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First published online June 24, 2005; 10.1104/pp.105.061192 Plant Physiology 138:1763-1773 (2005) © 2005 American Society of Plant Biologists Specificity in Ecological Interactions. Attack from the Same Lepidopteran Herbivore Results in Species-Specific Transcriptional Responses in Two Solanaceous Host Plants1,[w]Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, 07745 Jena, Germany
Model systems have proven enormously useful in elucidating the biochemical function of plant genes. However their ecological function, having been sculpted by evolutionary forces specific to a species, may be less conserved across taxa. Responses to wounding and herbivore attack differ among plant families and are known to be mediated by oxylipin, ethylene, and systemin-signaling networks. We analyzed transcriptional responses of two native Solanaceous species to the attack of an herbivore whose elicitors are known not to be influenced by diet. With The Institute for Genomic Research 10k-cDNA potato (Solanum tuberosum) microarray, we compared the transcriptional responses of Nicotiana attenuata with those of black nightshade (Solanum nigrum) when both were attacked by the Solanaceous generalist herbivore, Manduca sexta. Based on an NADH dehydrogenase subunit F phylogeny, S. nigrum is more closely related to potato than N. attenuata but responded significantly less to M. sexta attack. Apart from transcriptional differences anticipated from their differences in secondary metabolism, both species showed distinct transcriptional patterns (with only 10% overlap in significantly regulated genes), which point to fundamental differences in the signaling cascades and downstream genes mediating herbivore resistance. The lackluster transcriptional response of S. nigrum could not be attributed to its inability to respond to elicitation, because methyl jasmonate elicitation of S. nigrum resulted in a strong transcriptional response. Given that attack from the same herbivore elicits profoundly different responses in two Solanaceaous taxa, we conclude that blueprints for commonly regulated responses to plant-herbivore interactions appear unlikely.
Understanding the genetic basis of plant secondary metabolism will require multiple model systems (Kutchan, 2001
Three plant hormones, jasmonic acid (JA), ethylene (ET), and salicylic acid, mediate responses to wounding and attack from herbivores and pathogens in most taxa studied, but research on crosstalk among these signals has identified important differences at the family level. For example in Arabidopsis, wounding leads to the activation of two pathways: an oligosaccharide-dependent and a JA-dependent pathway in the damaged leaves (Walling, 2000
Within-family differences have been observed in the crosstalk between JA and ET signaling in the elicitation of defense responses. While JA and ET interact synergistically to elicit proteinase inhibitor expression in tomato, attack from Manduca sexta larvae in Nicotiana attenuata elicits an ET burst, which antagonizes the JA-mediated increase in nicotine (Kahl et al., 2000
Given this evidence for differences in defense signaling among several Solanaceous taxa, we were interested in a more thorough characterization of the potential differences in responses to herbivore attack within a plant family. For this analysis, we compared the herbivore-induced transcriptome of two native Solanaceous species, N. attenuata and S. nigrum, to attack from the same native herbivore, M. sexta larvae. Three aspects of this analysis make this a valuable comparison. First, we analyze the responses of two native plants in which the responses observed to herbivore attack are not confounded by a history of artificial selection for yield-associated traits. Second, we measure the responses to attack by a shared native herbivore (Fraenkel, 1959
In order to provide an unbiased comparison of the herbivore-regulated transcriptome in both species, we used a microarray with over 10,000 potato cDNAs (representing approximately a third of the potato genome). We were particularly interested in the scope of the response (How many genes are involved?) and the specificity of the response (How many transcripts are commonly and specifically regulated?). The potato microarray was established through the National Science Foundation Potato Functional Genomics project (http://www.tigr.org/tdb/potato) and is available from The Institute of Genomic Research (TIGR, Rockville, MD). The scope and specificity of the response could be influenced by the taxonomic similarity between the source of the genes on the array (potato) and the samples used in the hybridizations (S. nigrum and N. attenuata). To clarify the phylogentic relationship among the three species, we analyzed sequence similarities among the plastidial NADH dehydrogenase subunit F (ndhF) gene of several Solanacaeous species. Based on this analysis, S. nigrum is more closely related to potato than N. attenuata, which generated the expectation that the array analysis would likely reveal a stronger response from S. nigrum than from N. attenuata. However, we found the opposite to be true: S. nigrum showed a weaker response to M. sexta than N. attenuata. To test the hypothesis whether S. nigrum is generally less responsive, we examined the transcriptional responses of S. nigrum after elicitation by methyl jasmonate (MeJA), the volatile derivative of JA. MeJA is known to be both a product and elicitor of the oxilipin signaling pathway, the signal cascade that mediates many defense responses to herbivore and pathogen attack (Walling, 2000
Phylogenetic Analysis To clarify the phylogenetic relationship between N. attenuata and S. nigrum, we analyzed sequence similarities among the plastidial ndhF gene of several Solanaceous species. Based on this comparison, S. nigrum is more closely related to potato than N. attenuata, as demonstrated by a 97% homology between S. nigrum and potato and 94% between N. attenuata and potato (Fig. 1).
Microarray Analysis of M. sexta-Induced Responses
Three replicate TIGR chips were hybridized with RNA from thrice replicated M. sexta-infested N. attenuata plants and M. sexta-infested S. nigrum plants. Of 11,243 cDNAs, a total of 754 were regulated (mean ratio >1.5 or <0.67 for up- and down-regulated genes, respectively) in either N. attenuata, S. nigrum, or both species in response to M. sexta attack (Fig. 2
Signal Transduction Additionally to a common up-regulation of lysophospholipase and lipoxygenase (oxylipin signaling), N. attenuata and S. nigrum activate different signal cascades in response to leaf-chewing M. sexta larvae. Increases in genes coding for a G-protein-coupled receptor, a GTP-binding protein, phospolipase C, diacylglycerol kinase, calmodulin, annexin, a Ca2+-activated kinase, and a Ca2+-activated ion channel indicate calcium- and inositol phospholipid-based signaling, as well as G-protein-mediated signaling in N. attenuata. Moreover, the generation of 2-hydroperoxides by -dioxygenase ( -dox) and glucosylated salicylate by UDP-Glc:SA glucosyltransferase appears to be specific to N. attenuata, while a zeatin-glucosyltransferase and a 12-oxo-phytodienoate reductase seem to have in role in signaling in S. nigrum. An auxin-amino acid hydrolase and several kinases (calcium-dependent kinases, receptor kinases, and MAP kinases) are activated in both species.
Proteolysis
Secondary Metabolism
In contrast to S. nigrum, N. attenuata induces transcripts involved in the plastid-localized glyceraldehyde/pyruvate pathway (DOX synthase, DOX reductoisomerase) of IPP production, suggesting that not only sesquiterpenes but also mono- and diterpenes, are elicited in N. attenuata upon M. sexta herbivory. This is supported by the up-regulation of linalool synthase. IPP isomerase, which is recruited by both terpenoid pathways, is specifically up-regulated in N. attenuata.
Also in contrast to the response in S. nigrum, N. attenuata plants elicit a strong transcriptional commitment to the production of phenol-based secondary compounds. Starting with the synthesis of shikimate (dehydroquinate synthase, shikimate kinase, 3-phosphoshikimate 1-carboxyvinyltransferase, chorismate synthase), proceeding to the synthesis of prephenate (the committed step in Phe and Tyr synthesis catalyzed by chorismate mutase), continuing with the synthesis of cinnamic acid (Phe ammonia lyase), p-coumaric acid (cinnamate-4-hydroxylase), and p-coumaroyl-CoA (coumaric acid-CoA ligase), the genes providing the precursors for flavonoid and phenylpropanoid biosynthesis are induced. Transcripts related to flavonoid metabolism (UDP rhamnose-anthocyanidin-3-glucoside rhamnosyltransferase, dihydroflavonol reductase) and phenylpropanoid metabolism (p-coumaroyl shikimate 3'-hydroxylases, cinnamoyl-CoA reductase) were up-regulated as well. These results are consistent with the following earlier findings in the M. sexta-N. attenuata interaction: (1) The cloning of a UDP rhamnose-anthocyanidin-3-glucoside rhamnosyltransferase by differential display reverse transcription-PCR from M. sexta-induced N. attenuata plants (Voelckel and Baldwin, 2003
Proteinase inhibitor (PI) induction, an induced-defense response well characterized in Manduca-attacked N. attenuata (Zavala et al., 2004
Primary Metabolism
Stress Responses and Selected Genes
Verification of Microarray Data by TaqMan Real-Time PCR
The weaker response of S. nigrum to M. sexta herbivory in comparison to the response of N. attenuata raised the question whether S. nigrum was a nonresponding species. To test this hypothesis, we hybridized three additional microarrays with RNA from three biological replicates of MeJA-treated plants. Of 11,243 analyzed clones on the microarray, 339 were differentially regulated (263 > 1.5; 76 < 0.67) in S. nigrum in response to MeJA elicitation (about 3% of the total number of spotted clones; Supplemental Table III). In accordance with the ubiquitous role of oxilipins (JA, MeJA) in mediating plants' responses to herbivory, 72 genes are commonly up-regulated in S. nigrum in response to MeJA or to M. sexta (Fig. 5). Again LAP was among the highest up-regulated genes in MeJA-elicited plants and further up-regulated genes are involved in oxylipin biosynthesis (LOX), secondary metabolism (HMGR, farnesyl pyrophosphate synthase, PIs), synthesis of chaperones (luminal binding protein), to name just a few (Supplemental Table III). A majority of the up-regulated genes (191) were up-regulated only in MeJA-elicited plants clearly demonstrating that S. nigrum is fully capable of responding to elicitation. These genes included genes involved in secondary metabolism (e.g. shikimate 5-dehydrogenase), transcription factor genes (e.g. C2H2 zinc finger protein), genes related to ubiquitin-mediated proteolysis (clone nos. STMDG12, STMHH55), and genes coding for several cytochrome P450s. A subset of 33 genes were commonly up-regulated in MeJA-elicited S. nigrum and M. sexta-infested N. attenuata plants (Fig. 5B) and were dominated by genes involved in primary metabolism (carbohydrates) and secondary metabolism (phenylpropanoids, terpenoids). A similar-sized (33) subset of genes were commonly up-regulated among all three treatments and were dominated by genes related to oxylipin signaling and chaperones.
Small scale microarrays are often criticized for their bias in gene selection, which makes them suitable for answering the questions for which they were designed but unsuitable for other research questions. Here we used the potato 10 K-cDNA clone microarray (TIGR) to provide an unbiased comparison of the transcriptional responses of two Solanaceous species, N. attenuata and S. nigrum, to herbivory from the Solanaceous generalist, M. sexta. Based on the diversity of secondary metabolites produced by Solanaceous plants (e.g. Frohne and Jensen, 1992
The TIGR array analysis confirmed previously measured increases in the expression of jasmonate cascade genes and of genes known to be positively regulated by jasmonate signaling, such as genes involved in green leaf volatile, polyamine, or phenylpropanoid synthesis. Additionally, the TIGR array analysis found many more genes representing the above-mentioned branches of metabolism, including p-coumaroyl shikimate 3'-hydroxylase and cinnamoyl-CoA reductase (phenylpropanoids and their conjugates, Gang et al., 2002
Apart from the anticipated differences in alkaloid (steroidal alkaloids in S. nigrum) and alkaloid/polyamine precursor (putrescine in N. attenuata) formation, our analysis revealed the production of different defense metabolites in both species. N. attenuata predominantly elicited genes for the production of antinutritive polyphenol oxidases, phenylpropanoids and their precursors, and plastidic IPP, which is primarily channeled into mono- and diterpene synthesis (Lichtenthaler, 1999
Contrary to our assumption that the two species would activate a similar suite of signaling genes, N. attenuata and S. nigrum activated different sets of signaling genes and in N. attenuata more signaling cascades appeared to be up-regulated. JA signaling was regulated in both species; calcium-based signaling, inositol-phospholipid signaling, and G-protein-mediated signaling were found to be specific to N. attenuata, and cytokinin signaling was detected only in S. nigrum. While calcium-signaling has been implicated in systemin-mediated activation of phospholipase A2 and subsequent JA synthesis (Ryan, 2000
Our analysis also provided a deeper insight into the changes that accompany alterations in signaling and secondary metabolism, namely changes in carbohydrate and amino acid metabolism, nucleic acid and protein metabolism, or changes associated with other biotic or abiotic stressors. For example, both plants increased similar and dissimilar transcripts for chaperones, dehydration-related genes, and oxidative stress genes. Transcript levels of enzymes involved in protein degradation/processing were increased in both species but with distinct differences. Ubiquitin-related proteolysis, which plays an important role in eliminating misfolded or abnormal proteins that probably accumulate in stressed plants, is activated only in N. attenuata. Furthermore, ubiquitin-dependent protein turnover influences many cellular processes by modulating levels of regulatory proteins (Hare et al., 2003
In S. nigrum other genes involved in protein metabolism are induced by M. sexta herbivory, with the most dramatic example being a LAP gene whose expression was up-regulated 20-fold. LAPs are present in pro- and eukaryotes, and plant LAPs have been intensively studied in tomato, where they are elicited by JA, wounding, and pathogens and are present in floral tissues (Tu et al., 2003
When S. nigrum was treated with MeJA, a derivative of the jasmonate cascade that is largely responsible for mediating herbivore resistance, branches of secondary metabolism and signaling were activated that the previous microarray experiment had shown only for N. attenuata's responses to M. sexta attack. These included genes involved in phenylpropanoid and shikimate biosynthesis, the plastidic pathway of terpenoid production, genes involved in ubiquitin-mediated proteolysis, and a gene related to G protein signaling. Hence, the genuinely weaker transcriptional response of S. nigrum to M. sexta herbivory cannot be explained by S. nigrum's inability to respond to elicitation. N. attenuata has likely had a longer evolutionary association with M. sexta and hence has had more time to evolve a strong response to M. sexta attack. S. nigrum appears not to have evolved strong responses to this herbivore, but has to others, e.g. flea beetles (Schmidt et al., 2004 In summary, the transcriptional comparison of M. sexta-attacked N. attenuata and S. nigrum plants did not support the existence of a Solanaceous blueprint for herbivore defense. Most strikingly, the differences extended beyond the activation of different alkaloid pathways and included a profound divergence in signaling pathways mediating the elicited responses. The likely difference in the length of their evolutionary associations with M. sexta may account for the differences in their responses.
Plant and Insect Growth and Experimental Setup
Seeds of a Nicotiana attenuata inbred line were smoke germinated on Phytagel as described by Krugel et al. (2002)
Insect Treatment To determine whether first instar M. sexta larvae consume different amounts of leaf area from the two host plant species, we placed two freshly hatched caterpillars on each of another five plants per species and measured the amount of leaf material consumed after 24 h. After 24 h, the damaged leaves were harvested, scanned (HP Scanjet 8200, 300 dpi; Hewlett-Packard, Palo Alto, CA), the leaf area consumed was determined by counting pixels with image analysis software (Sigma Scan Pro 5, Point Richmond, CA), and the larvae were weighed. Five leaves were not included in the analysis because the caterpillars died or walked off the leaf during the experiment leaving n = 8 for N. attenuata and n = 7 for S. nigrum. The amount of leaf area consumed did not differ significantly between the two host species (N. attenuata 17.0 ± 2.9 mm2; S. nigrum 23.6 ± 3.0 mm2; t0.025, 13 = 1.375, P = 0.192). Lavae feeding on N. attenuata (2.7 ± 0.2 mg) tended to be slightly heavier than those feeding on S. nigrum (2.0 ± 0.1 mg).
MeJA Treatment
For gene expression analysis, we used two versions of the TIGR potato 10,000-clone cDNA microarray that contain 11,243 (version 10Kv1) and 11,512 (10Kv2) annotated cDNA clones spotted as duplicates on the array. Detailed information about this microarray can be found under http://www.tigr.org/tdb/potato/microarray_comp.shtml. For the transcriptional analysis of M. sexta-induced responses of N. attenuata and S. nigrum, we used array version 10Kv1; for the MeJA-elicited responses of S. nigrum we used array version 10Kv2. For comparisons of the datasets produced from the two versions of the microarray, we analyzed only the clones present on both versions of the array (11,243 clones). Gene expression data obtained from hybridizations of this potato microarray with a variety of Solanaceous species can be accessed through a database maintained at the TIGR Web site (http://www.tigr.org/tigr-scripts/sgedb/studies_SGED.pl) and thus compared and shared across different laboratories. Although Solanaceous species clearly differ in morphology, life cycle, secondary metabolism, tuber and fruit formation, etc., they have similar genomes with respect to gene content and genome organization (see transcriptional analysis of several Solanaceous plants by Robin Buell, http://www.tigr.org/tigr-scripts/sgedb/search2_std.pl?study_id=35). Plant material was ground under liquid nitrogen and total RNA was extracted with TRI Reagent (Sigma) according to the manufacturer's instructions. All steps of microarray processing (cDNA production, cDNA labeling, microarray hybridization, data quantification, data normalization using LOWESS) were carried out by the TIGR Expression Profiling Service according to published methods (http://www.tigr.org/tdb/potato/microarray_SOPs.shtml). The cDNAs hybridized to an individual array was produced from RNA extracted individually from the four plants of a control cage (Cy5 labeled) and the four plants of the treatment cage (Cy3 labeled). The three biological replicates of the M. sexta-N. attenuata elicitation experiment are named NA1, NA2, and NA3. SN1, SN2, and SN3 designated the corresponding replicate microarrays of the M. sexta-S. nigrum elicitation experiment; the arrays of the S. nigrum MeJA experiment are named SNmj1, SNmj2, and SNmj3. The raw data from the nine hybridizations including all details of the experiment are available from the TIGR Solanaceae Gene Expression Database (http://www.tigr.org/tigr-scripts/sgedb/search2_std.pl?study_id=53, experiment IDs 2450, 2455, 2460, 2465, 2470, 2475, 2928, 2929, 2930).
We analyzed the normalized data of the six microarrays with GeneSpring 6.1 (Silicon Genetics, Redwood City, CA) using Hierarchical Cluster Analysis. For further analysis we calculated the mean ER from the biological replicates and defined a transcript as being differentially regulated when the following criteria were fullfilled: (1) The ER was significantly different from 1 as determined by a Student's t test (P < 0.05); and (2) the ER exceeded the thresholds of 0.67 and 1.5 for down- and up-regulation, respectively. These criteria had been previously tested and found to give reproducible results (Heidel and Baldwin, 2004
We confirmed the microarray expression data using TaqMan real-time PCR (ABI PRISM 7700 Sequence Detection System; Applied Biosystems, Foster City, CA). Additionally, to test the suitability of this potato microarray for S. nigrum and N. attenuata, we chose to assay the species that is more distantly related to potato, namely N. attenuata (Fig. 1). We analyzed the three biological replicates of M. sexta-challenged N. attenuata using TaqMan probes for N. attenuata-specific genes that are homologous to genes present on the array, namely
We thank TIGR for generously providing the microarrays and the data acquisition, Dr. Ryan Oyama for invaluable support with the phylogenetic analysis, Jens Wurlitzer for help with the experiments, and Ben Bubner for TaqMan support. Received February 12, 2005; returned for revision April 5, 2005; accepted April 5, 2005.
1 This work was supported by the Max Planck Society and the Deutsche Forschungsgemeinschaft (FOR 456; BA2138/11).
2 These authors contributed equally to the paper.
3 Present address: John Innes Centre, Department of Disease and Stress Biology, Colney, Norwich NR4 7UH, UK.
[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.105.061192. * Corresponding author; e-mail baldwin{at}ice.mpg.de; fax: 493641571102.
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