- Research article
- Open Access
NaMYC2 transcription factor regulates a subset of plant defense responses in Nicotiana attenuata
© Woldemariam et al.; licensee BioMed Central Ltd. 2013
Received: 29 January 2013
Accepted: 25 April 2013
Published: 1 May 2013
To survive herbivore attack, plants have evolved potent mechanisms of mechanical or chemical defense that are either constitutively present or inducible after herbivore attack. Due to the costs of defense deployment, plants often regulate their biosynthesis using various transcription factors (TFs). MYC2 regulators belong to the bHLH family of transcription factors that are involved in many aspects of plant defense and development. In this study, we identified a novel MYC2 TF from N. attenuata and characterized its regulatory function using a combination of molecular, analytic and ecological methods.
The transcript and targeted metabolite analyses demonstrated that NaMYC2 is mainly involved in the regulation of the biosynthesis of nicotine and phenolamides in N. attenuata. In addition, using broadly-targeted metabolite analysis, we identified a number of other metabolite features that were regulated by NaMYC2, which, after full annotation, are expected to broaden our understanding of plant defense regulation. Unlike previous reports, the biosynthesis of jasmonates and some JA-/NaCOI1-dependent metabolites (e.g. HGL-DTGs) were not strongly regulated by NaMYC2, suggesting the involvement of other independent regulators. No significant differences were observed in the performance of M. sexta on MYC2-silenced plants, consistent with the well-known ability of this specialist insect to tolerate nicotine.
By regulating the biosynthesis of nicotine, NaMYC2 is likely to enhance plant resistance against non-adapted herbivores and contribute to plant fitness; however, multiple JA/NaCOI1-dependent mechanisms (perhaps involving other MYCs) that regulate separate defense responses are likely to exist in N. attenuata. The considerable variation observed amongst different plant families in the responses regulated by jasmonate signaling highlights the sophistication with which plants craft highly specific and fine-tuned responses against the herbivores that attack them.
In their natural habitats, plants are exposed to a number of abiotic (e.g. drought, ultra-violet radiation, salinity) and biotic (e.g. herbivore and/or pathogen attack, competition) stresses which strongly undermine their Darwinian fitness. To cope with herbivory, plants have evolved intricate defense mechanisms that include mechanical barriers, trichomes, thorns, latex, waxes, and a toxic-/anti-nutritive chemical arsenal deployed either constitutively (e.g. nicotine, glucosinolates) or following herbivore attack (e.g. hydroxygeranyllinalool-diterpene glycosides (HGL-DTGs), phenolamides, trypsin protease inhibitors) [1–3]. In addition, and in concert with these direct defenses, plants recruit predators or parasitoids of the attackers using informative volatile organic compounds or nutritional rewards [4–6]. However, the costs of defense responses [2, 7, 8] necessitate the development of stringent regulatory mechanisms and several families of plant transcription factors (TFs) (e.g. ERF, bZIP, MYB, bHLH and WRKY) have been shown to regulate plant defense against biotic and abiotic stresses [9–11]. Many of these transcription factors are co-induced in response to different stresses suggesting the existence of complex interaction [12–14].
In many plant species, the role of phytohormones in coordinating the development of defense responses has clearly been shown, frequently with cross-talk among them to achieve intricately fine-tuned response outcomes [15–18]. Specifically, the jasmonate signaling pathway plays a critical role in mediating defense responses against herbivores [19–21]. In response to herbivore attack, GLA1 enzymes release 18:3 α-linolenic acid (α-LeA) from chloroplast membranes. α-LeA is subsequently converted to oxophytodienoic acid (OPDA) in the chloroplasts by lipoxygenase (LOX), allene oxide synthase (AOS) and allene oxide cyclase (AOC) enzymes. OPDA is transported to peroxisomes and oxidized by OPDA reductase (OPR) forming jasmonic acid (JA). In the cytosol, JA is conjugated to isoleucine by JAR enzymes that produce the bioactive jasmonate, (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile) [22, 23]. JA-Ile associates with the SCFCOI1 complex, presumably to ubiquinate JAZ repressors and tag them for degradation by the 26S proteasome. In the absence of stressful conditions, MYC2 is repressed by the JAZ repressors, which recruit TOPLESS (TPL) as a co-repressor either directly through the EAR (Ethylene Response Factor-Associated Amphifilic Repression) motif or using the EAR motif of the NINJA (Novel Interactor of JAZ) protein [24, 25]. Degradation of JAZ proteins releases the MYC2 transcription factor from repression and reconfigures downstream transcriptional processes [11, 24, 26–28].
MYC2 is a member of the basic Helix-Loop-Helix (bHLH) family of transcription factors (TFs) [29, 30] that are characterized by structurally and functionally conserved domains in many plant species. One of these conserved domains, the basic (b) region, is used to bind to variants of the G-box hexamer (5'-CACNTG-3') found on the promoters of MYC2-regulated genes. The HLH and ZIP domains are used for homo-/hetero-dimerization, while the JID (JAZ Interacting Domain) domain is used to interact with JAZ proteins [11, 28, 29, 31–34].
MYC2 transcription factors participate in the regulation of many JA-dependent physiological processes: defense against herbivores/pathogens, drought tolerance, circadian clock, light signaling and root growth [11, 35–39]. Guo et al. , in a proteomic study that involved mock- or MeJA-treated wild type and myc2 plants, recently identified 27 differentially regulated, JA-inducible and MYC2 dependent proteins involved in glucosinolate metabolism (22%), stress and defense (33%), photosynthesis (22.2%), carbohydrate metabolism (7.4%), protein folding and degradation (11.1%), highlighting the very diverse roles of MYC2.
N. attenuata is a wild tobacco species native to the Great Basin Desert in Utah (USA) which our group has developed into an ecological plant model. The defense responses of this species against its specialist herbivore, Manduca sexta, are well studied, and include the production of potent secondary metabolites: nicotine, HGL-DTGs, phenolamides and protease inhibitors [10, 41–47]. In this study, we identified a putative MYC2 transcription factor in N. attenuata (NaMYC2) and characterized its role in defense response regulation using reverse genetic, transcriptomic and untargeted/targeted metabolomic approaches. Our transcriptomic and metabolomic data indicate a strong involvement of NaMYC2 in nicotine accumulation. However, silencing this gene had only a limited effect on the accumulation of other plant defense metabolites which strongly implicates the involvement of multiple independent and/or redundant transcriptional regulators in defense signaling of N. attenuata plants.
Results and discussion
NaMYC2 transcripts are induced after herbivory
Targeted analysis of secondary metabolite accumulation in MYC2-VIGS plants
Nicotine, phenolamides, hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) and phenolic compounds are among the potent, JA-dependent anti-herbivore compounds in N. attenuata[2, 10, 54, 55]. Their JA-dependent pattern of accumulation suggests that the biosynthesis of these compounds might be regulated by NaMYC2. To test this hypothesis, we used the MYC2-VIGS plants: previously, Saedler and Badwin  demonstrated that VIGS effectively knocks-down the expression of plant defense genes (e.g. PMT) in both leaves and roots of N. attenuata plants. Then, we used a targeted metabolomic approach to compare the accumulation of defensive secondary metabolites in untreated control and WOS-treated (24, 48 and 72 h) EV and MYC2-VIGS plants.
Overall, our results are consistent with the previous reports which demonstrated regulation of jasmonate-induced nicotine/alkaloid biosynthesis by MYC2 TFs. In N. tabacum Bright Yellow (BY-2) cells that were transformed with an inverted-repeat (ir)NtMYC2a/2b construct, the accumulations of nicotine and anatabine were significantly reduced compared to untransformed controls . The NtMYC2 protein was also shown to regulate nicotine biosynthesis either by directly binding to the promoters of nicotine biosynthetic genes in roots or activating NtERF189 which, in turn, activates genes involved in nicotine biosynthesis . In N. benthamiana, VIGS of two bHLH transcription factors (named NbbHLH1 and NbbHLH2) as well as NbERF1 and NbHB1 decreased MeJA-induced accumulation of nicotine . These results demonstrate both the regulatory functions of MYC2 and the involvement of a network of transcription factors in the regulation of nicotine biosynthesis. However, the functions of the tobacco MYC2 genes were not examined in the context of natural herbivore feeding; neither were the effects of these MYC2 genes on the accumulations of other tobacco defense metabolites (e.g. phenolamides, HGL-DTGs, etc.) studied. From the phylogenetic relationship of MYC/bHLH TFs in N. attenuata, N. tabacum and N. benthamiana (Figure 1) and our results, the presence of additional MYC TFs in N. attenuata is a reasonable prediction. Further characterization of these putative TFs might help to fully understand the biosynthesis and ecological consequences of nicotine/alkaloid biosynthesis. Moreover, characterization of additional regulators would complement the partial regulatory function of NaMYC2 in the control of different classes of N. attenuata defense metabolites, as demonstrated in the next sections.
Total hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) and TPI levels
Taken together and considering the JA-/COI1-dependence of HGL-DTG and TPI accumulation in N. attenuata, the biosynthesis of HGL-DTGs and TPIs in N. attenuata is likely regulated by a JA-dependent, but NaMYC2-independent mechanism. Alternatively, the function and/or synergism of an independent MYC2 gene in N. attenuata can explain the partial function of NaMYC2. In addition, similar to phenolamides, the accumulation of HGL-DTG and TPI is also strongly influenced by the developmental stage of the plants . Van Dam et al.  showed that the de novo synthesis of PIs is limited to the early stages of plant development and that flowering plants treated with methyl jasmonate did not significantly increase their local or systemic PI activity levels. In addition, damage to older leaves elicited a much weaker systemic response in younger leaves compared to younger source leaves, a pattern also reported from other studies in N. tabacum. Heiling et al. (2010) demonstrated that the concentrations of 17-hydroxygeranyllinalool diterpene glycosides (DTGs) were highest in most valuable young and reproductive tissues, which is required for effective defense of these tissues against herbivores in N. attenuata.
NaMYC2 and regulation of herbivory-induced phytohormone accumulation
Performance of the specialist herbivore on MYC2-VIGS plants
Large scale transcriptomic and metabolomic analysis of MYC2-silenced leaves
The role of MYC2 TFs in orchestrating plant defense and developmental processes in several plant species were previously reviewed [35, 68, 69]. As master regulators, MYC2 TFs may either directly regulate the genes responsible for defense metabolite biosynthesis or regulate their regulators [11, 68]. To provide information for further work, we used unbiased approaches and compared herbivore-induced (WOS) changes in the transcriptome and metabolome of EV and MYC2-VIGS N. attenuata plants.
NaMYC2 regulated transcriptome ofN. attenuata
In contrast to independently performed qRT-PCR measurement of transcript abundances of phenolamide biosynthetic genes, the microarray analysis did not identify these genes (PAL, AT1, DH29 and MYB8) as differentially regulated in MYC2-VIGS plants compared to EV-VIGS plants because these genes did not pass the strict statistical criteria set for selection of at least 2-fold down-regulated genes in microarray experiment. Nicotine biosynthesis genes are only expressed in the roots and therefore could not be evaluated in the leaf samples used for microarrays.
Silencing of NaMYC2 significantly affects the N. attenuata metabolome
In many plant species, attack from herbivores elicits a cascade of complex transcriptional and metabolic responses that improve plant defense. The effectiveness of plant defense depends on the efficiency by which the timing and duration of responses are regulated. In this study, we identified a MYC2 TF in N. attenuata and characterized its regulatory role using transcriptomic and metabolomic approaches. Transcriptionally, we showed that the expressions of many genes, including transcription factors, involved in plant development or defense responses were affected when MYC2 was silenced in N. attenuata. This was supported by the metabolomic data which identified a large number of differentially regulated molecular features following the silencing. Most importantly, as was previously reported in N. tabacum and N. benthamiana, we showed that NaMYC2 regulates the in planta accumulation of nicotine in N. attenuata leaves. The fact that MYC2 did not strongly affect the accumulation of other JA-dependent metabolites, HGL-DTGs and proteinase inhibitors, suggests that another MYC TF is likely involved in the process.
Despite the considerable conservation of the basic components of plant defense responses among different plant species, substantial variations exist in the responses outcomes which highlights between-species differences in downstream regulatory fine-tuning [31, 73]. For example, in contrast to the considerable similarity among members of the genus Nicotiana in the regulation of nicotine biosynthesis by MYC2 [52, 58, 59] (Figure 1), silencing MYC2 in N. attenuata did not have the exact same effects as reported in A. thaliana; we did not observe a role of MYC2 either in a positive feedback loop activating JA biosynthesis or in a negative feedback involving suppression of the jasmonate response through the activation of JAZ repressors [11, 74].
In addition, not all JA-dependent defense metabolites (e.g. HGL-DTGs) were regulated by MYC2 in N. attenuata. In fact, when compared against the diversity of defense metabolites in N. attenuata, the regulatory function of MYC2 is quite limited. This rather limited role suggests that other members of the bHLH family of transcription factors might be involved in the regulation of defense responses not regulated by MYC2. The recent identification of additional MYC2 TFs in A. thaliana[36, 37], N. tabacum[52, 58] and N. benthamiana with overlapping or distinct functions support this conjecture.
Indeed, we found an additional MYC2-like gene (KC906192) in diploid N. attenuata showing a 72.3% protein sequence identity with NaMYC2. In the phylogenetic analysis, MYC2-like protein clustered separately from the MYC2 clade of Solanaceae species, including N. tabacum MYC2a and MYC2b. When we briefly examined the function of MYC2-like gene in N. attenuata, interestingly, increased defense responses in MYC2-like-VIGS plants were observed (data not shown). This was in a strong contrast to silencing the NaMYC2 (and N. benthamiana genes bHLH1and bHLH2; ) but in agreement with the VIGS–induced silencing of the N. benthamiana bHLH3 (a gene fragment not included in phylogenetic tree shown in Figure 1), which increased the nicotine content in the VIGS-silenced N. benthamiana plants after foliar application of MeJA . Therefore, some of the MYC2-like genes may work as repressors of JA-induced responses, contributing to a fine-tuning of defense against herbivores, possibly by competing for promoter binding sites with the activator-type MYC2 genes. As previously demonstrated for the transient character of JA-Ile accumulation [62, 75], tight control of JA signaling is likely to be essential for plant responses to multiple biotic stresses in the environment. Identification and characterization of additional MYC2 TFs in N. attenuata and other plant species is likely to provide a more complete mechanistic picture of JA-regulated defense responses.
Considering the high degree of conservation in the binding site of MYC2 TFs in different species [29, 31], we believe future research in determining the binding sites of these TFs will be critical to understanding their function. When these binding sites are identified, additional MYC2-dependent genes or other transcription factors that respond to herbivory, disease, environmental stress or development can be more readily identified. It would be interesting to identify the interacting partners of MYC2 TFs in N. attenuata and characterize the mechanisms of interaction to understand how the signaling components evolved. In A. thaliana, transcriptional regulation by MYC2 requires interactions with important regulatory elements including members of the mediator complex proteins (e.g. MED25), chromatin-opening proteins like General Control Non-repressible 5 (GCN5), members of the histone acetyl transferase family and SPLAYED (SYD) [35, 76, 77]. Identification and characterization of homologues of these components in N. attenuata might test the generality of the signaling processes across different plant families.
Plant growth and treatments
N. attenuata seeds that were collected from its native habitat in Great Basin desert, Utah (USA) and inbred for 31 generations were used for the experiments. Seed germination and plant growth conditions were described in Krügel et al. . To experimentally simulate herbivory, we wounded fully expanded leaves of EV and MYC2-VIGS (n=5) N. attenuata plants with a serrated fabric pattern wheel and the wounds were treated with 20 μL of diluted (1:5, v/v in water) M. sexta oral secretions (WOS), while controls were collected from untreated plants. To evaluate performance of the specialist herbivore (M. sexta) on transformed plants, freshly hatched neonates were fed on EV and transformed plants (n = 20) and their masses were measured every 4 d.
Virus Induced Gene Silencing (VIGS)
Virus Induced Gene Silencing (VIGS) system, described in Saedler and Baldwin , was used to transiently silence MYC2 transcription factor. Briefly, we amplified ~250 bp fragment of the N. attenuata MYC2 using specific primers (Additional file 4: Table S3), cloned them into the PTV00 vector. We verified the clone by sequencing and transformed GV3101 strain of Agrobacterium tumefaciens with either untransformed plasmid (PTV00, control) or plasmids harboring the inserts (pTV-MYC2) and incubated them at 26°C for two days. On the day of infiltration, overnight cultures of all constructs and pBINTRA and pTVPDS were inoculated into YEP media containing antibiotics (Kanamycin 50 mg/L) and incubated (28°C) for 5 h. When the cultures attained an OD of 0.6 to 0.8, we centrifuged them (1,125g, 4°C for 5 min), resuspended the pellets in an equimolar mix (5 mM) of MgCl2 and MES and prepared a 1:1 mix of each construct with the helper strain pBINTRA. Using 1 mL syringes, we infiltrated the suspension into five leaves of 25 d old N. attenuata plants, covered them with plastic and left them in a dark chamber for 2 d. The plants were kept in the growth chamber under 16 h/day, 8 h/night light regime at 22°C. We monitored the spread of silencing using control plants infiltrated with the pTVPDS construct which induced leaf bleaching, while the efficiency of silencing was determined by measuring transcript abundances using qRT-PCR.
We treated fully elongated leaves of EV and MYC2-VIGS plants (n = 3) with WOS for 1h, collected and ground the leaves in liquid nitrogen and extracted RNA for the microarray analysis as described in Gillardoni et al. . After hybridization and array processing, we normalized (with the 75th percentile of the respective columns) and log2-transformed the raw expression values obtained from the "gProcessedSignal" column and processed them using Significance of Microarrays (SAM; http://www-stat.stanford.edu/~tibs/SAM/) package on Excel (Microsoft). For the analysis, we set the minimum fold change, delta and median FDR (%) values to 2, 0.69 and 15.8 (%) respectively. Genes that differed significantly in comparison to EV plants were annotated using Blast2Go  and grouped according to TAIR classification. The microarray data was deposited in GEO under the accession number GSE45608.
Transcript abundance measurement
We extracted total RNA from frozen leaf material of untreated or WOS-treated EV and MYC2-VIGS plants (n = 5) using TRIzol reagent (Invitrogen) as recommended by the manufacturer. We treated the total RNA with DNAse (RQ1 RNase-Free DNase; Promega) before synthesizing cDNA using oligo (dT)18 and Superscript II reverse transcriptase (Invitrogen). Transcript abundances were measured on Mx3005P Multiplex qPCR (Stratagene) with qPCR core kit for SYBR Green I (Eurogentec). Relative transcript abundances were determined by comparing sample fluorescence signals to dilution series of cDNA prepared from the 1 h WOS -treated samples, and examined on the same plate. Signals were then normalized by the average EF-1α transcript abundances determined separately for each sample. The primers used for qRT-PCR are listed in Additional file 4: Table S3. As there is a considerable similarity in protein coding sequences in multiple members in bHLH TF family, it may imply significant functional redundancy of these regulators in biological systems. We therefore carefully designed our primers in the 3’ non-translated end of the gene to amplify and detect specifically the NaMYC2 transcription factor (Additional file 1: Figure S2).
Fully-expanded leaves of EV and MYC2-VIGS plants (n = 5) were treated with WOS for 1 h or 2 h, collected and ground in liquid nitrogen and stored at −80°C until use. We homogenized about 200 mg powder in 1 mL ethyl acetate (containing 200 ng/mL D2-JA and 40 ng/mL D6-ABA, D4-SA and JA-13C6-Ile internal standards), centrifuged for 20 min (16,100g, 4°C) and transferred the supernatants into new tubes. After re-extracting the pellets with 0.5 mL ethyl acetate and combining the supernatants, we evaporated the ethyl acetate on a vacuum concentrator (Eppendorf) and resuspended the residue in 0.5 mL 70% methanol in water (v/v). Then, we centrifuged the re-suspended samples for 10 min (16,100 g, 4°C) and analyzed the supernatant (10 μL) on Varian 1200L Triple-Quadrupole-LC-MS (Varian) using a ProntoSIL® column (C18; 5 μm, 50 × 2 mm; Bischoff) attached to a precolumn (C18; 4 × 2 mm, Phenomenex). Detail measurement conditions are described in Woldemariam et al. .
Secondary metabolite analysis
To undertake targeted defense secondary metabolite (nicotine, total 17-hydroxygeranyllinalool diterpene glycosides [HGL-DTGs], caffeoylputrescine, dicaffeoylspermidine, chlorogenic acid and rutin) analysis, we treated leaves of EV and MYC2-VIGS (n = 5) plants with WOS for 24, 48 or 72 h, collected and ground the samples in liquid nitrogen. Control samples were collected without treatment. About 100 mg powder was extracted and analyzed on HPLC equipped with a photodiode array detector as previously described in Onkokesung et al. .
Untargeted metabolomic analysis
To undertake an unbiased metabolomic analysis, metabolites were extracted from leaves (n = 3) of EV and MYC2 silenced N. attenuata plants fed on for 4 d by neonates of M. sexta and analyzed on an HPLC 1100 Series system (Agilent, Palo Alto, USA) coupled to a MicroToF mass spectrometer (Bruker Daltonik, Bremen, Germany). The optimized analytic procedures are described in Gaquerel et al. . Briefly, peak picking, peak detection and RT corrections were performed by XCMS (and CAMERA) package using the following parameters: centWave method; ppm = 20; snthresh =10; peakwidth = between 5 and 18 s; minfrac=0.5; minsamp=1; bw=10; mzwid=0.01; sleep=0.001. To fill missing features, we used the FillPeaks function from XCMS. We exported the pre-processed data to Excel, filtered those features with RTs < 60 seconds and m/z < 80 and analyzed the processed data on Metaboanalyst 2.0 following the procedure described before .
We used STATVIEW (version 5.0; SAS Institute, Cary, NC, USA) software to perform statistical analyses with alpha level of 0.05 for all statistical tests.
We acknowledge the German Academic Exchange Service (DAAD) and the International Max Planck Research School (IMPRS) for financial support. Son Truong Dinh was also supported by the Vietnam Ministry of Agricultural and Rural Development and the Max Planck Society.
NaMYC2 GenBank Accession number: KC832837
NaMYC2-like GenBank Accession number: KC906192
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