A Kunitz trypsin inhibitor gene family from trembling aspen (Populus tremuloides Michx.): cloning, functional expression, and induction by wounding and herbivory

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Resistance against Leucoptera sinuella (Lepidoptera: Lyonetiidae) among hybrid clones of Populus spp. in central Chile

Leucoptera sinuella (Reutti) (Lepidoptera: Lyonetiidae) is a leaf miner specialist on Salicaceae recently introduced to Chile and Argentina, where it is causing economic damage to poplar plantations. We report a field survey in a poplar nursery naturally infested showing that regardless of the poplar hybrid taxon, high variability in resistance was observed among clones within families for oviposition and leaf-mining damage. A group of susceptible and resistant hybrid poplar clones was then selected for a laboratory evaluation of oviposition (antixenosis) and leaf-mining damage (antibiosis) on potted, rooted shoot cuttings. The concentration of condensed tannins (CTs) and salicinoid phenolic glucosides (SPGs) of the leaves of the selected clones from the laboratory study was also measured. Total oviposited eggs were positively correlated with leaf area, with the lowest oviposition on TMxT 11372 clone. The lowest percentage of mined leaf area was obtained for clones TMxT 11372, TMxT 11463, and TDxD 17574, but surprisingly no correlation between the percentage of mined leaf area and concentration of CTs and SPGs was found. Resistant poplar hybrids of our study could be suitable for breeding programs aimed for L. sinuella integrated pest management.

Proteomics and metabolomics reveal the mechanism underlying differential antioxidant activity among the organs of two base plants of Shiliang tea (Chimonanthus salicifolius and Chimonanthus zhejiangensis)

The leaves and branches of Chimonanthus salicifolius and Chimonanthus zhejiangensis are the base ingredients of Shiliang tea. In this study, proteomics and metabolomics were performed to understand the molecular mechanisms underlying antioxidant activity (AA) in the leaves and branches of the two species. Stress and redox related proteins are differentially expressed among organs. The abundance of isoprenoid pathway-related proteins is higher in leaves while the abundance of phenylpropanoid and flavonoid pathway-related proteins is higher in branches in both species. Metabolomics revealed the flavonoid composition and demonstrated that procyanidins are more abundant in branches. Superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), and AA are stronger in branches than leaves. Overall, branches might contribute to redox homeostasis through SOD/GSH-PX and flavonoids. Furthermore, the high level of AA of branches might be largely due to their increased accumulation of procyanidins.

Silencing of StRIK in potato suggests a role in periderm related to RNA processing and stress

BACKGROUND

The periderm is a protective barrier crucial for land plant survival, but little is known about genetic factors involved in its development and regulation. Using a transcriptomic approach in the cork oak (Q. suber) periderm, we previously identified an RS2-INTERACTING KH PROTEIN (RIK) homologue of unknown function containing a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm.

RESULTS

To gain insight into the function of RIK in the periderm, potato (S. tuberosum) tuber periderm was used as a model: the full-length coding sequence of RIK, hereafter referred to as StRIK, was isolated, the transcript profile analyzed and gene silencing in potato performed to analyze the silencing effects on periderm anatomy and transcriptome. The StRIK transcript accumulated in all vegetative tissues studied, including periderm and other suberized tissues such as root and also in wounded tissues. Downregulation of StRIK in potato by RNA interference (StRIK-RNAi) did not show any obvious effects on tuber periderm anatomy but, unlike Wild type, transgenic plants flowered. Global transcript profiling of the StRIK-RNAi periderm did show altered expression of genes associated with RNA metabolism, stress and signaling, mirroring the biological processes found enriched within the in silico co-expression network of the Arabidopsis orthologue.

CONCLUSIONS

The ubiquitous expression of StRIK transcript, the flower associated phenotype and the differential expression of StRIK-RNAi periderm point out to a general regulatory role of StRIK in diverse plant developmental processes. The transcriptome analysis suggests that StRIK might play roles in RNA maturation and stress response in the periderm.

Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus

Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.

Defense Priming in Nicotiana tabacum Accelerates and Amplifies 'New' C/N Fluxes in Key Amino Acid Biosynthetic Pathways

In the struggle to survive herbivory by leaf-feeding insects, plants employ multiple strategies to defend themselves. One mechanism by which plants increase resistance is by intensifying their responsiveness in the production of certain defense agents to create a rapid response. Known as defense priming, this action can accelerate and amplify responses of metabolic pathways, providing plants with long-lasting resistance, especially when faced with waves of attack. In the work presented, short-lived radiotracers of carbon administered as 11CO2 and nitrogen administered as 13NH3 were applied in Nicotiana tabacum, to examine the temporal changes in 'new' C/N utilization in the biosynthesis of key amino acids (AAs). Responses were induced by using topical application of the defense hormone jasmonic acid (JA). After a single treatment, metabolic partitioning of recently fixed carbon (designated 'new' carbon and reflected as 11C) increased through the shikimate pathway, giving rise to tyrosine, phenylalanine and tryptophan. Amplification in 'new' carbon fluxes preceded changes in the endogenous (12C) pools of these AAs. Testing after serial JA treatments revealed that fluxes of 'new' carbon were accelerated, amplified and sustained over time at this higher rate, suggesting a priming effect. Similar results were observed with recently assimilated nitrogen (designated 'new' nitrogen reflected as 13N) with its partitioning into serine, glycine and glutamine, which play important roles supporting the shikimate pathway and downstream secondary metabolism. Finally, X-ray fluorescence imaging revealed that levels of the element Mn, an important co-factor for enzyme regulation in the shikimate pathway, increased within JA treated tissues, suggesting a link between plant metal ion regulation and C/N metabolic priming.

LeBoldus J, Keefover‐Ring K, Azeem M, Chen J, Macaya‐Sanz D, MacDonald WL, Muchero W, DiFazio SP. Host plant genetic control of associated fungal and insect species in a Populus hybrid cross

Plants employ a diverse set of defense mechanisms to mediate interactions with insects and fungi. These relationships can leave lasting impacts on host plant genome structure such as rapid expansion of gene families through tandem duplication. These genomic signatures provide important clues about the complexities of plant/biotic stress interactions and evolution. We used a pseudo-backcross hybrid family to identify quantitative trait loci (QTL) controlling associations between Populus trees and several common Populus diseases and insects. Using whole-genome sequences from each parent, we identified candidate genes that may mediate these interactions. Candidates were partially validated using mass spectrometry to identify corresponding QTL for defensive compounds. We detected significant QTL for two interacting fungal pathogens and three insects. The QTL intervals contained candidate genes potentially involved in physical and chemical mechanisms of host-plant resistance and susceptibility. In particular, we identified adjoining QTLs for a phenolic glycoside and Phyllocolpa sawfly abundance. There was also significant enrichment of recent tandem duplications in the genomic intervals of the native parent, but not the exotic parent. Tandem gene duplication may be an important mechanism for rapid response to biotic stressors, enabling trees with long juvenile periods to reach maturity despite many coevolving biotic stressors.

Aboveground phytochemical responses to belowground herbivory in poplar trees and the consequence for leaf herbivore preference

Belowground (BG) herbivory can influence aboveground (AG) herbivore performance and food preference via changes in plant chemistry. Most evidence for this phenomenon derives from studies in herbaceous plants but studies in woody plants are scarce. Here we investigated whether and how BG herbivory on black poplar (Populus nigra) trees by Melolontha melolontha larvae influences the feeding preference of Lymantria dispar (gypsy moth) caterpillars. In a food choice assay, caterpillars preferred to feed on leaves from trees that had experienced attack by BG herbivores. Therefore, we investigated the effect of BG herbivory on the phytochemical composition of P. nigra trees alone and in combination with AG feeding by L. dispar caterpillars. BG herbivory did not increase systemic AG tree defences like volatile organic compounds, protease inhibitors and salicinoids. Jasmonates and salicylic acid were also not induced by BG herbivory in leaves but abscisic acid concentrations drastically increased together with proline and few other amino acids. Leaf coating experiments with amino acids suggest that proline might be responsible for the caterpillar feeding preference via presumptive phagostimulatory properties. This study shows that BG herbivory in poplar can modify the feeding preference of AG herbivores via phytochemical changes as a consequence of root-to-shoot signaling.

The effects of Enterolobium contortisiliquum serine protease inhibitor on the survival of the termite Nasutitermes corniger, and its use as affinity adsorbent to purify termite proteases

The immobilization of Enterolobium contortisiliquum protease inhibitor, EcTI-Sepharose, as an affinity chromatography matrix is a powerful biotechnological tool to purify targets from Nasutitermes corniger in the investigation of insecticidal properties of natural compounds.

Defence-related priming and responses to recurring drought: Two manifestations of plant transcriptional memory mediated by the ABA and JA signalling pathways

Collective evidence from agricultural practices and from scientific research has demonstrated that plants can alter their phenotypic responses to repeated biotic and abiotic stresses or their elicitors. A coordinated reaction at the organismal, cellular, and genome levels has suggested that plants can "remember" an earlier stress and modify their future responses, accordingly. Stress memory may increase a plant's survival chances by improving its tolerance/avoidance abilities and may provide a mechanism for acclimation and adaptation. Understanding the mechanisms that regulate plant stress memory is not only an intellectually challenging topic but has important implications for agricultural practices as well. Here, I focus exclusively on specific aspects of the transcription memory in response to recurring dehydration stresses and the memory-type responses to insect damage in a process known as "priming." The questions discussed are (a) whether/how the two memory phenomena are connected at the level of transcriptional regulation; (b) how differential transcription is achieved mechanistically under a repeated stress; and (c) whether similar molecular and/or epigenetic mechanisms are involved. Possible biological relevance of transcriptional stress memory and its preservation in plant evolution are also discussed.

Specificity of Herbivore Defense Responses in a Woody Plant, Black Poplar (Populus nigra)

The specificity of woody plant defense responses to different attacking herbivores is poorly known. We investigated the responses of black poplar (Populus nigra) to leaf feeding by three lepidopteran species (Lymantria dispar, Laothoe populi and Amata mogadorensis) and two leaf beetle species (Phratora vulgatissima and Chrysomela populi). Of the direct defenses monitored, increases in trypsin protease inhibitor activity and the salicinoid salicin were triggered by herbivore damage, but this was not herbivore-specific. Moreover, the majority of leaf salicinoid content was present constitutively and not induced by herbivory. On the other hand, volatile emission profiles did vary among herbivore species, especially between coleopterans and lepidopterans. Monoterpenes and sesquiterpenes were induced in damaged and adjacent undamaged leaves, while the emission of green leaf volatiles, aromatic and nitrogen-containing compounds (known to attract herbivore enemies) was restricted to damaged leaves. In conclusion, indirect defenses appear to show more specific responses to attacking herbivores than direct defenses in this woody plant.

Suppression of Plant Defenses by Herbivorous Mites Is Not Associated with Adaptation to Host Plants

Some herbivores suppress plant defenses, which may be viewed as a result of the coevolutionary arms race between plants and herbivores. However, this ability is usually studied in a one-herbivore-one-plant system, which hampers comparative studies that could corroborate this hypothesis. Here, we extend this paradigm and ask whether the herbivorous spider-mite Tetranychus evansi, which suppresses the jasmonic-acid pathway in tomato plants, is also able to suppress defenses in other host plants at different phylogenetic distances from tomatoes. We test this using different plants from the Solanales order, namely tomato, jimsonweed, tobacco, and morning glory (three Solanaceae and one Convolvulaceae), and bean plants (Fabales). First, we compare the performance of T. evansi to that of the other two most-commonly found species of the same genus, T. urticae and T. ludeni, on several plants. We found that the performance of T. evansi is higher than that of the other species only on tomato plants. We then showed, by measuring trypsin inhibitor activity and life history traits of conspecific mites on either clean or pre-infested plants, that T. evansi can suppress plant defenses on all plants except tobacco. This study suggests that the suppression of plant defenses may occur on host plants other than those to which herbivores are adapted.

The Mexican bean beetle (Epilachna varivestis) regurgitome and insights into beetle-borne virus specificity

For nearly 400 million years, insects and plants have been embattled in an evolutionary arms race. Insects have developed diverse feeding strategies and behaviors in an effort to circumvent and overcome an extensive collection of plant defense tactics. Sap-sucking insects often inject saliva into hosts plants, which contains a suite of effector proteins and even microbial communities that can alter the plant's defenses. Lacking salivary glands, leaf-feeding beetles represent an interesting group of phytophagous insects. Feeding beetles regurgitate onto leaf surfaces and it is thought that these oral secretions influence insect-plant interactions and even play a role in virus-vector specificity. Since the molecular and biological makeup of the regurgitant is virtually unknown, we carried out RNA sequencing and 16S rDNA analysis on a major soybean pest, Epilachna varivestis, to generate the first ever beetle "regurgitome" and characterize its microbiome. Interestingly, the regurgitant is comprised of a rich molecular assortment of genes encoding putative extracellular proteins involved in digestion, molting, immune defense, and detoxification. By carrying out plant inoculation assays, we reinforced the fundamental role of the regurgitant in beetle-borne virus specificity. Ultimately, these studies begin to characterize the importance of regurgitant in virus transmission and beetle-plant interactions.

Characterization of the Transcriptome and Gene Expression of Tetraploid Black Locust Cuttings in Response to Etiolation

Etiolation (a process of growing plants in partial or complete absence of light) promotes adventitious root formation in tetraploid black locust (Robinia pseudoacacia L.) cuttings. We investigated the mechanism underlying how etiolation treatment promotes adventitious root formation in tetraploid black locust and assessed global transcriptional changes after etiolation treatment. Solexa paired-end sequencing of complementary DNAs (cDNAs) from control (non-etiolated, NE) and etiolated (E) samples resulted in 107,564 unigenes. In total, 52,590 transcripts were annotated and 474 transcripts (211 upregulated and 263 downregulated) potentially involved in etiolation were differentially regulated. These genes were associated with hormone metabolism and response, photosynthesis, signaling pathways, and starch and sucrose metabolism. In addition, we also found significant differences of phytohormone contents, activity of following enzymes i.e., peroxidase, polyphenol oxidase and indole acetic acid oxidase between NE and E tissues during some cottage periods. The genes responsive to etiolation stimulus identified in this study will provide the base for further understanding how etiolation triggers adventitious roots formation in tetraploid black locus.

Acquiring nutrients from tree leaves: effects of leaf maturity and development type on a generalist caterpillar

The rapid growth and prolific reproduction of many insect herbivores depend on the efficiencies and rates with which they acquire nutrients from their host plants. However, little is known about how nutrient assimilation efficiencies are affected by leaf maturation or how they vary between plant species. Recent work showed that leaf maturation can greatly decrease the protein assimilation efficiency (PAE) of Lymantria dispar caterpillars on some tree species, but not on species in the willow family (Salicaceae). One trait of many species in the Salicaceae that potentially affects PAE is the continuous (or "indeterminate") development of leaves throughout the growing season. To improve our understanding of the temporal and developmental patterns of nutrient availability for tree-feeding insects, this study tested two hypotheses: nutrients (protein and carbohydrate) are more efficiently assimilated from immature than mature leaves, and, following leaf maturation, nutrients are more efficiently assimilated from indeterminate than determinate tree species. The nutritional physiology and growth of a generalist caterpillar (L. dispar) were measured on five determinate and five indeterminate tree species while their leaves were immature and again after they were mature. In support of the first hypothesis, caterpillars that fed on immature leaves had significantly higher PAE and carbohydrate assimilation efficiency (CAE), as well as higher protein assimilation rates and growth rates, than larvae that fed on mature leaves. Contrary to the second hypothesis, caterpillars that fed on mature indeterminate tree leaves did not have higher PAE than those that fed on mature determinate leaves, while CAE differed by only 3% between tree development types. Instead, "high-PAE" and "low-PAE" tree species were found across taxonomic and development categories. The results of this study emphasize the importance of physiological mechanisms, such as nutrient assimilation efficiency, to explain the large variation in host plant quality for insect herbivores.

Proteomic analysis reveals growth inhibition of soybean roots by manganese toxicity is associated with alteration of cell wall structure and lignification

Plant roots, the hidden half of plants, play a vital role in manganese (Mn) toxicity tolerance. However, molecular mechanisms underlying root adaptation to Mn toxicity remain largely unknown. In this study, soybean (Glycine max) was used to investigate alterations of root morphology and protein profiles in response to Mn toxicity. Results showed that soybean root growth was significantly inhibited by Mn toxicity. Subsequent proteomic analysis revealed that 31 proteins were successfully identified via MALDI TOF/TOF MS analysis including 21 unique up-regulated and 6 unique down-regulated proteins, which are mainly related to cell wall metabolism, protein metabolism and signal transduction. qRT-PCR analysis revealed that corresponding gene transcription patterns were correlated with accumulation of 14 of 21 up-regulated proteins, but only 1 of 6 down-regulated proteins, suggesting that most excess Mn up-regulated proteins are controlled at the transcriptional levels, while down-regulated proteins are controlled at the post-transcriptional levels. Furthermore, changes in abundances of GTP-binding nuclear protein Ran-3, expansin-like B1-like protein, dirigent protein and peroxidase 5-like protein strongly suggested that alteration of root cell wall structure and lignification might be associated with inhibited root growth. Taken together, this study was helpful to further understandings of adaptive strategies of legume roots to Mn toxicity.

SIGNIFICANCE

This study highlighted the effects of Mn toxicity on soybean root growth and its proteome profiles. Excess Mn treatments inhibited root growth. Comparative proteomic analysis was performed to analyze the changes in protein profiles of soybean roots in response to Mn toxicity. A total of 31 root proteins with differential abundances were identified and predominantly associated with signal transduction and cell wall metabolism. Among them, the abundances of the GTP-binding nuclear protein Ran-3 and Ran-binding protein 1 were significantly increased, suggesting that the proteins could be involved in the signaling network in soybean roots responsive to Mn toxicity. Interestingly, three 14-3-3 proteins were decreased by excess Mn at protein but not mRNA levels, suggesting that these proteins could be regulated at post-transcriptional modification under Mn excess conditions. Furthermore, changes in abundances of expansin-like B1-like protein, peroxidase 5-like protein, dirigent protein 2-like protein and dirigent protein strongly suggested that Mn toxicity could influence root cell wall modification, and thus inhibit root growth. This study provided significant insights into the potential molecular mechanisms underlying soybean root adaptation to Mn toxicity, which was mainly through alteration of root cell wall structure and lignification.

Pea weevil damage and chemical characteristics of pea cultivars determining their resistance to Bruchus pisorum L

Bruchus pisorum (L.) is one of the most intractable pest problems of cultivated pea in Europe. Development of resistant cultivars is very important to environmental protection and would solve this problem to a great extent. Therefore, the resistance of five spring pea cultivars was studied to B. pisorum: Glyans, Modus; Kamerton and Svit and Pleven 4 based on the weevil damage and chemical composition of seeds. The seeds were classified as three types: healthy seeds (type one), damaged seeds with parasitoid emergence holes (type two) and damaged seeds with bruchid emergence holes (type three). From visibly damaged pea seeds by pea weevil B. pisorum was isolated the parasitoid Triaspis thoracica Curtis (Hymenoptera, Braconidae). Modus, followed by Glyans was outlined as resistant cultivars against the pea weevil. They had the lowest total damaged seed degree, loss in weight of damaged seeds (type two and type three) and values of susceptibility coefficients. A strong negative relationship (r = -0.838) between the weight of type one seeds and the proportion of type three seeds was found. Cultivars with lower protein and phosphorus (P) content had a lower level of damage. The crude protein, crude fiber and P content in damaged seeds significantly or no significantly were increased as compared with the healthy seeds due to weevil damage. The P content had the highest significant influence on pea weevil infestation. Use of chemical markers for resistance to the creation of new pea cultivars can be effective method for defense and control against B. pisorum.

Influence of Genotype, Environment, and Gypsy Moth Herbivory on Local and Systemic Chemical Defenses in Trembling Aspen (Populus tremuloides)

Numerous studies have explored the impacts of intraspecific genetic variation and environment on the induction of plant chemical defenses by herbivory. Relatively few, however, have considered how those factors affect within-plant distribution of induced defenses. This work examined the impacts of plant genotype and soil nutrients on the local and systemic phytochemical responses of trembling aspen (Populus tremuloides) to defoliation by gypsy moth (Lymantria dispar). We deployed larvae onto foliage on individual tree branches for 15 days and then measured chemistry in leaves from: 1) branches receiving damage, 2) undamaged branches of insect-damaged trees, and 3) branches of undamaged control trees. The relationship between post-herbivory phytochemical variation and insect performance also was examined. Plant genotype, soil nutrients, and damage all influenced phytochemistry, with genotype and soil nutrients being stronger determinants than damage. Generally, insect damage decreased foliar nitrogen, increased levels of salicinoids and condensed tannins, but had little effect on levels of a Kunitz trypsin inhibitor, TI3. The largest damage-mediated tannin increases occurred in leaves on branches receiving damage, whereas the largest salicinoid increases occurred in leaves of adjacent, undamaged branches. Foliar nitrogen and the salicinoid tremulacin had the strongest positive and negative relationships, respectively, with insect growth. Overall, plant genetics and environment concomitantly influenced both local and systemic phytochemical responses to herbivory. These findings suggest that herbivory can contribute to phytochemical heterogeneity in aspen foliage, which may in turn influence future patterns of herbivory and nutrient cycling over larger spatial scales.

Characterization of an apple TT2-type R2R3 MYB transcription factor functionally similar to the poplar proanthocyanidin regulator PtMYB134

The apple MdMYB9 gene encodes a positive regulator of proanthocyanidin synthesis that activates anthocyanidin reductase promoters from apple and poplar via interaction with basic helix-loop-helix proteins. The regulation of proanthocyanidins (PAs, condensed tannins) is of great importance in food plants due to the many benefits of PAs in the human diet. Two candidate flavonoid MYB regulators, MdMYB9 and MdMYB11, were cloned from apple (Malus × domestica) based on their similarity to known MYB PA regulators. Transcript accumulation of both MdMYB9 and MdMYB11 was induced by high light and wounding, similar to the poplar (Populus spp) PA regulator PtMYB134. In transient activation assays with various basic helix-loop-helix (bHLH) co-regulators, MdMYB9 activated apple and poplar anthocyanidin reductase (ANR) promoters, while MdMYB11 showed no activity. Potential transcription factor binding elements were found within several ANR promoters, and the importance of the bHLH binding site (E-box) on ANR promoter activation was demonstrated via mutational analysis. The ability of MdMYB9 and PtMYB134 to reciprocally activate ANR promoters from both apple and poplar and to partner with heterologous bHLH co-factors from these plants confirms the high degree of conservation of PA regulatory complexes across species. The similarity in apple and poplar PA regulation suggests that regulatory genes from poplar could be effectively employed for metabolic engineering of the PA pathway in apple.

Molecular characterization of quinate and shikimate metabolism in Populus trichocarpa

The shikimate pathway leads to the biosynthesis of aromatic amino acids essential for protein biosynthesis and the production of a wide array of plant secondary metabolites. Among them, quinate is an astringent feeding deterrent that can be formed in a single step reaction from 3-dehydroquinate catalyzed by quinate dehydrogenase (QDH). 3-Dehydroquinate is also the substrate for shikimate biosynthesis through the sequential actions of dehydroquinate dehydratase (DQD) and shikimate dehydrogenase (SDH) contained in a single protein in plants. The reaction mechanism of QDH resembles that of SDH. The poplar genome encodes five DQD/SDH-like genes (Poptr1 to Poptr5), which have diverged into two distinct groups based on sequence analysis and protein structure prediction. In vitro biochemical assays proved that Poptr1 and -5 are true DQD/SDHs, whereas Poptr2 and -3 instead have QDH activity with only residual DQD/SDH activity. Poplar DQD/SDHs have distinct expression profiles suggesting separate roles in protein and lignin biosynthesis. Also, the QDH genes are differentially expressed. In summary, quinate (secondary metabolism) and shikimate (primary metabolism) metabolic activities are encoded by distinct members of the same gene family, each having different physiological functions.

A tandem Kunitz protease inhibitor (KPI106)-serine carboxypeptidase (SCP1) controls mycorrhiza establishment and arbuscule development in Medicago truncatula

Plant proteases and protease inhibitors are involved in plant developmental processes including those involving interactions with microbes. Here we show that a tandem between a Kunitz protease inhibitor (KPI106) and a serine carboxypeptidase (SCP1) controls arbuscular mycorrhiza development in the root cortex of Medicago truncatula. Both proteins are only induced during mycorrhiza formation and belong to large families whose members are also mycorrhiza-specific. Furthermore, the interaction between KPI106 and SCP1 analysed using the yeast two-hybrid system is specific, indicating that each family member might have a defined counterpart. In silico docking analysis predicted a putative P1 residue in KPI106 (Lys173) that fits into the catalytic pocket of SCP1, suggesting that KPI106 might inhibit the enzyme activity by mimicking the protease substrate. In vitro mutagenesis of the Lys173 showed that this residue is important in determining the strength and specificity of the interaction. The RNA interference (RNAi) inactivation of the serine carboxypeptidase SCP1 produces aberrant mycorrhizal development with an increased number of septated hyphae and degenerate arbuscules, a phenotype also observed when overexpressing KPI106. Protease and inhibitor are both secreted as observed when expressed in Nicotiana benthamiana epidermal cells. Taken together we envisage a model in which the protease SCP1 is secreted in the apoplast where it produces a peptide signal critical for proper fungal development within the root. KPI106 also at the apoplast would modulate the spatial and/or temporal activity of SCP1 by competing with the protease substrate.

Importance of protein quality versus quantity in alternative host plants for a leaf-feeding insect

The nutritional value of alternative host plants for leaf-feeding insects such as caterpillars is commonly measured in terms of protein quantity. However, nutritional value might also depend on the quality of the foliar protein [i.e., the composition of essential amino acids (EAAs)]. A lack of comparative work on the EAA compositions of herbivores and their host plants has hampered the testing of this hypothesis. We tested the "protein quality hypothesis" using the tree-feeding caterpillars of Lymantria dispar (gypsy moth) and two taxonomically unrelated host plants, red oak (Quercus rubra) and sugar maple (Acer saccharum). Because L. dispar has higher fitness on oak than on maple, support for the hypothesis would be found if protein were of higher quality from oak than from maple. The whole-body EAA composition of L. dispar larvae was measured to estimate its optimum dietary protein composition, which was compared with the EAA compositions of oak and maple leaves. Contrary to the protein quality hypothesis, the EAA compositions of oak and maple were not significantly different in the spring. The growth-limiting EAAs in both tree species were histidine and methionine. Similar results were observed in the summer, with the exception that the histidine composition of oak was between 10 and 15 % greater than in maple leaves. The two main factors that affected the nutritional value of protein from the tree species were the quantities of EAAs, which were consistently higher in oak, and the efficiency of EAA utilization, which decreased from 80 % in May to <50 % in August. We conclude that the relative nutritional value of red oak and sugar maple for L. dispar is more strongly affected by protein quantity than quality. Surveys of many wild herbaceous species also suggest that leaf-feeding insects would be unlikely to specialize on plants based on protein quality.

Stress inducible proteinase inhibitor diversity in Capsicum annuum

BACKGROUND

Wound-inducible Pin-II Proteinase inhibitors (PIs) are one of the important plant serine PIs which have been studied extensively for their structural and functional diversity and relevance in plant defense against insect pests. To explore the functional specialization of an array of Capsicum annuum (L.) proteinase inhibitor (CanPIs) genes, we studied their expression, processing and tissue-specific distribution under steady-state and induced conditions. Inductions were performed by subjecting C. annuum leaves to various treatments, namely aphid infestation or mechanical wounding followed by treatment with either oral secretion (OS) of Helicoverpa armigera or water.

RESULTS

The elicitation treatments regulated the accumulation of CanPIs corresponding to 4-, 3-, and 2-inhibitory repeat domains (IRDs). Fourty seven different CanPI genes composed of 28 unique IRDs were identified in total along with those reported earlier. The CanPI gene pool either from uninduced or induced leaves was dominated by 3-IRD PIs and trypsin inhibitory domains. Also a major contribution by 4-IRD CanPI genes possessing trypsin and chymotrypsin inhibitor domains was specifically revealed in wounded leaves treated with OS. Wounding displayed the highest number of unique CanPIs while wounding with OS treatment resulted in the high accumulation of specifically CanPI-4, -7 and -10. Characterization of the PI protein activity through two dimensional gel electrophoresis revealed tissue and induction specific patterns. Consistent with transcript abundance, wound plus OS or water treated C. annuum leaves exhibited significantly higher PI activity and isoform diversity contributed by 3- and 4-IRD CanPIs. CanPI accumulation and activity was weakly elicited by aphid infestation yet resulted in the higher expression of CanPI-26, -41 and -43.

CONCLUSIONS

Plants can differentially perceive various kinds of insect attacks and respond appropriately through activating plant defenses including regulation of PIs at transcriptional and post-translational levels. Based on the differentially elicited CanPI accumulation patterns, it is intriguing to speculate that generating sequence diversity in the form of multi-IRD PIs is a part of elaborative plant defense strategy to obtain a diverse pool of functional units to confine insect attack.

Herbivore-simulated induction of defenses in clonal networks of trembling aspen (Populus tremuloides)

Trembling aspen (Populus tremuloides Michx.) as a clonal tree species possesses a complex root system through which trees of the same or different clones are connected. Root connections have been studied with respect to resource sharing, but the nature, quantities or extent of what is shared between trees is relatively unknown. In this study, we posed the hypothesis that systemic defense induction signals could also spread through these root networks and trigger defenses in neighboring ramets before arrival of pests. Temporal expression pattern of Kunitz trypsin inhibitor (KTI) and dihydroflavonol reductase (DFR) genes, two markers of poplar defense, was followed by quantitative real-time polymerase chain reaction. The expression was quantified in systemic leaves of wounded and healthy plants that shared the same parental root and in untreated controls grown in separate pots. Untreated interconnected plants did not show induced resistance upon herbivore-simulated attack. Although wound-treated ramets induced defense genes, untreated interconnected plants produced an expression pattern similar to non-connected controls. Root connections do not automatically lead to induction of defensive traits that are expressed in plants directly under damage thought to simulate herbivory. Rather, it seems that other communication means such as airborne volatiles can serve as signal transmission pathways among neighboring plants.

The polyphenol oxidase gene family in poplar: phylogeny, differential expression and identification of a novel, vacuolar isoform

Polyphenol oxidases (PPOs) are oxidative enzymes that convert monophenols and o-diphenols to o-quinones using molecular oxygen. The quinone products are highly reactive following tissue damage and can interact with cellular constituents and cause oxidative browning and cross-linking. The induction of PPO in some plants as a result of wounding, herbivore attack, or pathogen infection has implicated them in defense. However, PPO-like enzymes that act as specific hydroxylases, for example in lignan and pigment biosynthesis, have also been discovered. Here, we present the first genome-enabled analysis of a PPO gene family. The Populus trichocarpa genome was found to contain a minimum of nine complete PPO genes, and seven of these were characterized further. The PPO gene family includes both recently duplicated and divergent sequences that are 36-98% identical at the amino acid level. Gene expression profiling in poplar tissues and organs revealed that the PPO genes are all differentially expressed during normal development, but that only a small subset of PPO genes are significantly upregulated by wounding, methyl jasmonate or pathogen infection. Our studies also identified PtrPPO13, a novel PPO gene that is predicted to encode an N-terminal signal peptide. Transient expression of green fluorescent protein fusions demonstrated its localization to the vacuolar lumen. Together, our findings show that the poplar PPO family is diverse and is likely linked to diverse physiological functions.

NtKTI1, a Kunitz trypsin inhibitor with antifungal activity from Nicotiana tabacum, plays an important role in tobacco's defense response

A cDNA library from tobacco inoculated with Rhizoctonia solani was constructed, and several cDNA fragments were identified by differential hybridization screening. One cDNA clone that was dramatically repressed, NtKTI1, was confirmed as a member of the Kunitz plant proteinase inhibitor family. RT-PCR analysis revealed that NtKTI1 was constitutively expressed throughout the whole plant and preferentially expressed in the roots and stems. Furthermore, RT-PCR analysis showed that NtKTI1 expression was repressed after R. solani inoculation, mechanical wounding and salicylic acid treatment, but was unaffected by methyl jasmonate, abscisic acid and NaCl treatment. In vitro assays showed that NtKTI1 exerted prominent antifungal activity towards R. solani and moderate antifungal activity against Rhizopus nigricans and Phytophthora parasitica var. nicotianae. Bioassays of transgenic tobacco demonstrated that overexpression of NtKTI1 enhanced significantly the resistance of tobacco against R. solani, and the antisense lines exhibited higher susceptibility than control lines towards the phytopathogen. Taken together, these studies suggest that NtKTI1 may be a functional Kunitz trypsin inhibitor with antifungal activity against several important phytopathogens in the tobacco defense response.

Thaumatin-like proteins are differentially expressed and localized in phloem tissues of hybrid poplar

BACKGROUND

Two thaumatin-like proteins (TLPs) were previously identified in phloem exudate of hybrid poplar (Populus trichocarpa x P. deltoides) using proteomics methods, and their sieve element localization confirmed by immunofluorescence. In the current study, we analyzed different tissues to further understand TLP expression and localization in poplar, and used immunogold labelling to determine intracellular localization.

RESULTS

Immunofluorescence using a TLP antiserum confirmed the presence of TLP in punctate, organelle-like structures within sieve elements. On western blots, the antiserum labeled two constitutively expressed proteins with distinct expression patterns. Immunogold labelling suggested that TLPs are associated with starch granules and starch-containing plastids in sieve elements and phloem parenchyma cells. In addition, the antiserum recognized TLPs in the inner cell wall and sieve plate region of sieve elements.

CONCLUSIONS

TLP localization in poplar cells and tissues is complex. TLP1 is expressed predominantly in tissues with a prominent vascular system such as midveins, petioles and stems, whereas the second TLP is primarily expressed in starch-storing plastids found in young leaves and the shoot apex.

Induction of acid phosphatase transcripts, protein and enzymatic activity by simulated herbivory of hybrid poplar

Herbivory and wounding upregulate a large suite of defense genes in hybrid poplar leaves. A strongly wound- and herbivore-induced gene with high similarity to Arabidopsis vegetative storage proteins (VSPs) and acid phosphatase (AP) was identified among genes strongly expressed during the poplar herbivore defense response. Phylogenetic analysis showed that the putative poplar acid phosphatase (PtdAP1) gene is part of an eight-member AP gene family in poplar, and is most closely related to a functionally characterized soybean nodule AP. Unlike the other poplar APs, PtdAP1 is expressed in variety of tissues, as observed in an analysis of EST data. Following wounding, the gene shows an expression profile similar to other known poplar defense genes such as protease inhibitors, chitinase, and polyphenol oxidase. Significantly, we show for the first time that subsequent to the wound-induction of PtdAP1 transcripts, AP protein and activity increase in extracts of leaves and other tissues. Although its mechanism of action is as yet unknown, these results suggest in hybrid poplar PtdAP1 is likely a component of the defense response against leaf-eating herbivores.

Poplar defense against insects: genome analysis, full-length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz-type protease inhibitor family

*Kunitz protease inhibitors (KPIs) feature prominently in poplar defense responses against insects. The increasing availability of genomics resources enabled a comprehensive analysis of the poplar (p)KPI family. *Using genome analysis, expressed sequence tag (EST) mining and full-length (FL)cDNA cloning we established an inventory and phylogeny of pKPIs. Microarray and real-time PCR analyses were used to profile pKPI gene expression following real or simulated insect attack. Proteomics of insect midgut content was used to monitor stability of pKPI protein. *We identified 31 pKPIs in the genome and validated gene models by EST mining and cloning of 41 unique FLcDNAs. Genome organization of the pKPI family, with six poplar-specific subfamilies, suggests that tandem duplications have played a major role in its expansion. pKPIs are expressed throughout the plant and many are strongly induced by insect attack, although insect-specific signals seem initially to suppress the tree pKPI response. We found substantial peptide coverage for a potentially intact pKPI protein in insect midgut after eating poplar leaves. *These results highlight the complexity of an important defense gene family in poplar with regard to gene family size, differential constitutive and insect-induced gene expression, and resilience of at least one pKPI protein to digestion by herbivores.

Regulation of isoprene emission from poplar leaves throughout a day

Isoprene is a biogenic hydrocarbon that significantly affects tropospheric chemistry. Numerous plant species, including many trees, emit isoprene. Isoprene is synthesized by isoprene synthase (IspS), from dimethylallyl diphosphate (DMADP) made by the methylerythritol 4-phosphate (MEP) pathway. It has been demonstrated that in developing leaves, isoprene emission is regulated by transcriptional control of IspS, while in mature leaves subjected to changing growth temperature, regulation of emission is shared between IspS and DMADP supply from the MEP pathway. Isoprene emission also varies throughout a day, with circadian regulation implicated. This study investigated changes in isoprene emission capacity, and expression of IspS and the enzymes of the MEP pathway throughout several days, with Populus trichocarpa grown at different temperatures to induce different levels of isoprene emission. Isoprene emission capacity exhibited ultradian regulation, with a period of about 12 h; peak capacity was observed at 0300 and 1500 h daily. Several of the enzymes of the MEP pathway had previously been suggested to have regulatory roles in the production of other plastidic terpenoids, and transcript accumulation for these enzymes, combined with in silico promoter analyses, supported a regulatory role for deoxyxylulose 5-phosphate synthase (DXS) in particular.

Analysis of the poplar phloem proteome and its response to leaf wounding

Phloem exudate collected from hybrid poplar (Populus trichocarpa x Populus deltoides) was estimated to have more than 100 proteins, of which 48 were identified using LC-MS/MS. Comparative two-dimensional gel electrophoresis demonstrated that two phloem exudate proteins were significantly (P<0.05) upregulated 24 h after leaf wounding. These were identified as pop3/SP1 and a thaumatin-like protein. This is the first characterization of a phloem proteome from a tree species.

The wound-, pathogen-, and ultraviolet B-responsive MYB134 gene encodes an R2R3 MYB transcription factor that regulates proanthocyanidin synthesis in poplar

In poplar (Populus spp.), the major defense phenolics produced in leaves are the flavonoid-derived proanthocyanidins (PAs) and the salicin-based phenolic glycosides. Transcriptional activation of PA biosynthetic genes leading to PA accumulation in leaves occurs following herbivore damage and mechanical wounding as well as infection by the fungal biotroph Melampsora medusae. In this study, we have identified a poplar R2R3 MYB transcription factor gene, MYB134, that exhibits close sequence similarity to the Arabidopsis (Arabidopsis thaliana) PA regulator TRANSPARENT TESTA2 and that is coinduced with PA biosynthetic genes following mechanical wounding, M. medusae infection, and exposure to elevated ultraviolet B light. Overexpression of MYB134 in poplar resulted in transcriptional activation of the full PA biosynthetic pathway and a significant plant-wide increase in PA levels, and electrophoretic mobility shift assays showed that recombinant MYB134 protein is able to bind to promoter regions of PA pathway genes. MYB134-overexpressing plants exhibited a concomitant reduction in phenolic glycoside concentrations and other minor alterations to levels of small phenylpropanoid metabolites. Our data provide insight into the regulatory mechanisms controlling stress-induced PA metabolism in poplar, and the identification of a regulator of stress-responsive PA biosynthesis constitutes a valuable tool for manipulating PA metabolism in poplar and investigating the biological functions of PAs in resistance to biotic and abiotic stresses.

Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi

In natural conditions, plants are subjected to a combination of biotic stresses and often have to cope with simultaneous pathogen infections. In this report, we aim to understand the global transcriptional response of hybrid poplar NM6 (Populus nigra x P. maximowiczii) to infection by two biotrophic Melampsora fungi, Melampsora larici-populina and M. medusae f. sp. deltoidae. These pathogens triggered different responses after inoculation of poplar leaves. Transcript profiling using the GeneChip Poplar Genome Array revealed a total of 416 differentially expressed transcripts whose expression level was > or = twofold relative to controls. Interestingly, approximately half of the differentially expressed genes in infected leaves showed altered expression following interaction with either of the Melampsora spp. We also infected poplar leaves simultaneously with both Melampsora spp. to investigate potential interaction between the responses to the individual pathogens during a mixed infection. For this mixed inoculation, the number of differentially expressed transcripts increased to 648 and our analysis showed that infection with both fungi also induced a common set of genes. The genes induced after Melampsora spp. infection were mainly related to primary and secondary metabolic processes, cell-wall reinforcement and lignification, defense and stress-related mechanisms, and signal perception and transduction.

Trypsin inhibitors in passion fruit (Passiflora f. edulis flavicarpa) leaves: accumulation in response to methyl jasmonate, mechanical wounding, and herbivory

This work investigates the effect of methyl jasmonte (MeJa), mechanical wounding, and herbivory caused by larval feeding of a specialist insect ( Agraulis vanillae vanillae) upon trypsin inhibitory activity in passion fruit leaves. Despite the fact that all treatments caused accumulation of trypsin inhibitors (TIs), higher levels were observed in MeJa treated leaves when plants were assayed 24 and 48 h after stimulus. Concerning both mechanically injured plants and attacked ones, a systemic induction was observed. Partially purified inhibitors from MeJa exposed plants were further characterized by X-ray film contact print technique and N-terminal sequence. Such analysis indicated that the TIs identified belong to the Kunitz family. Moreover, the partially purified inhibitors strongly inhibited trypsin-like digestive enzymes from sugar cane stalk borer ( Diatraea saccharalis) in vitro. Our results further support the protective function of wound-inducible trypsin inhibitors and their potential as tools to improve important crop species against insect predation through genetic engineering.

The accumulation of a Kunitz trypsin inhibitor from chickpea (TPI-2) located in cell walls is increased in wounded leaves and elongating epicotyls

Here, we report the identification and characterization of CaTPI-2, which is a member of a Cicer arietinum gene family encoding Kunitz-type proteinase inhibitors with at least two members -CaTPI-1 and CaTPI-2. The widespread mRNA accumulation of CaTPI-2 in all the different organs of 4-day-old etiolated seedlings and in stem internodes differs from the more specific Cicer arietinum Trypsin Proteinase Inhibitor-1 (CaTPI-1) transcription. After the generation of polyclonal antibodies against the recombinant Trypsin Proteinase Inhibitor-2 (TPI-2) protein, the protein was located in the cell walls of vegetative organs. The decrease found in both transcription and TPI-2 protein levels when the epicotyls aged, together with the wider and more intensive immunostaining of the protein in apical zones of epicotyls and radicles, in consonance with their higher elongation rate, indicated a relationship of the TPI-2 protein with the elongation process. CaTPI-2 mRNA levels were increased by wounding in both epicotyls and leaves. The accumulation of CaTPI-2 mRNA in seedlings, which was further amplified by mechanical wounding in epicotyls and leaves, suggests the involvement of TPI-2 in the response to wounds. Our results indicate that TPI-2 protein has features different from those of the former characterized Trypsin Proteinase Inhibitor-1 (TPI-1), such as its different gene regulation under light, a different cellular location and its upregulation by wounding, which implies a function different from that of TPI-1 in chickpea metabolism.

Functional analysis of the Kunitz trypsin inhibitor family in poplar reveals biochemical diversity and multiplicity in defense against herbivores

We investigated the functional and biochemical variability of Kunitz trypsin inhibitor (KTI) genes of Populus trichocarpa x Populus deltoides. Phylogenetic analysis, expressed sequence tag databases, and western-blot analysis confirmed that these genes belong to a large and diverse gene family with complex expression patterns. Five wound- and herbivore-induced genes representing the diversity of the KTI gene family were selected for functional analysis and shown to produce active KTI proteins in Escherichia coli. These recombinant KTI proteins were all biochemically distinct and showed clear differences in efficacy against trypsin-, chymotrypsin-, and elastase-type proteases, suggesting functional specialization of different members of this gene family. The in vitro stability of the KTIs in the presence of reducing agents and elevated temperature also varied widely, emphasizing the biochemical differences of these proteins. Significantly, the properties of the recombinant KTI proteins were not predictable from primary amino acid sequence data. Proteases in midgut extracts of Malacosoma disstria, a lepidopteran pest of Populus, were strongly inhibited by at least two of the KTI gene products. This study suggests that the large diversity in the poplar (Populus spp.) KTI family is important for biochemical and functional specialization, which may be important in the maintenance of pest resistance in long-lived plants such as poplar.

Regulation of isoprene emission in Populus trichocarpa leaves subjected to changing growth temperature

The hydrocarbon isoprene is emitted in large quantities from numerous plant species, and has a substantial impact on atmospheric chemistry. Temperature affects isoprene emission at several levels: the temperature at which emission is measured, the temperature at which leaves develop, and the temperatures to which a mature leaf is exposed in the days prior to emission measurement. The molecular regulation of the response to the last of these factors was investigated in this study. When plants were grown at 20 degrees C and moved from 20 to 30 degrees C and back, or grown at 30 degrees C and moved from 30 to 20 degrees C and back, their isoprene emission peaked within 3 h of the move and stabilized over the following 3 d. Trees that developed at 20 degrees C and experienced 30 degrees C episodes had higher isoprene emission capacities than did leaves grown exclusively at 20 degrees C, even 2 weeks after the last 30 degrees C episode. The levels and extractable activities of isoprene synthase protein, which catalyses the synthesis of isoprene, and those of dimethylallyl diphosphate (DMADP), its substrate, alone could not explain observed variations in isoprene emission. Therefore, we conclude that control of isoprene emission in mature leaves is shared between isoprene synthase protein and DMADP supply.

Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding

Background

The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions.

Results

As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa × P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in poplar leaves attacked by forest tent caterpillars.

Conclusion

This study has generated a high-quality FLcDNA resource for poplar and the third largest FLcDNA collection published to date for any plant species. We successfully used the FLcDNA sequences to reassess gene prediction in the poplar genome sequence, perform comparative sequence annotation, and identify differentially expressed transcripts associated with defense against insects. The FLcDNA sequences will be essential to the ongoing curation and annotation of the poplar genome, in particular for targeting gaps in the current genome assembly and further improvement of gene predictions. The physical FLcDNA clones will serve as useful reagents for functional genomics research in areas such as analysis of gene functions in defense against insects and perennial growth. Sequences from this study have been deposited in NCBI GenBank under the accession numbers EF144175 to EF148838.

Priming defense genes and metabolites in hybrid poplar by the green leaf volatile cis-3-hexenyl acetate

* Herbivore-induced plant volatiles (HIPVs), in addition to attracting natural enemies of herbivores, can serve a signaling function within plants to induce or prime defenses. However, it is largely unknown, particularly in woody plants, which volatile compounds within HIPV blends can act as signaling molecules. * Leaves of hybrid poplar saplings were exposed in vivo to naturally wound-emitted concentrations of the green leaf volatile (GLV) cis-3-hexenyl acetate (z3HAC) and then subsequently fed upon by gypsy moth larvae. Volatiles were collected throughout the experiments, and leaf tissue was collected to measure phytohormone concentrations and expression of defense-related genes. * Relative to controls, z3HAC-exposed leaves had higher concentrations of jasmonic acid and linolenic acid following gypsy moth feeding. Furthermore, z3HAC primed transcripts of genes that mediate oxylipin signaling and direct defenses, as determined by both qRT-PCR and microarray analysis using the AspenDB 7 K expressed sequence tags (EST) microarray containing c. 5400 unique gene models. Moreover, z3HAC primed the release of terpene volatiles. * The widespread priming response suggests an adaptive benefit to detecting z3HAC as a wound signal. Thus, woody plants can detect and use z3HAC as a signal to prime defenses before actually experiencing damage. GLVs may therefore have important ecological functions in arboreal ecosystems.

Poplar defense against insect herbivoresThis review is one of a selection of papers published in the Special Issue on Poplar Research in Canada

The availability of a poplar ( Populus trichocarpa Torr & A. Gray, black cottonwood) genome sequence is enabling new research approaches in angiosperm tree biology. Much of the recent genomics research in poplars has been on wood formation, growth and development, resistance to abiotic stress and pathogens, motivated, at least in part, by the fact that poplars provide an important system for large-scale, short-rotation plantation forestry in the Northern Hemisphere. To sustain productivity and ecosystem health of natural and planted poplar forests it is of critical importance to also develop a better understanding of the molecular mechanisms of defense and resistance of poplars against insect pests. Previous research has established a solid foundation of the chemical ecology of poplar defense against insects. This review summarizes some of the relevant literature on defense against insect herbivores in poplars with an emphasis on molecular, biochemical, and emerging genomic research in this important field within forest biotechnology and chemical ecology. Following a general introduction, we provide a brief overview of some of the most relevant insect pests of poplars; we then describe some of the general defense strategies of poplars along with selected examples of their activities. We conclude with a summary of emerging results and perspectives from recent advances in genomics research on poplar defense against insects.

Shoot–root defense signaling and activation of root defense by leaf damage in poplarThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada

Shoot–root systemic defense signaling of hybrid poplar (Populus trichocarpa Torr. & A. Gray × Populus deltoides Bartr. ex Marsh.) was investigated with molecular techniques to extend existing knowledge of poplar defense. Treatment of roots with methyl jasmonate demonstrated that transcripts of PtdTI3, a poplar trypsin inhibitor and marker of poplar defense responses, can be induced in poplar roots as well as leaves. Moreover, simulated herbivory of poplar leaves with methyl jasmonate treatment or wounding with pliers also induced PtdTI3 mRNA in roots, which implies downward, or basipetal, systemic signaling from shoots to roots. In addition, the inducible root-defense response comprised both increased PtdTI3 protein levels and trypsin-inhibitor activity. The inducible systemic response was further investigated with comparative macroarray analyses which indicated that in addition to PtdTI3, other genes respond in roots after wounding and methyl jasmonate treatment of leaves. The majority of the 17 genes encode previously identified leaf herbivory defense genes; however, some genes strongly up-regulated in leaves were not induced in roots. The identification of multiple defense genes that are inducible in roots following leaf damage is clear evidence of a systemic defense response in roots and the presence of basipetal shoot–root defense signaling.

The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins

The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to poplar leaf rust (Melampsora medusae) infection was studied using the Populus 15.5K cDNA microarray. Pronounced changes in the transcriptome were observed, with approximately 20% of genes on the array showing either induction or repression of transcription within the 9-day infection timecourse. A small number of pathogen-defense genes encoding PR-1, chitinases, and other pathogenesis-related proteins were consistently upregulated throughout the experimental period, but most genes were affected only at individual timepoints. The largest number of changes in gene expression was observed late in the infection at 6 to 9 days postinoculation (dpi). At these timepoints, genes encoding enzymes required for proanthocyanidin (condensed tannin) synthesis were upregulated dramatically. Phytochemical analysis confirmed that, late in the infection, proanthocyanidin levels increased in infected leaves. Strongly M. medusae-repressed genes at 9 dpi included previously characterized wound- and herbivore-induced defense genes, which suggests antagonism between the tree responses to insect feeding and M. medusae infection. In this highly compatible plant-pathogen interaction, we postulate that the biotrophic pathogen evades detection and suppresses early host responses.

A chickpea Kunitz trypsin inhibitor is located in cell wall of elongating seedling organs and vascular tissue

Kunitz proteinase inhibitors in legumes have mainly been described as defence and storage proteins. Here, we report a Kunitz trypsin inhibitor, encoded by the CaTPI-1 gene from Cicer arietinum. The transcription of this gene mainly occurs in seedling vegetative organs, and is affected by the light and growth stages. The recombinant TPI-1 protein expressed in E. coli was seen to be an efficient inhibitor of trypsin. After the generation of polyclonal antibodies against recombinant TPI-1 protein, the protein was located in the cell wall of elongating epicotyls and radicles by Western-blot experiments, in agreement with the transcription pattern. These results, together with the fact that both CaTPI-1 mRNA and protein levels decreased with epicotyl growth, suggest a possible role in the elongation of seedling epicotyls and radicles. Immunolocalization analyses of the TPI-1 protein indicated that it is abundant in the cell walls of both immature primary xylem cells and surrounding parenchyma cells. This location has led us to explore potential functions for TPI-1 protein in vascular tissue during seedling elongation.

Populus: a model system for plant biology

With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.

Molecular Evolution of a Small Gene Family of Wound Inducible Kunitz Trypsin Inhibitors in Populus

Maximum likelihood models of codon substitutions were used to analyze the molecular evolution of a Kunitz trypsin inhibitor (KTI) gene family in Populus and Salix. The methods support previous assertions that the KTI genes comprise a rapidly evolving gene family. Models that allow for codon specific estimates of the ratio of nonsynonymous to synonymous substitutions (omega) among sites detect positive Darwinian selection at several sites in the KTI protein. In addition, branch-specific maximum likelihood models show that there is significant heterogeneity in omega among branches of the KTI phylogeny. In particular, omega is substantially higher following duplication than speciation. There is also evidence for significant rate heterogeneity following gene duplication, suggesting different evolutionary rates in newly arisen gene duplicates. The results indicate uneven evolutionary rates both between sites in the KTI protein and among different lineages in the KTI phylogeny, which is incompatible with a neutral model of sequence evolution.

Genomics of hybrid poplar (Populus trichocarpa× deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences

As part of a genomics strategy to characterize inducible defences against insect herbivory in poplar, we developed a comprehensive suite of functional genomics resources including cDNA libraries, expressed sequence tags (ESTs) and a cDNA microarray platform. These resources are designed to complement the existing poplar genome sequence and poplar (Populus spp.) ESTs by focusing on herbivore- and elicitor-treated tissues and incorporating normalization methods to capture rare transcripts. From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139,007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385,000 publicly available Populus ESTs. Clustering and assembly of 107,519 3'-end ESTs resulted in 14,451 contigs and 20,560 singletons, altogether representing 35,011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45,000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15,496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (-)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant-insect interactions in poplar.

Expression of poplar chitinase in tomato leads to inhibition of development in colorado potato beetle

The previously described poplar chitinase, WIN6, is induced during infestation by gypsy moth (Lymantria dispar L.) larvae, thus suggesting a role in defense against insect pests. To test this hypothesis, we produced tomato seedlings infected with a recombinant potato virus X (PVX), which produces WIN6, and tested its insecticidal properties on Colorado potato beetle [CPB; Leptinotarsa decemlineata (Say)], which is a serious pest of tomatoes and other crops. The advantage of PVX is that plant material is ready for insect bioassay within 3-4 weeks of constructing the recombinant virus. Considering that production of transgenic tomato seedlings using Agrobacterium takes at least 6 months, this hastens the rate at which genes can be examined. Upon insect bioassay, only 47% CPB neonates feeding on leaves containing >0.3% w/w WIN6 developed to 2nd instar while 93% of controls reached 2nd instar. To our knowledge this is the first plant chitinase that retards development of an insect pest.