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First published online October 28, 2005; 10.1104/pp.105.067058 Plant Physiology 139:1268-1283 (2005) © 2005 American Society of Plant Biologists 12-Oxo-Phytodienoic Acid Triggers Expression of a Distinct Set of Genes and Plays a Role in Wound-Induced Gene Expression in Arabidopsis1,[w]Department of Bioscience, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226–8501, Japan (N.T., Y.S.-S., T.O., A.K., K.K., K.-i.T.); Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226–8501, Japan (T.A., K.Y., Y.K.); Kazusa DNA Research Institute, 2–6–7 Kazusa-kamatari, Kisarazu, Chiba 292–0812, Japan (N.S., H.S., D.S.); Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3–8–1 Komaba, Meguro, Tokyo 153–8902, Japan (T.M.); and Department of Bioscience, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, and Research Center for the Evolving Earth and Planets, 4259 Nagatsuta, Midori-ku, Yokohama 226–8501, Japan (H.O.)
Jasmonic acid (JA) and methyl jasmonate (MeJA), collectively known as JAs, regulate diverse physiological processes in plants, including the response to wounding. Recent reports suggest that a cyclopentenone precursor of JA, 12-oxo-phytodienoic acid (OPDA), can also induce gene expression. However, little is known about the physiological significance of OPDA-dependent gene expression. We used microarray analysis of approximately 21,500 Arabidopsis (Arabidopsis thaliana) genes to compare responses to JA, MeJA, and OPDA treatment. Although many genes responded identically to both OPDA and JAs, we identified a set of genes (OPDA-specific response genes [ORGs]) that specifically responded to OPDA but not to JAs. ORGs primarily encoded signaling components, transcription factors, and stress response-related genes. One-half of the ORGs were induced by wounding. Analysis using mutants deficient in the biosynthesis of JAs revealed that OPDA functions as a signaling molecule in the wounding response. Unlike signaling via JAs, OPDA signaling was CORONATINE INSENSITIVE 1 independent. These results indicate that an OPDA signaling pathway functions independently of JA/MeJA signaling and is required for the wounding response in Arabidopsis.
Plants synthesize various fatty acid derivatives having biological activity. Among these, jasmonic acid (JA) and methyl jasmonate (MeJA), collectively known as jasmonates (JAs), are the best characterized. JAs are cyclopentanone compounds derived from linolenic acid via an octadecanoid pathway consisting of several enzymatic steps (Fig. 1). The early steps of this pathway occur in chloroplasts, where linolenic acid is converted to 12-oxo-phytodienoic acid (OPDA) by means of the three enzymes, lipoxygenase, allene oxide synthase (AOS), and allene oxide cyclase (Bell et al., 1995  ; Laudert et al., 1996; Stenzel et al., 2003). OPDA is subsequently reduced in a cyclopentenone ring by a peroxisome-localized enzyme, 12-oxo-phytodienoic acid reductase 3 (OPR3). The reaction product then undergoes three cycles of  -oxidation in the peroxisome, generating JA (Stintzi and Browse, 2000; Strassner et al., 2002; Reumann et al., 2004).
There have been numerous physiological analyses of the function of JAs. The role of JAs in the response to biotic stresses, such as insect or fungal attack (McConn et al., 1997 ; Ozawa et al., 2000), and abiotic stresses, such as mechanical wounding (Baldwin et al., 1997; Creelman and Mullet, 1997; Reymond et al., 2000; Richard et al., 2000), has been well documented. JAs also play important roles in anther development (Feys et al., 1994; McConn and Browse, 1996; Xie et al., 1998) and in the regulation of many other plant developmental processes (Creelman and Mullet, 1997). Several components are involved in signaling via JAs. One such component, CORONATINE INSENSITIVE 1 (COI1), contains an F-box motif that has similarity to F-box proteins involved in targeting proteins for removal by ubiquitination (Xie et al., 1998; del Pozo and Estelle, 2000). Thus, COI1 is thought to be involved in protein ubiquitination and degradation regulated by JAs. COI1 is now thought to be a central component of signaling pathways involving JAs.
Recently, OPDA, an intermediate in the biosynthesis of JAs, has been shown to be the biologically active molecule. An opr3 Arabidopsis (Arabidopsis thaliana) mutant that could not produce JA was identified that exhibits delayed anther dehiscence, resulting in male sterility (Sanders et al., 2000 In this study, we analyzed OPDA-dependent gene expression by comparing responses to OPDA and JAs using DNA microarrays covering 80% of the Arabidopsis genome. We identified a group of genes, designated ORGs (OPDA-specific response genes), which responded to OPDA but not to JAs. OPDA treatment of coi1 mutants demonstrated that ORG expression is independent of the COI1-dependent JA signaling pathway. Using the OPDA and JAs biosynthetic mutants aos and opr3 (Fig. 1), we showed that the normal response to wounding was impaired in aos but not in opr3 mutants. These results demonstrate that OPDA is a lipid signal mediator in vivo, regulating ORGs that function during the wounding response.
Identification of Response Genes for OPDA and JAs by Microarray Analysis To comprehensively evaluate the effect of OPDA, JA, and MeJA on the transcription of Arabidopsis genes in general, we used an oligonucleotide array covering 21,500 genes, corresponding to 80% of the genome. A time-course experiment was performed to analyze gene expression at 0, 30, and 180 min after treatment with OPDA, JA, or MeJA. After eliminating error spots, as described in "Materials and Methods," we calculated the normalized fold expression of 20,095 genes for each treatment. Scatter plots comparing expression between the three treatments were drawn on a logarithmic scale using the normalized fold expression of each gene. A higher correlation between JA and MeJA treatment was observed at 30 and 180 min (0.64 and 0.85, respectively) than that observed between OPDA and JAs treatment. Most of the genes that responded to JA treatment responded equivalently to MeJA treatment. The correlation coefficients of OPDA versus JA and OPDA versus MeJA were, respectively, 0.48 and 0.47 at 30 min and 0.77 and 0.76 at 180 min. As shown in Figure 2, A, B, D, and E, spots corresponding to up- or down-regulated genes (red or green spots, respectively) were observed specifically along axial lines. This result demonstrates that a group of genes responded to OPDA but not to JA or MeJA; these genes were termed OPDA-specific response genes, or ORGs. The analysis also revealed a large number of genes that responded to OPDA as well as JA and MeJA. From this comprehensive gene expression analysis, we concluded that OPDA regulates the expression of a distinct set of genes that are not regulated by JAs, in addition to genes that respond to all three compounds.
Validation of ORGs by Northern-Blot Analysis Based on the microarray results, ORGs were defined as follows (for a detailed description, see "Materials and Methods"). Up-regulated ORGs were induced more than 3-fold by OPDA but less than 2-fold by JA and MeJA (Table I; Supplemental Table I). Down-regulated ORGs were repressed more than 3-fold by OPDA but less than 2-fold by JA and MeJA (Table II). Genes corresponding to 172 loci (157 induced and 15 repressed) satisfied these criteria. For identification of ORGs, we also applied hierarchical clustering for 1,078 genes whose expression responded more than 3-fold to any of three treatments. By this clustering, 214 ORG genes were also found (193 induced 21 repressed; see Supplemental Table II and Supplemental Fig. 1). Basically, most of genes identified in former criteria were included in latter criteria (144 induced and 11 repressed). We therefore used the gene list obtained by the former criteria for further analysis.
To verify that OPDA modulates ORG expression independently of JAs, we assessed the expression profile of selected putative ORGs by northern blotting. Consistent with the microarray data, northern analysis showed that the expression of ZAT10 (At1g27730), AtERF5 (At5g47230), DREB2A (At5g05410), GST6 (At2g47730), and FAD-OXR (FAD-linked oxidoreductase; At4g20860) increased upon OPDA treatment but did not respond to JAs (Fig. 3A). The expression of AtVSP2 (At5g24770), a known jasmonate-responsive gene (Berger et al., 1995 ), increased similarly in response to each treatment. ZAT10, AtERF5, and DREB2A are known transcription factors related to the response to various abiotic stresses (Liu et al., 1998; Fujimoto et al., 2000; Ohta et al., 2001; Lee et al., 2002). GST6 and FAD-OXR are also induced in stress responses (Dittrich and Kutchan, 1991; Chen et al., 1996). Expression of the transcription factor genes ZAT10 and AtERF5 was detected within 30 min of OPDA treatment and decreased thereafter. On the other hand, expression of GST6 and FAD-OXR was induced at a later time (around 180 min).
To confirm the induction of ORGs, we used an opr3 mutant, which lacks an enzyme catalyzing the reduction of the cyclopentenone ring of OPDA (Fig. 1) and thus is deficient in JAs (Stintzi and Browse, 2000 ; Stintzi et al., 2001). As shown in Figure 3B, the induction of ZAT10 and FAD-OXR by OPDA was equivalent in the opr3 mutant and wild-type strain (Wassilewskija [Ws] background). Similar results were obtained for AtERF5, DREB2A, and GST6 (data not shown). These results demonstrate that OPDA, but not JAs, regulates the expression of these representative ORGs. In contrast, the induction of AtVSP2 by OPDA was abolished in the opr3 mutant, but was induced by OPDA and JAs in wild-type plants (Fig. 3, A and B), indicating that AtVSP2 responds specifically to JAs. This result also showed that exogenous OPDA could be converted to JA within 180 min under these experimental conditions, given that AtVSP2 expression in OPDA-treated wild-type plants became evident after this time.
Of the 172 ORGs, 123 (70%) were annotated using locus annotation from The Arabidopsis Information Resource (Rhee et al., 2003
We also identified genes that responded to JAs (JRGs), according to the criteria described in "Materials and Methods." Briefly, genes that were induced or repressed more than 3-fold by both JA and MeJA were selected as JRGs. A total of 449 loci (371 induced and 78 repressed) satisfied these criteria (Supplemental Table III). This group mainly included genes involved in metabolic pathways, such as ascorbate and glutathione metabolism, JA biosynthesis, and indole glucosinolate synthesis, which are known to be regulated by JAs (Brader et al., 2001
Although the exact role of OPDA is unclear since it is a precursor of JA, it is expected to have a related physiological function. JAs have a pivotal role in the wounding response (Reymond and Farmer, 1998
To determine whether OPDA is required to induce expression of ORGs in wounded plants in vivo, the expression of ZAT10, FAD-OXR, and AtERF5 in mechanically wounded plants was quantified for two JA biosynthesis mutants (Fig. 1): opr3, which has a defect in JA biosynthesis, and aos, which lacks both OPDA and JA (Stintzi and Browse, 2000
Figure 4A also indicates that, even in the aos mutant, about one-half of the wound-induced expression of ZAT10, FAD-OXR, and AtERF5 was not abolished. Recently, various oxylipins were shown to function as signaling molecules that induce gene expression (Gerwick et al., 1991 ; Howe and Schilmiller, 2002; Weber, 2002). Since most oxylipins are derived from linolenic acid, it would be expected that the residual response to wounding seen in the aos mutant is mediated by oxylipins derived from linolenic acid. Therefore, we treated wild-type (Col) and mutant (aos) plants with linolenic acid and analyzed the expression levels of ZAT10 and AtVSP2 by northern blotting. ZAT10 and AtVSP2 mRNAs accumulated in Col (Fig. 4C). In aos, the ZAT10 mRNA level was reduced compared with wild-type plants (Fig. 4C), and expression of AtVSP2 expression was completely lost.
COI1 is required for the response to JAs (Feys et al., 1994
OPC8:0 and OPC6:0 Also Induce the Expression of ORGs
OPDA and JA have a similar structural backbone, a consequence of the fact that OPDA is the precursor of JA before reduction and
OPDA Regulation of Gene Expression Is Distinct from JAs
JAs are important regulators of plant responses to environmental stresses, such as wounding, insect attack, and infection (Creelman and Mullet, 1997
We used genome-wide expression analysis to identify genes that respond to OPDA, JA, and MeJA, and identified a large number of OPDA response genes, ORGs distinct from those that respond to JAs, or JRGs (Fig. 2; Supplemental Fig. 1). The characteristics of ORGs and JRGs differ greatly (Tables I and II; Supplemental Table III). A significant proportion of ORGs are signaling components and transcriptional factors, whereas JRGs mainly include enzymes involved in metabolic pathways for jasmonates, ascorbate, glutathione, and indole glucosinolate (Brader et al., 2001
The above results indicate that OPDA and JAs have distinct functions in gene regulation, suggesting that OPDA itself functions as a signaling molecule. The
JAs are essential in vivo regulators of defense responses (Reymond and Farmer, 1998
In the aos mutant, approximately 50% of ORG expression remained. Recently, various oxylipins derived from linolenic acid were shown to accumulate and induce gene expression in plants (Howe and Schilmiller, 2002
Wounding induced the expression of 74 ORGs. These included many signal transduction components and transcription factors (Tables I and II), suggesting that OPDA is required upstream of the wounding response. Wounding causes the accumulation of reactive oxygen species, resulting in oxidative stress (Olson and Varner, 1993 We found that OPDA modulates a distinct set of genes via a COI1-independent signaling pathway. We also propose that OPDA plays a role in the wounding response. The precise function of OPDA in physiological events is still largely unknown. In further analyses of OPDA, isolation of mutants in which OPDA signaling or OPDA level is specifically altered will be a key step to complete our understanding of oxylipin signaling in plant cells.
Plant Materials, Chemical Treatments, and Wounding
For chemical treatments, Arabidopsis (Arabidopsis thaliana; Col Ws, aos, opr3, and coi1-16) were grown in Murashige and Skoog liquid medium (Murashige and Skoog, 1962
For northern-blot analyses, total RNA was extracted from Arabidopsis by the phenol/SDS method (Chirgwin et al., 1979
The Arabidopsis 2 oligo microarray and the Agilent Linear Amplification/Labeling kit (Agilent Technologies) were used for DNA microarray analyses, all of which were conducted in biological duplicate. The quality of total RNA samples was verified using the RNA 6000 Nano Assay (Agilent Technologies). Sample amplification, labeling, and hybridization essentially followed the protocol recommended by Agilent Technologies. Briefly, 500 ng of each total RNA sample was reverse transcribed into cDNA using the T7 promoter primer. Labeled cRNA was synthesized from the cDNA. The reaction was performed in a solution containing dNTP mix, cyanine 3-dCTP (for treated samples) or cyanine 5-dCTP (for untreated samples; Perkin-Elmer), and T7 RNA Polymerase, and incubated at 40°C for 2 h. To remove unincorporated nucleotides, the labeled cRNA was purified using the RNeasy mini kit (Qiagen). Hybridization was performed in 500 µL of a hybridization mixture containing cRNA probes, the labeled orientation marker (Deposition Control SP300; Operon Technologies), and Cot-1 DNA (Invitrogen) at 60°C for 17 h. The glass slides were then washed and scanned using an Agilent microarray scanner (Agilent Technologies). See also Supplemental File 1, MIAME-compliant description.
Spot intensities were quantified, background subtracted, and dye normalized by Agilent Feature Extraction software. Using the spot intensity, a base-10 logarithmic value of relative expression to control (RE) of each gene was determined by the same software (data available in Supplemental Table IV). Then we calculated "normalized fold expression" from RE to unify the duplicate data and to compare between treatments using Microsoft Excel as below.
For treatment tr = {OPDA, JA, MeJA }, replicate r = {1,2}, time t = {30 min, 180 min}, and gene g:
 is SD. Since OPDA, JA, and MeJA were applied in the same way for liquid cultured plants, for all these data:
Wounding treatment was performed on 21-d-old seedlings grown on MS medium containing agarose. Thus, wounding data were treated independently.
We obtained biologically duplicate data for every treatment. To unify the duplicate data, we calculated weighted averages based on a flag (PosAndSignif flag) in Agilent microarray. In the Agilent microarray, if genes showed significantly higher expression than microarray background, the genes were flagged as 1; otherwise 0 for each Green and Red channel. We did not use the data if at least one of the PosAndSignif flags for Green or Red channels was 0. And if the flags for both of the duplicate data were 0, the gene (locus) was removed from all subsequent analyses. For the remaining 20,095 loci, normalized fold expression was determined.
To screen ORGs, JRGs, and wounding response genes (WRGs), normalized fold expression of each gene was calculated as described above. Then, maximum normalized fold expression (MAF) and minimum normalized fold expression (MIF) were calculated as follows.
The MAF and MIF of OPDA, JA, MeJA, and wound treatment were calculated for each gene (MAFOPDA, MIFOPDA, MAFJA, MIFJA, MAFMeJA, MIFMeJA, MAFwound, and MIFwound, respectively). For ORGs, we selected genes using the following criteria: For up-regulated ORGs, MAFOPDA was more than 3 and both MAFJA and MAFMeJA were less than 2; for down-regulated ORGs, MIFOPDA was less than 0.33 and both MIFJA and MIFMeJA were more than 0.5. A total of 172 genes (157 induced, 15 repressed) fulfilled the criteria. For JRGs, we selected genes having both MAFJA and MAFMeJA of more than 3 or both MIFJA and MIFMeJA of less than 0.33. A total of 449 genes (371 induced, 78 repressed) fulfilled these criteria. For WRGs, we selected genes having MAFwound of more than 3 or MIFwound of less than 0.33; 1,721 genes (1,035 genes induced, 696 repressed, 10 genes overlapped in both categories) fulfilled these criteria.
Total RNA (5 µg) was prepared from untreated or treated plants as described. The RNA was electrophoresed on a 1.2% agarose/formaldehyde gel and blotted onto a nylon membrane. Probes were prepared from plasmid DNAs of AV544343, AV521889, AV546998, AV537643, AV544278, and AV532124 (accession nos. reported by Asamizu et al. [2000]
We thank Dr. J. Browse, Dr. J.H. Park and Dr. K.A. Feldmann, and Dr. J. Turner for kindly providing opr3, aos, and coi1-16 seeds, respectively. Received June 11, 2005; returned for revision August 31, 2005; accepted September 5, 2005.
1 This work was supported in part by the New Energy and Industrial Technology Development Organization, Japan (performed as part of the project Development of Fundamental Technologies for Controlling the Production of Industrial Materials by Plants).  The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Hiroyuki Ohta (hohta@bio.titech.ac.jp).
[w] The online version of this article contains Web-only data. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.067058. * Corresponding author; e-mail hohta{at}bio.titech.ac.jp; fax 81–45–924–5823.
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