (HMGR), basic pathogenesis related (PR) genes, systemic acquired resistance gene 8.2 (Sar 8.2), and harpin-induced gene1 (Hin1). To identify the transcription factor(s) involved in the activation of these defense genes, we performed gel-mobility shift assays using nuclear extracts from NtMEK2DD plants. Among the common cis-acting elements present in the promoters of defense-related genes, we observed a strong increase in the binding activity to the W box in nuclear extracts from the NtMEK2DD plants but not the control NtMEK2KR plants. The elevated W-box-binding activity in the nuclear extracts cannot be reversed by phosphatase treatment, excluding the possibility of a direct phosphorylation regulation of WRKY transcription factors by SIPK/WIPK. Instead, we observed a rapid increase in the expression of several WRKY genes in the NtMEK2DD plants. These results suggest that the increase in W-box-binding activity after SIPK/WIPK activation is a result of WRKY gene activation, and the NtMEK2-SIPK/WIPK cascade is involved in regulating the expression of genes ranging from transcription factors to defense genes further downstream during plant defense responses.

A “Whirly” Transcription Factor Is Required for Salicylic Acid-Dependent Disease Resistance in Arabidopsis

Transcriptional reprogramming is critical for plant disease resistance responses; its global control is not well understood. Salicylic acid (SA) can induce plant defense gene expression and a long-lasting disease resistance state called systemic acquired resistance (SAR). Plant-specific "Whirly" DNA binding proteins were previously implicated in defense gene regulation. We demonstrate that the potato StWhy1 protein is a transcriptional activator of genes containing the PBF2 binding PB promoter element. DNA binding activity of AtWhy1, the Arabidopsis StWhy1 ortholog, is induced by SA and is required for both SA-dependent disease resistance and SA-induced expression of an SAR response gene. AtWhy1 is required for both full basal and specific disease resistance responses. The transcription factor-associated protein NPR1 is also required for SAR. Surprisingly, AtWhy1 activation by SA is NPR1 independent, suggesting that AtWhy1 works in conjunction with NPR1 to transduce the SA signal. Our analysis of AtWhy1 adds a critical component to the SA-dependent plant disease resistance response.

The tomato transcription factor Pti4 regulates defense-related gene expression via GCC box and non-GCC box cis elements

The tomato transcription factor Pti4, an ethylene-responsive factor (ERF), interacts physically with the disease resistance protein Pto and binds the GCC box cis element that is present in the promoters of many pathogenesis-related (PR) genes. We reported previously that Arabidopsis plants expressing Pti4 constitutively express several GCC box-containing PR genes and show reduced disease symptoms compared with wild-type plants after inoculation with Pseudomonas syringae pv tomato or Erysiphe orontii. To gain insight into how genome-wide gene expression is affected by Pti4, we used serial analysis of gene expression (SAGE) to compare transcripts in wild-type and Pti4-expressing Arabidopsis plants. SAGE provided quantitative measurements of >20,000 transcripts and identified the 50 most highly expressed genes in Arabidopsis vegetative tissues. Comparison of the profiles from wild-type and Pti4-expressing Arabidopsis plants revealed 78 differentially abundant transcripts encoding defense-related proteins, protein kinases, ribosomal proteins, transporters, and two transcription factors (TFs). Many of the genes identified were expressed differentially in wild-type Arabidopsis during infection by Pseudomonas syringae pv tomato, supporting a role for them in defense-related processes. Unexpectedly, the promoters of most Pti4-regulated genes did not have a GCC box. Chromatin immunoprecipitation experiments confirmed that Pti4 binds in vivo to promoters lacking this cis element. Potential binding sites for ERF, MYB, and GBF TFs were present in statistically significantly increased numbers in promoters regulated by Pti4. Thus, Pti4 appears to regulate gene expression directly by binding the GCC box and possibly a non-GCC box element and indirectly by either activating the expression of TF genes or interacting physically with other TFs.

Two MAPK cascades, NPR1, and TGA transcription factors play a role in Pto-mediated disease resistance in tomato

The tomato Pto kinase confers resistance to the causative agent of bacterial speck disease, Pseudomonas syringae pv. tomato, by recognizing the pathogen effector proteins AvrPto or AvrPtoB. Pto-mediated resistance requires multiple signal transduction pathways and has been shown to activate many defense responses including an oxidative burst, rapid changes in the expression of over 400 genes, and localized cell death. We have tested the role in Pto-mediated resistance in tomato of a set of 21 genes from other species known to be involved in defense-related signaling. Expression of each gene was suppressed by virus-induced gene silencing (VIGS) and the effect on disease symptoms and bacterial growth during the tomato-Pseudomonas incompatible interaction was determined. We found that Pto-mediated resistance was compromised by silencing of genes encoding two mitogen-activated protein (MAP) kinase kinases, MEK1 and MEK2, two MAP kinases, NTF6 and wound-induced protein kinase (WIPK), a key regulator of systemic acquired resistance (SAR), NPR1, and two transcription factors, TGA1a and TGA2.2. A lesser impact on Pto-mediated resistance was observed in plants silenced for RAR1 and COI1. The identification of nine genes that play a role in resistance to bacterial speck disease both advances our knowledge of Pto signal transduction and demonstrates the conservation of many defense signaling components among diverse plant species.

Isolation of tobacco ubiquitin-conjugating enzyme cDNA in a yeast two-hybrid system with tobacco ERF3 as bait and its characterization of specific interaction

Tobacco ETHYLENE-RESPONSIVE FACTOR3 (ERF3) is a member of the ERF-domain transcription factors and has a transcriptional repressor activity, whereas other ERF proteins show activation activity. To understand the regulation of ERF3-repressor activity, protein(s) were screened which interact with ERF3 in a yeast two-hybrid system. A partial sequence (B8) of NtUBC2, a tobacco ubiquitin-conjugating enzyme was isolated. This B8 specifically interacted with ERF3 in the yeast two-hybrid system. Further analyses revealed that the region unique to ERF3 interacted with B8. The physiological functions of NtUBC2 and the stability of ERF3 are discussed in relation to the regulation of the repression activity of ERF3.

Members of the Arabidopsis WRKY group III transcription factors are part of different plant defense signaling pathways

WRKY proteins are a large group of transcription factors restricted to the plant kingdom. In Arabidopsis thaliana, the gene family consists of 74 members. Here, we analyzed the expression of all 13 members of one main WRKY subgroup and found that the majority are responsive both to pathogen infection and to salicylic acid. Temporal expression studies during compatible, incompatible, and nonhost interactions and employing plant defense-signaling mutants allowed us to define four distinct WRKY subsets responding to different signaling queues along defense pathways. These subsets did not reflect phylogenetic relationships. Promoter studies of one member, AtWRKY54, using a reporter gene construct in transgenic Arabidopsis plants, revealed that regulatory regions mediating pathogen and SA inducibility are clearly separable. In an AtWRKY54 knockout line, resistance to Peronospora parasitica was not compromised, but the transient expression kinetics of several WRKY genes was affected, suggesting both the existence of functional redundancy and intense cross-talk between signaling networks.

Molecular characterization and expression analysis of 1-aminocyclopropane-1-carboxylate oxidase homologs from potato under abiotic and biotic stresses

In this work, we report cloning of two full-length 1-aminocyclopropane-1-carboxylate oxidase (ACO) cDNAs (ACO1 and ACO2) from potato (Solanum tuberosum) and their expression in potato tissues. The sequence data indicate that the two cDNAs share a high degree of homology with each other, and with known ACO genes from other plant species, including monocots and dicots. However, these potato genes lack homology at the 5' and 3' ends, despite similarities in their open reading frames and encoded amino acids. Phylogenetic analysis places them in two subfamilies of ACOs. The genes are tissue specific: expression is high in leaves and low in roots and tubers. In sprouts and tubers, ACO1 is induced by heat (40 degrees C) and cold (0 degrees C) stresses, whereas ACO2 is induced only by cold (0 degrees C). ACO1 is markedly induced in leaves by wounding, soil-flooding, and exogenous application of 1-aminocyclopropane-1-carboxylic acid (ACC). In contrast, ACO2 induction is lower under these treatments. ACO1 and ACO2 are regulated very differently in potato leaves with respect to senescence. ACO2 expression is unaffected by senescence, whereas that of ACO1 is closely related to the age and senescence in both attached and detached leaves. Exogenous ACC not only induces ACO1, but also accelerates leaf senescence. ACO1 transcripts are induced significantly in leaves, stems, and tubers in the Potato virus A (PVA)-resistant potato cultivar Shepody when graft inoculated with PVA.

Isolation and characterization of a novel ribosome-inactivating protein from root cultures of pokeweed and its mechanism of secretion from roots

Ribosome-inactivating proteins are N-glycosidases that remove a specific adenine from the sarcin/ricin loop of the large rRNA, thus arresting protein synthesis at the translocation step. In the present study, a novel type I ribosome-inactivating protein, termed PAP-H, was purified from Agrobacterium rhizogenes-transformed hairy roots of pokeweed (Phytolacca americana). The protein was purified by anion- and cation-exchange chromatography. PAP-H has a molecular mass of 29.5 kD as detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its isoelectric point was determined to be 7.8. Yeast (Saccharomyces cerevisiae) ribosomes incubated with PAP-H released the 360-nucleotide diagnostic fragment from the 26S rRNA upon aniline treatment, an indication of its ribosome-inactivating activity. Using immunofluorescence microscopy, PAP-H was found to be located in the cell walls of hairy roots and root border cells. PAP-H was determined to be constitutively secreted as part of the root exudates, with its secretion enhanced by a mechanism mediated by ethylene induction. Purified PAP-H did not show in vitro antifungal activity against soil-borne fungi. In contrast, root exudates containing PAP-H as well as additional chitinase, beta-1,3-glucanase, and protease activities did inhibit the growth of soil-borne fungi. We found that PAP-H depurinates fungal ribosomes in vitro and in vivo, suggesting an additive mechanism that enables PAP-H to penetrate fungal cells.

Identification of a novel nuclear factor-binding site in the Pisum sativum sad gene promoters

DNA fragments containing the 5' promoter regions of the Pisum sativum sadA and sadC genes were amplified from genomic DNA, cloned and sequenced. These sequences contain a number of conserved cis-acting elements, which are potentially involved in stress-induced transcription of the sad genes. To determine whether any of the identified elements are active in binding nuclear factors in vitro, 11 60-bp overlapping (by 30 bp) DNA probe fragments covering the proximal sadC promoter sequence (360 bp) were used in electrophoretic mobility shift assays with competition. Binding activities were compared in nuclear extracts from control, UV-B-stressed and wounded pea leaves. The pattern of DNA binding was almost identical with all three extracts, with one 30-bp region being the predominant site for factor binding. Using overlapping sub-fragments of this region, the majority of the specific binding could be attributed to the novel 11-bp GC-rich sequence GTGGCGCCCAC. An almost identical sequence is conserved in the sadA promoter. This motif has features in common with a number of recognised cis-elements, which suggests a possible binding site for factors which play a role in regulating sad gene transcription.

Ethylene-responsive genes are differentially regulated during abscission, organ senescence and wounding in peach (Prunus persica)

Ethylene-responsive genes from peach (Prunus persica, L. Batsch) were isolated by differential screening of a cDNA library constructed from abscission zones in which cell separation had been evoked by treatment with the ethylene analogue propylene. DNA and deduced protein sequences of four selected clones, termed Prunus persica Abscission zone (PpAz), revealed homology to thaumatin-like proteins (PpAz8 and PpAz44), to proteins belonging to the PR4 class of pathogenesis-related (PR) proteins (PpAz89), and to fungal and plant beta-D-xylosidases (PpAz152). Expression analyses conducted on embrioctomized and CEPA-treated fruitlets as well as on fruit explants have shown that PpAz8, PpAz44 and PpAz89 are preferentially transcribed in the cells of the fruit abscission zone rather than in the non-zone tissues. The PpAz152 transcript showed a different accumulation pattern being consistently and promptly induced by wounding and only slightly stimulated by propylene. By contrast, a complex pattern of transcript accumulation was found for the four genes in response to the wounding of leaves and during organ development and senescence. Based on this evidence, the existence of multiple regulatory pathways underlying the differential expression of the four PpAz genes in the different tissues and physiological processes is hypothesized.