Regulation of a chitinase gene promoter by ethylene and elicitors in bean protoplasts

De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development

BACKGROUND

Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The flowering and fruit set are particularly prolonged processes, lasting between one to three months, generating important differences in physiological ages of the fruit within the same tree. So far there is no detailed genomic information regarding this species, being the cultivar 'Hass' especially important for avocado growers worldwide. With the aim to explore the fruit avocado transcriptome and to identify candidate biomarkers to monitore fruit development, we carried out an RNA-Seq approach during 4 stages of 'Hass' fruit development: 150 days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest).

RESULTS

The 'Hass' de novo transcriptome contains 62,203 contigs (x̅=988 bp, N50 = 1050 bp). We found approximately an 85 and 99% of complete ultra-conserved genes in eukaryote and plantae database using BUSCO (Benchmarking Universal Single-Copy Orthologs) and CEGMA (Core Eukaryotic Gene Mapping Approach), respectively. Annotation was performed with BLASTx, resulting in a 58% of annotated contigs (90% of differentially expressed genes were annotated). Differentially expressed genes analysis (DEG; with False Discovery Rate ≤ 0.01) found 8672 genes considering all developmental stages. From this analysis, genes were clustered according to their expression pattern and 1209 genes show correlation with the four developmental stages.

CONCLUSIONS

Candidate genes are proposed as possible biomarkers for monitoring the development of the 'Hass' avocado fruit associated with lipid metabolism, ethylene signaling pathway, auxin signaling pathway, and components of the cell wall.

The Correlation between Chitin and Acidic Mammalian Chitinase in Animal Models of Allergic Asthma

Asthma is the result of chronic inflammation of the airways which subsequently results in airway hyper-responsiveness and airflow obstruction. It has been shown that an elicited expression of acidic mammalian chitinase (AMCase) may be involved in the pathogenesis of asthma. Our recent study has demonstrated that the specific suppression of elevated AMCase leads to reduced eosinophilia and Th2-mediated immune responses in an ovalbumin (OVA)-sensitized mouse model of allergic asthma. In the current study, we show that the elicited expression of AMCase in the lung tissues of both ovalbumin- and Der P2-induced allergic asthma mouse models. The effects of allergic mediated molecules on AMCase expression were evaluated by utilizing promoter assay in the lung cells. In fact, the exposure of chitin, a polymerized sugar and the fundamental component of the major allergen mite and several of the inflammatory mediators, showed significant enhancement on AMCase expression. Such obtained results contribute to the basis of developing a promising therapeutic strategy for asthma by silencing AMCase expression.

Epitope-tagged protein-based artificial miRNA screens for optimized gene silencing in plants

Artificial miRNA (amiRNA) technology offers highly specific gene silencing in diverse plant species. The principal challenge in amiRNA application is to select potent amiRNAs from hundreds of bioinformatically designed candidates to enable maximal target gene silencing at the protein level. To address this issue, we developed the epitope-tagged protein-based amiRNA (ETPamir) screens, in which single or multiple potential target genes encoding epitope-tagged proteins are constitutively or inducibly coexpressed with individual amiRNA candidates in plant protoplasts. Accumulation of tagged proteins, detected by immunoblotting with commercial tag antibodies, inversely and quantitatively reflects amiRNA efficacy in vivo. The core procedure, from protoplast isolation to identification of optimal amiRNA, can be completed in 2-3 d. The ETPamir screens circumvent the limited availability of plant antibodies and the complexity of plant amiRNA silencing at target mRNA and/or protein levels. The method can be extended to verify predicted target genes for endogenous plant miRNAs.

The tomato ethylene receptor LE-ETR3 (NR) is not involved in mediating ozone sensitivity: causal relationships among ethylene emission, oxidative burst and tissue damage

The causal relationships among ethylene emission, oxidative burst and tissue damage, and the temporal expression patterns of some ethylene biosynthetic and responsive genes, were examined in the Never ripe (Nr) tomato (Lycopersicon esculentum) mutant and its isogenic wild type (cv. Pearson), to investigate the role played by the ethylene receptor LE-ETR3 (NR) in mediating the plant response to ozone (O(3)). Tomato plants were used in a time-course experiment in which they were exposed to acute O(3) fumigation with 200 nl l(-1) O(3) for 4 h. The pattern of leaf lesions indicated similar sensitivities to O(3) for cv. Pearson and Nr. In both genotypes, O(3) activated a hydrogen peroxide (H(2)O(2))-dependent oxidative burst, which was also ethylene-driven in Nr leaves. Ozone induced some ethylene and jasmonate biosynthetic and inducible genes, although with different timings and to different extents in the two genotypes. The overall data indicate that Nr retains partial sensitivity to ethylene, suggesting only a marginal role of the NR receptor in mediating the complex response of tomato plants to O(3).

Ethylene induces antifreeze activity in winter rye leaves

Antifreeze activity is induced by cold temperatures in winter rye (Secale cereale) leaves. The activity arises from six antifreeze proteins that accumulate in the apoplast of winter rye leaves during cold acclimation. The individual antifreeze proteins are similar to pathogenesis-related proteins, including glucanases, chitinases, and thaumatin-like proteins. The objective of this study was to study the regulation of antifreeze activity in response to ethylene and salicyclic acid, which are known regulators of pathogenesis-related proteins induced by pathogens. Nonacclimated plants treated with salicylic acid accumulated apoplastic proteins with no antifreeze activity. In contrast, when nonacclimated plants were exposed to ethylene, both antifreeze activity and the concentration of apoplastic protein increased in rye leaves. Immunoblotting revealed that six of the seven accumulated apoplastic proteins consisted of two glucanases, two chitinases, and two thaumatin-like proteins. The ethylene-releasing agent ethephon and the ethylene precursor 1-aminocyclopropane-1-carboxylate also induced high levels of antifreeze activity at 20 degrees C, and this effect could be blocked by the ethylene inhibitor AgNO(3). When intact rye plants were exposed to 5 degrees C, endogenous ethylene production and antifreeze activity were detected within 12 and 48 h of exposure to cold, respectively. Rye plants exposed to drought produced both ethylene and antifreeze activity within 24 h. We conclude that ethylene is involved in regulating antifreeze activity in winter rye in response to cold and drought.

Oligosaccharides potentiate methyl jasmonate-induced production of paclitaxel in Taxus canadensis

The interdependence of methyl jasmonate (MJ) with chitin and chitosan derived elicitors in formation of paclitaxel was studied using plant cell suspension cultures of Taxus canadensis. Induction of paclitaxel biosynthesis was enhanced when MJ and elicitors were added 8 days after culture transfer compared to treatments in which only MJ or only elicitors were added. The enhancement of the paclitaxel biosynthesis response to MJ concentration was roughly linear between 0 and 200 µM using colloidal chitin or oligosaccharides of chitin and chitosan as elicitors. MJ concentrations greater than 200 µM were inhibitory. In kinetic studies, culture growth and substrate utilization were inhibited when the cultures were elicited with 100 µM MJ and with 0.63 mg l(-1) N-acetylchitohexaose and with 100 µM MJ alone; paclitaxel yields were 10-fold greater under the latter condition than the former. Ethylene biosynthesis by the cell cultures in response to elicitation is implicated in regulation of the response.

Ethylene regulates the susceptible response to pathogen infection in tomato

Ethylene evolution occurs concomitantly with the progression of disease symptoms in response to many virulent pathogen infections in plants. A tomato mutant impaired in ethylene perception-Never ripe-exhibited a significant reduction in disease symptoms in comparison to the wild type after inoculations of both genotypes with virulent bacterial (Xanthomonas campestris pv vesicatoria and Pseudomonas syringae pv tomato) and fungal (Fusarium oxysporum f sp lycopersici) pathogens. Bacterial spot disease symptoms were also reduced in tomato genotypes impaired in ethylene synthesis (1-aminocyclopropane-1-carboxylic acid deaminase) and perception (14893), thereby corroborating a reducing effect for ethylene insensitivity on foliar disease development. The reduction in foliar disease symptoms in Never ripe plants was a specific effect of ethylene insensitivity and was not due to reductions in bacterial populations or decreased ethylene synthesis. PR-1B1 mRNA accumulation in response to X. c. vesicatoria infection was not affected by ethylene insensitivity, indicating that ethylene is not required for defense gene induction. Our findings suggest that broad tolerance of diverse vegetative diseases may be achieved via engineering of ethylene insensitivity in tomato.

Regulation of sesquiterpene cyclase gene expression. Characterization of an elicitor- and pathogen-inducible promoter

The promoter for a tobacco (Nicotiana tabacum) sesquiterpene cyclase gene, a key regulatory step in sesquiterpene phytoalexin biosynthesis, has been analyzed. The EAS4 promoter was fused to the beta-glucuronidase (GUS) reporter gene, and the temporal and spatial expression patterns of GUS activity were examined in stably transformed plants and in transient expression assays using electroporated protoplasts of tobacco. No GUS activity was observed in any tissues under normal growth conditions. A low level of GUS activity was detected in wounded leaf, root, and stem tissues, whereas a much higher level was observed when these tissues were challenged with elicitors or microbial pathogens. The GUS expression pattern directed by the EAS4 promoter was identical to the induction patterns observed for the endogenous sesquiterpene cyclase genes. Neither exogenous salicylic acid nor methyl jasmonate induced GUS expression; and H2O2 induced GUS expression to only a limited extent. Although the EAS4 promoter contains cis-sequences resembling previously identified transcriptional control motifs, other cis-sequences important for quantitative and qualitative gene expression were identified by deletion and gain-of-function analyses. The EAS4 promoter differs from previously described pathogen-/elicitor-inducible promoters because it only supports inducible gene expression and directs unique spatial expression patterns.

The isolation and characterization of type II metallothionein-like genes from tomato (Lycopersicon esculentum L.)

Two cDNAs encoding putative metallothionein (MT)-like peptides have been isolated from tomato (L. esculentum L.). The predicted protein products of these two cDNAs (LeMT(A) and LeMT(B)) are 72 and 83 amino acids respectively and both encode peptides with arrangements of cysteine residues characteristic of type II plant MTs. In other plants which possess more than one gene expressing MT proteins of the same type, the products are closely related or identical, but LeMT(A) and LeMT(B) constitute two different classes of message, and encode two different protein products. Northern blot analysis of LeMT(A) and LeMT(B) showed that transcripts of both MT-like genes were more abundant in leaves than roots in tomato plants grown without addition of extra metal ions, a characteristic of type II MTs. A genomic clone corresponding to LeMT(B) (LeMT(B)) was isolated and sequenced. The 5'-flanking region of LeMT(B) was shown to contain a putative metal regulatory element (MRE) which suggests the possibility of metal-regulated transcription. In addition, the upstream region also contains a G-box like motif (CACGTG) and an 8 bp sequence (AATTCAAA) found within the promoters of genes shown to be ethylene-responsive.

Chitinase gene expression in transgenic plants: a molecular approach to understanding plant defence responses

Recent studies suggest that the production of enzymes capable of degrading the cell walls of invading phytopathogenic fungi may be an important component of the defence response of plants. In this chapter, we summarize recent progress on the isolation and characterization of chitinolytic enzymes from higher plants. Emphasis is placed on experiments designed to study the regulation of chitinase gene expression in response to ethylene treatment or pathogen ingress and on determining the role of this enzyme in plant defence. The production of transgenic plants with enhanced resistance to attack by the fungal pathogen Rhizodonia solani is discussed.

Structure and expression of three genes encoding ACC oxidase homologs from melon (Cucumis melo L.)

The enzyme ACC oxidase catalyses the last step of ethylene biosynthesis in plants, converting 1-aminocyclopropane-1-carboxylic acid (ACC) to ethylene. We have previously described the isolation and characterization of a cDNA clone (pMEL1) encoding an ACC oxidase homolog from melon (Cucumis melo L.). Here we report the isolation and characterization of three genomic clones, corresponding to three putative members of the ACC oxidase gene family in melon. All are transcriptionally active. The sequences of these genes have been determined. One genomic clone (CM-ACO1), corresponding to the cDNA previously isolated, presents a coding region interrupted by three introns. Its transcription initiation site has been defined with RNA from ripe fruit and ethylene-treated leaves. The other two genes (CM-ACO2, CM-ACO3) have only two introns, at positions identical to their counterparts in CM-ACO1. The degree of DNA homology in the coding regions of CM-ACO2 and CM-ACO3 relative to CM-ACO1 is 59% and 75%, respectively. CM-ACO2 and CM-ACO3 are 59% homologous in their coding regions. These three genes have close homology to PH-ACO3, a member of the ACC oxidase multigene family of petunia. The predicted amino acid sequences of CM-ACO1 and CM-ACO3 are 77% to 81% identical to those encoded by the tomato and petunia genes, while the deduced amino acid sequence of CM-ACO2 shows only 42% to 45% homology. RT-PCR analysis using gene-specific primers shows that the three genes are differentially expressed during development, ethylene treatment and wounding. CM-ACO1 is induced in ripe fruit and in response to wounding and to ethylene treatment in leaves. CM-ACO2 is detectable at low level in etiolated hypocotyls. CM-ACO3 is expressed in flowers and is not induced by any of the stimuli tested.

Characterization of two class II chitinase genes from peanut and expression studies in transgenic tobacco plants

Two different genes encoding class II chitinases from peanut (Arachis hypogaea L. cv. NC4), A.h.Chi2;1 and A.h.Chi2;2, have been cloned. In peanut cell suspension cultures, mRNA levels of A.h.Chi2;2 increased after ethylene or salicylate treatment and in the presence of conidia from Botrytis cinerea. The second gene, A.h.Chi2;1, was only expressed after treatment with the fungal spores. Transgenic tobacco plants containing the complete peanut A.h.Chi2;1 gene exhibited essentially the same expression pattern in leaves as observed in peanut cell cultures. Expression characteristics of transgenic tobacco carrying a promoter-GUS fusion of A.h.Chi2;1 are described.

Tansley Review No. 86 Accumulation of phytoalexins: defence mechanism and stimulus response system

Phytoalexin synthesis is a defence-response- that is characterized by a requirement for a number of distinct elements, all of which must be present for the response to be expressed fully. These same elements: a signal, a cellular receptor, a signal transduction system and a responsive metabolic system, are also used to describe a stimulus-response system. A number of molecular species can function as signal molecules or elicitors of phytoalexin synthesis, including poly- and oligosaccharides, proteins and polypeptides, and fatty acids. Few receptors for elicitors have been identified but those that have been are proteins located on the plasma membrane of the plant. Induction of phytoalexin synthesis involves selective and co-ordinated activation of specific defence response genes, including those encoding the enzymes of phytoalexin synthesis, and these genes constitute the responsive metabolic system. The separate, and distant, locations of the receptor and the responsive genes means that the event in which the signal is perceived by the receptor must be relayed to the genes by means of a second messenger system. Several second messengers are candidates for such a coupling- or signal transduction-system, including udenosine-3',5'-cyclic monophosphate, Ca²⁺ , diacylglycerol and inositol 1,4,5-trisphosphate, active oxygen species and jasmonic acid. Each has been examined as a possible component of the signal transduction system mediating between the elicitor receptor interaction and the phytoalexin synthesis it induces. Analysis of the signalling events is made complex by the simultaneous solicitation by the invading micro-organism of several defence responses, each of which might involve elements of a different signal system. The same complexity is evident which the role of phytoalexin accumulation in resistance is analysed. Evaluation of the contribution made by phytoalexin accumulation towards resistance has been attempted by the use of various inhibitors and enhancers of the process. Transgenic and mutant plants with specific alterations in one or more ot those elements necessary for the plant to respond to the signals for phytoalexin synthesis and other defence responses, are beginning to aid resolution of the complex pattern ot signalling events and the respective roles of the inducible defence mechanisms in resistance. CONTENTS Summary 1 I. Introduction 2 II. Chemistry of phytoalexins 3 III. Phytoalexin accumulation as a determinant of resistance 6 IV. Elicitation of phytoalexin accumulation 11 References 34.

A GCC element and a G-box motif participate in ethylene-induced expression of the PRB-1b gene

The PRB-1b gene codes for a basic-type pathogenesis-related protein and is activated at the transcriptional level by the plant hormone ethylene. To identify cis-acting DNA elements essential for ethylene induction, deleted and mutant forms of the PRB-1b promoter, fused to the beta-glucuronidase (GUS) coding region, were introduced in transgenic tobacco plants. A 73 bp fragment (X1 region) of the PRB-1b promoter, located between positions -213 and -141, was sufficient to confer ethylene responsiveness to the reporter gene. The X1 region contains a TAAGAGCCGCC motif (GCC-box) well conserved in several ethylene-inducible genes. A substitution mutation in this sequence, in the context of a 213 bp PRB-1b promoter, completely abolished ethylene induction in transgenic tobacco, defining this conserved motif as part of a cis-acting element responsive to ethylene. Three other mutations in the X1 region caused a pronounced decrease in the PRB-1b promoter activity in transgenic plants, but did not affect ethylene inducibility. One of them, localized in a G-box like motif (CACGTG), disrupted the binding site for a nuclear factor, as observed in gel-shift analysis. Interestingly, the mobility of the complex formed on the G-box element was dependent on its phosphorylation state. These results suggest that a cis-acting element involved in the perception of the ethylene signal resides in a GCC motif and acts in concert with additional elements in the regulation of ethylene-induced PRB-1b expression.

DNA-protein interactions on a cis-DNA element essential for ethylene regulation

The PRB-1b gene encodes for a basic-type component of the pathogenesis-related PR-1 protein family. In leaves of tobacco plants, PRB-1b mRNA accumulation is rapidly induced by the application of exogenous ethylene. Promoter deletion analysis was performed in transgenic tobacco plants to delineate cis-acting elements necessary for ethylene responsiveness of the PRB-1b gene. The promoter sequence from position -213 was sufficient to enhance a 20 fold increase of beta-glucuronidase reporter gene expression in transgenic tobacco leaves exposed to 20 microliters/l of ethylene, however -141 bp were not. The functional study was correlated with in vitro analysis of the nuclear protein-DNA complexes formed on the promoter element identified as necessary for ethylene induction. Gel-shift analysis using restriction fragments spanning the sequence between position -237 and -143 revealed two distinct nuclear protein-DNA interactions. The protein-binding sequences were mapped to the contiguous regions G (-200 to -178) and Y (-179 to -154) by gel-shift analysis using oligonucleotides. Fractionation of crude nuclear extract by heparin-agarose chromatography resulted in the differential elution of the two binding activities. The DNA-nuclear protein interactions characterized in vitro can be part of the molecular events which mediate the transcriptional regulation of the PRB-1b gene by ethylene.

Identification of an ethylene-responsive region in the promoter of a fruit ripening gene

Transcription of the E4 gene is controlled by an increase in ethylene concentration during tomato fruit ripening. To investigate the molecular basis for ethylene regulation, we have examined the E4 promoter to identify cis elements and trans-acting factors that are involved in E4 gene expression. In transgenic tomato plants a chimeric gene construct containing a 1.4-kilobase E4 promoter fused to a beta-glucuronidase reporter gene is rapidly induced by ethylene in ripening fruit. Deletion of E4 promoter sequences to 193 base pairs reduces the level of GUS activity but does not affect ethylene induction. Transient expression of E4 promoter-luciferase chimeric gene constructs containing various deletions, introduced into tomato fruit pericarp by particle bombardment, indicates that a positive ethylene-responsive region is localized between nucleotides -161 and -85 relative to the transcription start site. DNase I footprint analysis shows that a nuclear factor in unripe fruit interacts specifically with sequences in this element, from -142 to -110, which are required for the ethylene response. The DNase I footprint of this factor is reduced in ethylene-treated unripe fruit and undetectable in ripe fruit. Based on the correlation of a nuclear factor binding site with promoter sequences required for ethylene induction, we propose that this in vitro DNA-binding activity may represent a factor that is involved in ethylene-regulated E4 gene expression.

Characterization of an ethylene-responsive glutathione S-transferase gene cluster in carnation

In this paper we present the structural analysis of two tightly linked genes from the glutathione S-transferase (GST) gene family in carnation (Dianthus caryophyllus). Southern blot analysis and restriction endonuclease mapping revealed a single cloned region of the carnation genome was highly homologous to the previously characterized ethylene-responsive GST mRNA expressed in flower petals during senescence. Nucleotide sequencing of this region revealed the presence of two tandemly arranged genes designated GST1 and GST2. Comparison of the nucleotide sequences of the cloned genomic region with the previously characterized GST cDNA clone pSR8 revealed that GST1 contains the entire transcription unit in 10 exons interrupted by 9 introns. The transcription unit of GST2 was found to be very similar to GST1 with complete conservation of intron position. In addition, the length and nucleotide sequences of the two genes' introns were highly conserved. GST2 was not completely represented by the cloned genomic region, missing the 3' portion of the transcription unit. Primer extension analysis indicated a single transcriptional start site for transcripts which accumulate in senescing carnation petals. The 5'-flanking sequences of GST1 and GST2 were compared and regions of homology and divergence identified. These upstream sequences were compared with other plant ethylene-responsive genes and GST genes and several sequence motifs of potential importance in the regulation of GST expression were identified. A chimeric gene constructed between -1457 bp of the 5'-flanking DNA of GST1 and the coding region of beta-glucuronidase was found to confer ethylene-inducible expression in flower petals following delivery of the construct into tissue by particle bombardment.

Analysis of regulatory elements involved in stress-induced and organ-specific expression of tobacco acidic and basic beta-1,3-glucanase genes

Infection of tobacco by tobacco mosaic virus (TMV) induces coordinate expression of genes encoding acidic and basic beta-1,3-glucanase isoforms. These genes are differentially expressed in response to other treatments. Salicylate treatment induces acidic glucanase mRNA to a higher level than basic glucanase mRNA. Ethylene treatment and wounding strongly induce the basic glucanase genes but have little effect on genes encoding the acidic isoforms. Furthermore, the basic glucanase genes are constitutively expressed in roots and lower leaves of healthy plants, whereas the acidic glucanase genes are not. In order to investigate how these expression patterns are established, we fused promoter regions of an acidic and a basic glucanase gene to the beta-glucuronidase (GUS) reporter gene and examined expression of these constructs in transgenic tobacco plants. A fragment of 1750 bp and two 5'-truncated fragments of 650 bp and 300 bp of the acidic glucanase promoter were tested for induction of GUS gene expression after salicylate treatment and TMV infection. Upstream sequences of 1750 bp and 650 bp were sufficient for induction of the reporter gene by salicylate treatment and TMV infection, but the activity of the 300 bp fragment was strongly reduced. The results suggest that the 1750 bp upstream sequence of the acidic glucanase gene contains multiple regulatory elements. For the basic glucanase promoter it is shown that 1476 bp of upstream sequences were able to drive expression in response to TMV infection and ethylene treatment, but no response was found to incision wounding. Furthermore, high GUS activity was found in lower leaves and roots of healthy transgenic plants, carrying the 1476 bp basic glucanase promoter/GUS construct. When the promoter was truncated up to position -446 all activity was lost, indicating that the region between -1476 and -446 of the basic glucanase promoter is necessary for organ-specific and developmentally regulated expression as well as for induced expression in response to infection and other stress treatments.