Jasmonate signaling: toward an integrated view

Ethylene response factor NtERF91 positively regulates alkaloid accumulations in tobacco (Nicotiana tabacum L.)

Tobacco alkaloid metabolism is regulated by various transcription factors (TFs). Here, we have characterized a non-NIC2 locus gene, Ethylene Response Factor 91 (ERF91), function in regulation of alkaloid accumulation in tobacco. NtERF91 was preferentially expressed in roots and induced by jasmonic acid. Additionally, NtERF91 was able to in vitro bind to the NtPMT2 and NtQPT2 promoters via directly targeting the GCC-box elements and transactivate NtQPT2 gene expression. Ectopic overexpression of NtERF91 not only increased the expression of most nicotine biosynthetic genes, but also altered alkaloid accumulation profile, resulting in dramatically anatabine accumulation. We conclude that NtERF91 plays an overlapped but distinct role in regulating tobacco alkaloid accumulations.

Multi-phased internalization of murine norovirus (MNV) in Arabidopsis seedlings and its potential correlation with plant defensive responses

Norovirus is a highly infectious human pathogen that causes acute foodborne diseases worldwide. As global diet patterns have begun to incorporate a higher consumption of fresh agricultural products, the internalization of norovirus into plants has emerged as a potential threat to human health. Here, we demonstrated that murine norovirus (MNV1) was internalized into Arabidopsis in multiple phases, and this internalization was correlated with Arabidopsis innate immunity responses. Under hydroponic conditions, continuous treatment of MNV1 retarded root growth and facilitated flower development of Arabidopsis without causing necrotic lesions. Examination of viral titers and RNA levels revealed that MNV1 was internalized into Arabidopsis in at least three different phases. In response to MNV1 treatment, the Arabidopsis defensive marker PR1 (a salicylic acid signaling marker) was transiently up-regulated at the early stage. PDF1.2, a jasmonic acid signaling marker, exhibited a gradual induction over time. Noticeably, Arabidopsis RNS1 (T2 ribonuclease) was rapidly induced by MNV1 and exhibited anti-correlation with the internalization of MNV1. Exposure to recombinant Arabidopsis RNS1 protein reduced the viral titers and degraded MNV1 RNA in vitro. In conclusion, the internalization of MNV1 into Arabidopsis was fluctuated by mutual interactions that were potentially regulated by Arabidopsis immune systems containing RNS1.

JAZ proteins modulate seed germination through interaction with ABI5 in bread wheat and Arabidopsis

Appropriate regulation of crop seed germination is of significance for agriculture production. In this study, we show that TaJAZ1, most closely related to Arabidopsis JAZ3, negatively modulates abscisic acid (ABA)-inhibited seed germination and ABA-responsive gene expression in bread wheat. Biochemical interaction assays demonstrate that the C-terminal part containing the Jas domain of TaJAZ1 physically interacts with TaABI5. Similarly, Arabidopsis jasmonate-ZIM domain (JAZ) proteins also negatively modulate ABA responses. Further we find that a subset of JAZ proteins could interact with ABI5 using the luciferase complementation imaging assays. Choosing JAZ3 as a representative, we demonstrate that JAZ3 interacts with ABI5 in vivo and represses the transcriptional activation activity of ABI5. ABA application could abolish the enrichment of JAZ proteins in the ABA-responsive gene promoter. Furthermore, we find that ABA application could induce the expression of jasmonate (JA) biosynthetic genes and then increase the JA concentrations partially dependent on the function of ABI5, consequently leading to the degradation of JAZ proteins. This study sheds new light on the crosstalk between JA and ABA in modulating seed germination in bread wheat and Arabidopsis.

Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the huanglongbing-associated fruit abscission

Citrus greening disease or huanglongbing (HLB) is associated with excessive pre-harvest fruit drop. To understand the mechanisms of the HLB-associated fruit abscission, transcriptomes were analyzed by RNA sequencing of calyx abscission zones (AZ-C) of dropped "Hamlin" oranges from HLB-diseased trees upon shaking the trees (Dd), retained oranges on diseased trees (Rd), dropped oranges from healthy shaken trees (Dh), and retained oranges on healthy trees (Rh). Cluster analysis of transcripts indicated that Dd had the largest distances from all other groups. Comparisons of transcriptomes revealed 1047, 1599, 813, and 764 differentially expressed genes (DEGs) between Dd/Rd, Dd/Dh, Dh/Rh, and Rd/Rh. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated hormone signaling, defense response, and secondary metabolism were involved in HLB-associated fruit abscission. Ethylene (ET) and jasmonic acid (JA) synthesis/signaling-related genes were upregulated in Dd, while other phytohormone-related genes were generally downregulated. In addition, genes related to JA/ET-activated defense response were upregulated in Dd as well. Consistent with the phytohormone gene expression data, increased levels (p < 0.05) of ET and JA, and a decreased level (p < 0.05) of abscisic acid were found in Dd compared with Rd, Dh or Rh. Lasiodiploidia theobromae level in Dd AZ-C was higher than the other fruit types, confirmed by qPCR, indicating AZ-C secondary fungal infection of HLB fruit may exacerbate their abscission. This information will help formulate effective strategies to control HLB-related abscission.

Targeted transcriptional and proteomic studies explicate specific roles of Bacillus subtilis iturin A, fengycin, and surfactin on elicitation of defensive systems in mandarin fruit during stress

Application of Bacillus cyclic lipopeptides (CLPs); fengycin, iturin A and surfactin has shown a great potential in controlling the spread of green mold pathogen invasion (Penicillium digitatum) in wounded mandarin fruit during postharvest period. The limited defensive protein profiles followed specific expression of pivotal genes relating to plant hormone mediating signaling pathways of the CLPs’ action on stimulating host plant resistance have been exhibited. The present study aimed to elucidate the specific effect of individual CLP obtained from Bacillus subtilis ABS-S14 as elicitor role on activation of plant defensive system at transcriptional and proteomic levels with and without P. digitatum co-application in mandarin fruit. Fengycin and iturin A elevated the gene expression of PAL, ACS1, ACO, CHI, and GLU while significantly stimulating plant POD transcription was only detected in the treatments of surfactin both with and without following P. digitatum. An increase of LOX and PR1 gene transcripts was determined in the treatments of individual CLP with fungal pathogen co-application. Fengycin activated production of unique defensive proteins such as protein involved in ubiquinone biosynthetic process in treated flavedo without P. digitatum infection. Proteins involved in the auxin modulating pathway were present in the iturin A and surfactin treatments. CLP-protein binding assay following proteome analysis reveals that iturin A attached to 12-oxophytodienoate reductase 2 involved in the oxylipin biosynthetic process required for jasmonic acid production which is implicated in induced systemic resistance (ISR). This study suggests specific elicitor action of individual CLP, particularly iturin A showed the most powerful in stimulating the ISR system in response to stresses in postharvest mandarins.

Insights into stress responses in mandarins triggered by Bacillus subtilis cyclic lipopeptides and exogenous plant hormones upon Penicillium digitatum infection

Bacillus subtilis CLP extract activates defense gene expression and increases the unique protein production involving in pathways of ISR, SAR, ubiquitin-proteasome system, and glycolysis for stress responses in flavedo tissues. Cyclic lipopeptides (CLPs) of Bacillus subtilis ABS-S14 had ability to activate plant defensive pathways, increase resistance and control green mold rot caused by Penicillium digitatum in mandarin fruit. The current study investigated transcriptional and proteomic data to highlight the unique induction effect of CLPs produced by B. subtilis ABS-S14 on the defense mechanism of mandarins in response to P. digitatum attack, and their differences from those following the exogenous plant hormone application. The proteomic patterns of the flavedo tissues as affected by Bacillus CLP extract, salicylic acid (SA), methyl jasmonate (MeJA), and ethephon (Et) were explored. qPCR analysis revealed the great effects of CLP extract in enhancing the transcription of PAL, ACS1, GLU, POD, and PR1. Tryptic peptides by LC-MS analysis between treatments with and without fungal infection were compared. B. subtilis CLP extract empowered the plant's immune response to wound stress by the significant production of calmodulin-binding receptor-like cytoplasmic kinase 2, molybdenum cofactor sulfurase, and NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase. Ubiquitin carrier protein abundance was developed only in the treated flavedo with CLP extract coupled with P. digitatum infection. The gene expression and overall proteome findings involving pathways of ubiquitin proteasome system, ISR, SAR, and energy production provide a new insight into the molecular mechanisms of the antagonist B. subtilis ABS-S14 inducing resistance against green mold in mandarins.

Proteomic Analysis and Functional Validation of a Brassica oleracea Endochitinase Involved in Resistance to Xanthomonas campestris

Black rot is a severe disease caused by the bacterium Xanthomonas campestris pv. campestris (Xcc), which can lead to substantial losses in cruciferous vegetable production worldwide. Although the use of resistant cultivars is the main strategy to control this disease, there are limited sources of resistance. In this study, we used the LC-MS/MS technique to analyze young cabbage leaves and chloroplast-enriched samples at 24 h after infection by Xcc, using both susceptible (Veloce) and resistant (Astrus) cultivars. A comparison between susceptible Xcc-inoculated plants and the control condition, as well as between resistant Xcc-inoculated plants with the control was performed and more than 300 differentially abundant proteins were identified in each comparison. The chloroplast enriched samples contributed with the identification of 600 additional protein species in the resistant interaction and 900 in the susceptible one, which were not detected in total leaf sample. We further determined the expression levels for 30 genes encoding the identified differential proteins by qRT-PCR. CHI-B4 like gene, encoding an endochitinase showing a high increased abundance in resistant Xcc-inoculated leaves, was selected for functional validation by overexpression in Arabidopsis thaliana. Compared to the wild type (Col-0), transgenic plants were highly resistant to Xcc indicating that CHI-B4 like gene could be an interesting candidate to be used in genetic breeding programs aiming at black rot resistance.

Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes

Mitochondria play crucial roles in regulating multiple biological processes particularly electron transfer and energy metabolism in eukaryotic cells. Exposure to water-deficit or dehydration may affect mitochondrial function, and dehydration response may dictate cell fate decisions. iTRAQ-based quantitative proteome of a winter legume, chickpea, demonstrated the central metabolic alterations in mitochondria, presumably involved in dehydration adaptation. Three-week-old chickpea seedlings were subjected to progressive dehydration and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical characteristics and mitochondrial architecture. The proteomics analysis led to the identification of 40 dehydration-responsive proteins whose expressions were significantly modulated by dehydration. The differentially expressed proteins were implicated in different metabolic processes, with obvious functional tendencies toward purine-thiamine metabolic network, pathways of carbon fixation and oxidative phosphorylation. The linearity of dehydration-induced proteome alteration was examined with transcript abundance of randomly selected candidates under multivariate stress conditions. The differentially regulated proteins were validated through sequence analysis. An extensive sequence based localization prediction revealed >62.5% proteins to be mitochondrial resident by, at least, one prediction algorithm. The results altogether provide intriguing insights into the dehydration-responsive metabolic pathways and useful clues to identify crucial proteins linked to stress tolerance. BIOLOGICAL SIGNIFICANCE: Investigation on plant mitochondrial proteome is of significance because it would allow a better understanding of mitochondrial function in plant adaptation to stress. Mitochondria are the unique organelles, which play a crucial role in energy metabolism and cellular homeostasis, particularly when exposed to stress conditions. Chickpea is one of the cultivated winter legumes, which enriches soil nitrogen and has very low water footprint and thus contributes to fortification of sustainable agriculture. We therefore examined the dehydration-responsive mitochondrial proteome landscape of chickpea and queried whether molecular interplay of mitochondrial proteins modulate dehydration tolerance. A total of 40 dehydration-induced mitochondrial proteins were identified, predicted to be involved in key metabolic processes. Our future efforts would focus on understanding both posttranslational modification and processing for comprehensive characterization of mitochondrial protein function. This approach will facilitate mining of more biomarkers linked to the tolerance trait and contribute to crop adaptation to climate change.

High temperatures change the perspective: Integrating hormonal responses in citrus plants under co-occurring abiotic stress conditions

Plants growing in the field are subjected to multiple stress factors acting simultaneously. Abnormally high temperatures are expected to affect wild plants and crops in the next years due to global warming. In this work, we have studied physiological, hormonal and molecular responses of the citrus rootstock, Carrizo citrange (Poncirus trifoliata L. Raf. × Citrus sinensis L. Osb.) subjected to wounding or high salinity occurring individually or in combination with heat stress. According to our results, combination of high salinity and heat stress aggravated the negative effects of salt intoxication in Carrizo. The high transpiration rate caused by high temperatures counteracted physiological responses of plants to salt stress and increased Cl^- intake in leaves. In addition, 12-oxo-phytodienoic acid accumulated specifically under combination of wounding and heat stress, whereas at low temperatures, wounded plants accumulated jasmonic acid (JA) and JA-isoleucine (JA-Ile). Moreover, an antagonism between salicylic acid (SA) and JA was observed, and wounded plants subjected to high temperatures did not accumulate JA nor JA-Ile whereas SA levels increased (via isochorismate synthase biosynthetic pathway). Wounded plants did not accumulate abscisic acid (ABA) but its catabolite phaseic acid. This could act as a signal for the upregulation of (ABA)-RESPONSIVE ELEMENT (ABRE)-BINDING TRANSCRIPTION FACTOR 2 (CsAREB2) and RESPONSIVE TO DISSECATION 22 (CsRD22) in an ABA-independent way. This work uncovers some mechanisms that explain Carrizo citrange tolerance to high temperatures together with different hormonal signals in response to specific stresses. It is suggested that co-occurring abiotic stress conditions can modify (either enhance or reduce) the hormonal response to modulate specific responses.

Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-resistant and susceptible sweetpotato cultivars

Transcriptome analysis was performed on the roots of susceptible and resistant sweetpotato cultivars infected with the major root-knot nematode species Meloidogyne incognita. In addition, we identified a transcription factor-mediated defense signaling pathway that might function in sweetpotato-nematode interactions. Root-knot nematodes (RKNs, Meloidogyne spp.) are important sedentary endoparasites of many agricultural crop plants that significantly reduce production in field-grown sweetpotato. To date, no studies involving gene expression profiling in sweetpotato during RKN infection have been reported. Therefore, in the present study, transcriptome analysis was performed on the roots of susceptible (cv. Yulmi) and resistant (cv. Juhwangmi) sweetpotato cultivars infected with the widespread, major RKN species Meloidogyne incognita. Using the Illumina HiSeq 2000 platform, we generated 455,295,628 pair-end reads from the fibrous roots of both cultivars, which were assembled into 74,733 transcripts. A number of common and unique genes were differentially expressed in susceptible vs. resistant cultivars as a result of RKN infection. We assigned the differentially expressed genes into gene ontology categories and used MapMan annotation to predict their functional roles and associated biological processes. The candidate genes including hormonal signaling-related transcription factors and pathogenesis-related genes that could contribute to protection against RKN infection in sweetpotato roots were identified and sweetpotato-nematode interactions involved in resistance are discussed.

The formation and accumulation of protein-networks by physical interactions in the rapid occlusion of laticifer cells in rubber tree undergoing successive mechanical wounding

BACKGROUND

Although the wound response of plants has been extensively studied, little is known of the rapid occlusion of wounded cell itself. The laticifer in rubber tree is a specific type of tissue for natural rubber biosynthesis and storage. In natural rubber production, tapping is used to harvest the latex which flows out from the severed laticifer in the bark. Therefore, study of the rapid wound-occlusion of severed laticifer cells is important for understanding the rubber tree being protected from the continuously mechanical wounding.

RESULTS

Using cytological and biochemical techniques, we revealed a biochemical mechanism for the rapid occlusion of severed laticifer cells. A protein-network appeared rapidly after tapping and accumulated gradually along with the latex loss at the severed site of laticifer cells. Triple immunofluorescence histochemical localization showed that the primary components of the protein-network were chitinase, β-1,3-glucanase and hevein together with pro-hevein (ProH) and its carboxyl-terminal part. Molecular sieve chromatography showed that the physical interactions among these proteins occurred under the condition of neutral pH. The interaction of β-1,3-glucanase respectively with hevein, chitinase and ProH was testified by surface plasmon resonance (SPR). The interaction between actin and β-1,3-glucanase out of the protein inclusions of lutoids was revealed by pull-down. This interaction was pharmacologically verified by cytochalasin B-caused significant prolongation of the duration of latex flow in the field.

CONCLUSIONS

The formation of protein-network by interactions of the proteins with anti-pathogen activity released from lutoids and accumulation of protein-network by binding to the cytoskeleton are crucial for the rapid occlusion of laticifer cells in rubber tree. The protein-network at the wounded site of laticifer cells provides not only a physical barrier but also a biochemical barrier to protect the wounded laticifer cells from pathogen invasion.

Genome-wide identification of tomato (Solanum lycopersicum L.) lipoxygenases coupled with expression profiles during plant development and in response to methyl-jasmonate and wounding

Lipoxygenases (LOXs) (EC 1.13.11.12) catalyze the oxygenation of fatty acids and produce oxylipins including the plant hormone jasmonate (jasmonic acid/methyl jasmonate; MeJA). Little is known about the tomato LOX gene family members that impact tomato growth and development, and less so about their feed-back regulation in response to MeJA. We present genome wide identification of 14 LOX gene family members in tomato which map unevenly on 12 chromosomes. The characteristic structural features of 9-LOX and 13-LOX tomato gene family, their protein domains/features, and divergence are presented. Quantification of the expression patterns of all the 14 SlLOX gene members segregated the members based on differential association with growth, development, or fruit ripening. We also identified those SlLOX genes whose transcription responds to exogenous MeJA and/or wounding stress. MeJA-based feedback regulation that involves activation of specific members of LOX genes is defined. Specific nature of SlLOX gene regulation in tomato is defined. The novel data on dynamics of SlLOX gene expression should help catalyze future strategies to elucidate role(s) of each gene member in planta and for crop biotechnological intervention.

Terpene Synthase Genes in Quercus robur - Gene Characterization, Expression and Resulting Terpenes Due to Cockchafer Feeding

Root herbivory caused by larvae of the forest cockchafer (Melolontha hippocastani) enhances the impact of drought on trees, particularly in oak forest rejuvenations. In Germany, geographically distant oak stands show differences in infestation strength by the forest cockchafer. While in Southwestern Germany this insect causes severe damage, oak forests in northern Germany are rarely infested. It is known that root-released volatile organic compounds (VOCs) are perceived by soil herbivores, thus guiding the larvae toward the host roots. In this work, we exposed seedlings of two distant oak provenances to forest cockchafer larvae and studied their population genetic properties, their root-based VOC chemotypes, their attraction for larvae and terpene synthase gene expression. Based on nuclear and chloroplast marker analysis, we found both oak populations to be genetically highly variable while showing typical patterns of migration from different refugial regions. However, no clear association between genetic constitution of the different provenances and the abundance of cockchafer populations on site was observed. In contrast to observations in the field, bioassays revealed a preference of the larvae for the northeastern oak provenance. The behavior of larvae was most likely related to root-released volatile terpenes and benzenoids since their composition and quantity differed between oak populations. We assume repellent effects of these compounds because the populations attractive to insects showed low abundance of these compounds. Five different oak terpene synthase (TPS) genes were identified at the genomic level which can be responsible for biosynthesis of the released terpenes. TPS gene expression patterns in response to larval feeding revealed geographic variation rather than genotypic variation. Our results support the assumption that root-released VOC are influencing the perception of roots by herbivores.

Genome-wide identification and analysis of the COI gene family in wheat (Triticum aestivum L.)

Background

COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCF^COI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown that COIs are involved in pollen fertility. In this study, we identified and characterized COI genes in the wheat genome and analyzed expression patterns under abiotic stress.

Results

A total of 18 COI candidate sequences for 8 members of COI gene family were isolated in wheat (Triticum aestivum L.). Phylogenetic and structural analyses showed that these COI genes could be divided into seven distinct subfamilies. The COI genes showed high expression in stamens and glumes. The qRT-PCR results revealed that wheat COIs were involved in several abiotic stress responses and anther/glume dehiscence in the photoperiod-temperature sensitive genic male sterile (PTGMS) wheat line BS366.

Conclusions

The structural characteristics and expression patterns of the COI gene family in wheat as well as the stress-responsive and differential tissue-specific expression profiles of each TaCOI gene were examined in PTGMS wheat line BS366. In addition, we examined SA- and MeJA-induced gene expression in the wheat anther and glume to investigate the role of COI in the JA signaling pathway, involved in the regulation of abnormal anther dehiscence in the PTGMS wheat line. The results of this study contribute novel and detailed information about the TaCOI gene family in wheat and could be used as a benchmark for future studies of the molecular mechanisms of PTGMS in other crops.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5116-9) contains supplementary material, which is available to authorized users.

Contrasting nutrient-disease relationships: Potassium gradients in barley leaves have opposite effects on two fungal pathogens with different sensitivities to jasmonic acid

Understanding the interactions between mineral nutrition and disease is essential for crop management. Our previous studies with Arabidopsis thaliana demonstrated that potassium (K) deprivation induced the biosynthesis of jasmonic acid (JA) and increased the plant's resistance to herbivorous insects. Here, we addressed the question of how tissue K affects the development of fungal pathogens and whether sensitivity of the pathogens to JA could play a role for the K-disease relationship in barley (Hordeum vulgare cv. Optic). We report that K-deprived barley plants showed increased leaf concentrations of JA and other oxylipins. Furthermore, a natural tip-to-base K-concentration gradient within leaves of K-sufficient plants was quantitatively mirrored by the transcript levels of JA-responsive genes. The local leaf tissue K concentrations affected the development of two economically important fungi in opposite ways, showing a positive correlation with powdery mildew (Blumeria graminis) and a negative correlation with leaf scald (Rhynchosporium commune) disease symptoms. B. graminis induced a JA response in the plant and was sensitive to methyl-JA treatment whereas R. commune initiated no JA response and was JA insensitive. Our study challenges the view that high K generally improves plant health and suggests that JA sensitivity of pathogens could be an important factor in determining the exact K-disease relationship.

Phytohormones as targets for improving plant productivity and stress tolerance

In this review, we summarize the results of experiments that lead to altered levels of phytohormones in transgenic plants to improve plant productivity. The available data indicate that manipulating the level of phytohormones might also be a promising way to enhance the environmental stress tolerance of crop plants. In the regulation of the level of phytohormones, both biosynthesis and their catabolism pathways can be targeted for engineering purposes. Moreover, the signaling pathways of phytohormones should explored in this respect. In genetic modifications, conditional promoters must be developed to avoid undesired effects on growth. In order to find a practical application, the effects of genetic modifications should be further verified under field conditions and over a longer time scale.

SUMO Suppresses the Activity of the Jasmonic Acid Receptor CORONATINE INSENSITIVE1

Plants respond rapidly to sudden environmental cues, often responding prior to changes in the hormone levels that coordinate these responses. How this is achieved is not fully understood. The integrative role of the phytohormone jasmonic acid (JA) relies upon the plant's ability to control the levels of JASMONATE ZIM (JAZ) domain-containing repressor proteins. Here, we demonstrate that regardless of intrinsic JA levels, Small Ubiquitin-like Modifier (SUMO)-conjugated JAZ proteins inhibit the JA receptor CORONATINE INSENSITIVE1 (COI1) from mediating non-SUMOylated JAZ degradation. The SUMO-deconjugating proteases OVERLY TOLERANT TO SALT1 (OTS1) and OTS2 regulate JAZ protein SUMOylation and stability. The ots1 ots2 double mutants accumulate SUMOylated and non-SUMOylated JAZ repressor proteins but show no change in endogenous JA levels compared with wild-type plants. SUMO1-conjugated JAZ proteins bind to COI1 independently of the JA mimic coronatine. SUMO inhibits JAZ binding to COI1. We identify the SUMO interacting motif in COI1 and demonstrate that this is vital to SUMO-dependent inhibition of COI1. Necrotroph infection of Arabidopsis thaliana promotes SUMO protease degradation, and this increases JAZ SUMOylation and abundance, which in turn inhibits JA signaling. This study reveals a mechanism for rapidly regulating JA responses, allowing plants to adapt to environmental changes.

Tricarboxylates Induce Defense Priming Against Bacteria in Arabidopsis thaliana

Exposure of plants to biotic stress results in an effective induction of numerous defense mechanisms that involve a vast redistribution within both primary and secondary metabolisms. For instance, an alteration of tricarboxylic acid (TCA) levels can accompany the increase of plant resistance stimulated by various synthetic and natural inducers. Moreover, components of the TCA flux may play a role during the set-up of plant defenses. In this study, we show that citrate and fumarate, two major components of the TCA cycle, are able to induce priming in Arabidopsis against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Both citrate and fumarate show no direct antimicrobial effect and therefore enhanced bacterial resistance found in planta is solely based on the induction of the plant defense system. During the priming phase, both TCA intermediates did not induce any changes in transcript abundances of a set of defense genes, and in phytohormones and camalexin levels. However, at early time points of bacterial challenge, citrate induced a stronger salicylic acid and camalexin accumulation followed later by a boost of the jasmonic acid pathway. On the other hand, adaptations of hormonal pathways in fumarate-treated plants were more complex. While jasmonic acid was not induced, mutants impaired in jasmonic acid perception failed to mount a proper priming response induced by fumarate. Our results suggest that changes in carboxylic acid abundances can enhance Arabidopsis defense through complex signaling pathways. This highlights a promising feature of TCAs as novel defense priming agents and calls for further exploration in other pathosystems and stress situations.

Impact of drought and salt stress on the biosynthesis of alkaloids in Chelidonium majus L

When plants are exposed to various stress situations, their alkaloid concentration frequently is enhanced. This well-known phenomenon is presumably due to a passively enhanced rate of biosynthesis, caused by greatly elevated concentrations of NADPH in stressed plants. Here, we used Chelidonium majus L. plants, which accumulate high concentrations of dihydrocoptisine in their leaves, to study the impact of drought and salt stress on the biosynthesis and accumulation of alkaloids. In comparison to well-watered controls, in the transcriptome of the gene encoding the key enzyme in alkaloid biosynthesis, stylopine synthase, is enhanced in stressed C. majus plants. If we presuppose that increased transcript levels correlate with increased enzymatic activity of the gene products, these data indicate, for the first time, that stress-related increases in alkaloid concentration might not only be caused by the well-known stress-related passive shift, but may also be due to an enhancement of enzymatic capacity.

Mechanisms of resistance in the rice cultivar Manikpukha to the rice stem nematode Ditylenchus angustus

The incompatible interaction between the rice cultivar Manikpukha and the rice stem nematode Ditylenchus angustus has been reported recently. This research focuses on the underlying mechanisms of resistance in Manikpukha. Invasion, post-infection development and reproduction of D. angustus were compared in compatible and incompatible interactions to identify the stage in which resistance occurs. The results indicate that resistance in Manikpukha is associated with reduced development and reproduction, implying that resistance acts post-invasion. We studied the possible involvement of three classical defence hormones, salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), in response to infection in a compatible interaction using biosynthesis/signalling-deficient transgenic rice lines. All three hormones appear to have an influence on the basal defence of Nipponbare against the stem nematode. Although hormone application increases basal defences, expression studies and hormone analyses after nematode infection in Manikpukha did not show a clear involvement of the hormone defense pathways for SA, ET and JA. However, it seems that OsPAL1 plays a pivotal role in resistance, indicating that the phenylpropanoid pathway and its products might be key players in the incompatible interaction. Lignin measurement showed that, although basal levels are similar, Manikpukha had a significantly higher lignin content on nematode infection, whereas it was decreased in the susceptible cultivar. The results presented here show that SA, ET and JA are involved in basal defences, but the resistance of Manikpukha against D. angustus probably relies on products of the phenylpropanoid pathway.

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

In plants, there can be a trade-off between resource allocations to growth vs defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction. We studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny. We used partial correlations of individual transcripts (expressed sequence tags, ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, for example, those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs. A terpenoid ABC transporter gene showed strongest correlations (P = 0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P = 0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P = 0.004) represented the uncovered positive correlations. Our study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.

Spatio-temporal profiling of abscisic acid, indoleacetic acid and jasmonic acid in single rice seed during seed germination

Abscisic acid (ABA), indoleacetic acid (IAA) and jasmonic acid (JA) are plant hormones that were reported to play indispensable roles during seed germination. However, the interactions between these plant hormones during rice seed germination have still not been explored clearly. A sensitive method for determination of these plant hormones would be beneficial for the exploration of such interactions. Herein, we present a liquid chromatography coupled with mass spectrometry (LC-MS) method for the quantification of ABA, IAA and JA in a single tissue of rice seed to investigate the spatio-temporal distribution of these plant hormones during rice seed germination. To this end, an in silico strategy was developed in order to select a derivatization reagent with an ideal sensitivity of MS detection. This strategy was confirmed with experimental studies on three reagents N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide (EDC), N,N-dimethylethylenediamine (DMED), and N-(acridin-9-yl)-2-bromoacetamide (AYBA) and their formic acid derivatives. Our results from the in silico and LC-MS experiments show that AYBA is a good derivatization reagent for ABA, IAA and JA due to its reasonable ionization efficiency in electrospray ionization mass spectrometry (ESI-MS) and excellent hydrophobicity. Finally, a sensitive LC-MS method upon AYBA was established for the determination of ABA, IAA and JA in germinated seeds. Good linearities for ABA, IAA, and JA were obtained with correlation coefficients greater than 0.99. The limits of detection (LODs) were in the range of 0.14-0.16 pg mL^-1. The method exhibits good precisions with RSD 1.5%-13.8% (intra-day) and 1.2%-7.3% (inter-day) and acceptable recoveries (88.6%-102.9%, n = 6). Finally, the method was successfully employed in the spatio-temporal profiling of ABA, IAA and JA in a single tissue of rice seed during rice seed germination.

Attenuated accumulation of jasmonates modifies stomatal responses to water deficit

To determine whether drought-induced root jasmonate [jasmonic acid (JA) and jasmonic acid-isoleucine (JA-Ile)] accumulation affected shoot responses to drying soil, near-isogenic wild-type (WT) tomato (Solanum lycopersicum cv. Castlemart) and the def-1 mutant (which fails to accumulate jasmonates during water deficit) were self- and reciprocally grafted. Rootstock hydraulic conductance was entirely rootstock dependent and significantly lower in def-1, yet def-1 scions maintained a higher leaf water potential as the soil dried due to their lower stomatal conductance (gs). Stomatal sensitivity to drying soil (the slope of gsversus soil water content) was low in def-1 self-grafts but was normalized by grafting onto WT rootstocks. Although soil drying increased 12-oxo-phytodienoic acid (OPDA; a JA precursor and putative antitranspirant) concentrations in def-1 scions, foliar JA accumulation was negligible and foliar ABA accumulation reduced compared with WT scions. A WT rootstock increased drought-induced ABA and JA accumulation in def-1 scions, but decreased OPDA accumulation. Xylem-borne jasmonates were biologically active, since supplying exogenous JA via the transpiration stream to detached leaves decreased transpiration of WT seedlings but had the opposite effect in def-1. Thus foliar accumulation of both ABA and JA at WT levels is required for both maximum (well-watered) gs and stomatal sensitivity to drying soil.

GhJAZ2 attenuates cotton resistance to biotic stresses via the inhibition of the transcriptional activity of GhbHLH171

Plants have evolved effective mechanisms to protect themselves against multiple stresses, and employ jasmonates (JAs) as vital defence signals to defend against pathogen infection. The accumulation of JA, induced by signals from biotic and abiotic stresses, results in the degradation of Jasmonate-ZIM-domain (JAZ) proteins, followed by the de-repression of JAZ-repressed transcription factors (such as MYC2) to activate defence responses and developmental processes. Here, we characterized a JAZ family protein, GhJAZ2, from cotton (Gossypium hirsutum) which was induced by methyl jasmonate (MeJA) and inoculation of Verticillium dahliae. The overexpression of GhJAZ2 in cotton impairs the sensitivity to JA, decreases the expression level of JA-response genes (GhPDF1.2 and GhVSP) and enhances the susceptibility to V. dahliae and insect herbivory. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that GhJAZ2 may be involved in the regulation of cotton disease resistance by interaction with further disease-response proteins, such as pathogenesis-related protein GhPR10, dirigent-like protein GhD2, nucleotide-binding site leucine-rich repeat (NBS-LRR) disease-resistant protein GhR1 and a basic helix-loop-helix transcription factor GhbHLH171. Unlike MYC2, overexpression of GhbHLH171 in cotton activates the JA synthesis and signalling pathway, and improves plant tolerance to the fungus V. dahliae. Molecular and genetic evidence shows that GhJAZ2 can interact with GhbHLH171 and inhibit its transcriptional activity and, as a result, can restrain the JA-mediated defence response. This study provides new insights into the molecular mechanisms of GhJAZ2 in the regulation of the cotton defence response.

Bacillus cereus AR156 Activates Defense Responses to Pseudomonas syringae pv. tomato in Arabidopsis thaliana Similarly to flg22

Bacillus cereus AR156 (AR156) is a plant growth-promoting rhizobacterium capable of inducing systemic resistance to Pseudomonas syringae pv. tomato in Arabidopsis thaliana. Here, we show that, when applied to Arabidopsis leaves, AR156 acted similarly to flg22, a typical pathogen-associated molecular pattern (PAMP), in initiating PAMP-triggered immunity (PTI). AR156-elicited PTI responses included phosphorylation of MPK3 and MPK6, induction of the expression of defense-related genes PR1, FRK1, WRKY22, and WRKY29, production of reactive oxygen species, and callose deposition. Pretreatment with AR156 still significantly reduced P. syringae pv. tomato multiplication and disease severity in NahG transgenic plants and mutants sid2-2, jar1, etr1, ein2, npr1, and fls2. This suggests that AR156-induced PTI responses require neither salicylic acid, jasmonic acid, and ethylene signaling nor flagella receptor kinase FLS2, the receptor of flg22. On the other hand, AR156 and flg22 acted in concert to differentially regulate a number of AGO1-bound microRNAs that function to mediate PTI. A full-genome transcriptional profiling analysis indicated that AR156 and flg22 activated similar transcriptional programs, coregulating the expression of 117 genes; their concerted regulation of 16 genes was confirmed by real-time quantitative polymerase chain reaction analysis. These results suggest that AR156 activates basal defense responses to P. syringae pv. tomato in Arabidopsis, similarly to flg22.

The Elongator complex-associated protein DRL1 plays a positive role in immune responses against necrotrophic fungal pathogens in Arabidopsis

DEFORMED ROOT AND LEAVES1 (DRL1) is an Arabidopsis homologue of the yeast TOXIN TARGET4 (TOT4)/KILLER TOXIN-INSENSITIVE12 (KTI12) protein that is physically associated with the RNA polymerase II-interacting protein complex named Elongator. Mutations in DRL1 and Elongator lead to similar morphological and molecular phenotypes, suggesting that DRL1 and Elongator may functionally overlap in Arabidopsis. We have shown previously that Elongator plays an important role in both salicylic acid (SA)- and jasmonic acid (JA)/ethylene (ET)-mediated defence responses. Here, we tested whether DRL1 also plays a similar role as Elongator in plant immune responses. Our results show that, although DRL1 partially contributes to SA-induced cytotoxicity, it does not play a significant role in SA-mediated expression of PATHOGENESIS-RELATED genes and resistance to the virulent bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. In contrast, DRL1 is required for JA/ET- and necrotrophic fungal pathogen Botrytis cinerea-induced defence gene expression and for resistance to B. cinerea and Alternaria brassicicola. Furthermore, unlike the TOT4/KTI12 gene which, when overexpressed in yeast, confers zymocin resistance, a phenotype of the tot4/kti12 mutant, overexpression of DRL1 does not change B. cinerea-induced defence gene expression and resistance to this pathogen. Finally, DRL1 contains an N-terminal P-loop and a C-terminal calmodulin (CaM)-binding domain and is a CaM-binding protein. We demonstrate that both the P-loop and the CaM-binding domain are essential for the function of DRL1 in B. cinerea-induced expression of PDF1.2 and ORA59, and in resistance to B. cinerea, suggesting that the function of DRL1 in plant immunity may be regulated by ATP/GTP and CaM binding.

New ionic liquids based on systemic acquired resistance inducers combined with the phytotoxicity reducing cholinium cation

Systemic acquired resistance (SAR) is one of the most promising ways to support plants in the fight against viruses.

Proteomic Analysis Reveals Coordinated Regulation of Anthocyanin Biosynthesis through Signal Transduction and Sugar Metabolism in Black Rice Leaf

Black rice (Oryza sativa L.) is considered to be a healthy food due to its high content of anthocyanins in the pericarp. The synthetic pathway of anthocyanins in black rice grains has been identified, however, the proteomic profile of leaves during grain development is still unclear. Here, isobaric Tags Relative and Absolute Quantification (iTRAQ) MS/MS was carried out to identify statistically significant changes of leaf proteome in the black rice during grain development. Throughout three sequential developmental stages, a total of 3562 proteins were detected and 24 functional proteins were differentially expressed 3–10 days after flowering (DAF). The detected proteins are known to be involved in various biological processes and most of these proteins were related to gene expression regulatory (33.3%), signal transduction (16.7%) and developmental regulation and hormone-like proteins (12.5%). The coordinated changes were consistent with changes in regulatory proteins playing a leading role in leaves during black rice grain development. This indicated that signal transduction between leaves and grains may have an important role in anthocyanin biosynthesis and accumulation during grain development of black rice. In addition, four identified up-regulated proteins associated with starch metabolism suggested that the remobilization of nutrients for starch synthesis plays a potential role in anthocyanin biosynthesis of grain. The mRNA transcription for eight selected proteins was validated with quantitative real-time PCR. Our results explored the proteomics of the coordination between leaf and grain in anthocyanins biosynthesis of grain, which might be regulated by signal transduction and sugar metabolism in black rice leaf.

Transcription Factor AsMYC2 Controls the Jasmonate-Responsive Expression of ASS1 Regulating Sesquiterpene Biosynthesis in Aquilaria sinensis (Lour.) Gilg

Sesquiterpenes are one of the most important defensive secondary metabolite components of agarwood. Agarwood, which is a product of the Aquilaria sinensis response to external damage, is a fragrant and resinous wood that is widely used in traditional medicines, incense and perfume. We previously reported that jasmonic acid (JA) plays an important role in promoting agarwood sesquiterpene biosynthesis and induces expression of the sesquiterpene synthase ASS1, which is a key enzyme that is responsible for the biosynthesis of agarwood sesquiterpenes in A. sinensis. However, little is known about this molecular regulation mechanism. Here, we characterized a basic helix-loop-helix transcription factor, AsMYC2, from A. sinensis as an activator of ASS1 expression. AsMYC2 is an immediate-early jasmonate-responsive gene and is co-induced with ASS1. Using a combination of yeast one-hybrid assays and chromatin immunoprecipitation analyses, we showed that AsMYC2 bound the promoter of ASS1 containing a G-box motif. AsMYC2 activated expression of ASS1 in tobacco epidermis cells and up-regulated expression of sesquiterpene synthase genes (TPS21 and TPS11) in Arabidopsis, which was also promoted by methyl jasmonate. Our results suggest that AsMYC2 participates in the regulation of agarwood sesquiterpene biosynthesis in A. sinensis by controlling the expression of ASS1 through the JA signaling pathway.

Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. To advance our understanding of the architecture and dynamic regulation of the JA gene regulatory network, we performed a high-resolution RNA-seq time series of methyl JA-treated Arabidopsis thaliana at 15 time points over a 16-h period. Computational analysis showed that methyl JA (MeJA) induces a burst of transcriptional activity, generating diverse expression patterns over time that partition into distinct sectors of the JA response targeting specific biological processes. The presence of transcription factor (TF) DNA binding motifs correlated with specific TF activity during temporal MeJA-induced transcriptional reprogramming. Insight into the underlying dynamic transcriptional regulation mechanisms was captured in a chronological model of the JA gene regulatory network. Several TFs, including MYB59 and bHLH27, were uncovered as early network components with a role in pathogen and insect resistance. Analysis of subnetworks surrounding the TFs ORA47, RAP2.6L, MYB59, and ANAC055, using transcriptome profiling of overexpressors and mutants, provided insights into their regulatory role in defined modules of the JA network. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints and validates previously unknown regulators, and provides a valuable resource for functional studies on JA signaling components in plant defense and development.

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

Soybean cyst nematode (SCN) is the most damaging pest of soybean worldwide. The molecular mechanism of SCN resistance remains largely unknown. We conducted a global RNA-seq comparison between a resistant genotype (S54) and a susceptible genotype (S67) of Glycine soja, the wild progenitor of soybean, to understand its regulatory network in SCN defense. The number of differentially expressed genes (DEGs) in S54 (2,290) was much larger than that in S67 (555). A number of defense-related genes/pathways were significantly induced only in S54, while photosynthesis and several metabolic pathways were affected in both genotypes with SCN infection. These defense-associated DEGs were involved in pathogen recognition, calcium/calmodulin-mediated defense signaling, jasmonic acid (JA)/ethylene (ET) and sialic acid (SA)-involved signaling, the MAPK signaling cascade, and WRKY-involved transcriptional regulation. Our results revealed a comprehensive regulatory network involved in SCN resistance and provided insights into the complex molecular mechanisms of SCN resistance in wild soybean.

Transcriptome Analysis of the Effects of Shell Removal and Exogenous Gibberellin on Germination of Zanthoxylum Seeds

The zanthoxylum seeds are oil-rich and have a very thick, dense and oily shell. In the natural conditions the seeds have a very low germination rate. Prior to treatment with GAs to promote germination, the seeds were usually soaked in sulfuric acid to remove shells easily. A high-throughput sequencing of mRNAs was performed to investigate the effects of the above treatments on the germination of zanthoxylum seeds. Seven libraries were assembled into 100,982 unigenes and 59,509 unigenes were annotated. We focused on the expression profiles of the key genes related to the oil metabolisms and hormone regulations during seed germination. Our data indicated the endogenous ABA of seeds was rich. The effects that the exogenous GAs promoted germination were apparent in the secong day of germination. Especially, for the first time our results indicated the exogenous GAs lowered the aerobic metabolism including the oil metabolisms during imbibition. We inferred that the exogenous GAs had inhibitory effects on the oil metabolisms to avoide oxidative damages to the imbibed seeds, and the seed shell played the role similiar to the exogenous GAs in the initial stage of germination in the natural conditions.

High temperature effects on Pi54 conferred resistance to Magnaporthe oryzae in two genetic backgrounds of Oryza sativa

The global temperatures are predicted to rise due to climate change. However, knowledge on the mechanisms underlying the effect of high temperature (HT) on plant pathogen interaction is limited. We investigated the effect of elevated temperature on host phenotypic, biochemical and gene expression patterns in the rice-Magnaporthe oryzae (Mo) pathosystem using two genetic backgrounds, Co39 (Oryzae sativa-indica) and LTH (O. sativa-japonica) with (CO and LT) and without (Co39 and LTH) R gene (Pi54). After exposure to 28°C and 35°C the two genetic backgrounds showed contrasting responses to Mo. At 28°C, CO, Co39 and LTH displayed a more severe disease phenotype than LT. Surprisingly, CO became resistant to Mo after exposure to 35°C. CO and LT were used for further analysis to determine the defence related biochemical and transcriptome changes associated with HT induced resistance. Pre-exposure to 35°C triggered intense callose deposits and cell wall fluorescence of the attacked epidermal cells, as well as, increased hydrogen peroxide (H₂O₂) and salicylic acid (SA) levels. Transcriptional changes due to combined stress (35°C+Mo) were largely overridden by pathogen infection in both backgrounds, suggesting that the plants tended to shift their response to the pathogen. However, significant differences in global gene expression patterns occurred between CO and LT in response to both single (35°C and Mo) and double stress (35°C+Mo). Collectively, our results suggest that rice lines carrying Pi54 respond to Mo by rapid induction of callose and H₂O₂, and that these resistance mechanisms are amplified at HT. The relative difference in disease severity between CO and LT at 28°C suggests that the genetic background of japonica rice facilitates the function of Pi54 more than the background of indica rice. The phenotypic plasticity and gene expression differences between CO and LT reveal the presence of intricate background specific molecular signatures that may potentially influence adaptation to plant stresses.

NO dioxygenase- and peroxidase-like activity of Arabidopsis phytoglobin 3 and its role in Sclerotinia sclerotiorum defense

Phytoglobin 3 appears to be ubiquitous in plants, yet there has been dearth of evidence for their potent physiological functions. Previous crystallographic studies suggest a potential NO dioxygenase like activity of Arabidopsis phytoglobin 3 (AHb3). The present work examined the in vivo function of AHb3 in plant physiology and its role in biotic stress using Arabidopsis- Sclerotinia sclerotorium pathosystem. The gene was found to be ubiquitously expressed in all plant tissues, with moderately increased expression in roots. Its expression was induced upon NO, H₂O₂ and biotic stress. A C-terminal tagged GFP version of the wild type protein revealed its enhanced accumulation in the guard cells. AHb3-GFP was found to be partitioned majorly into the nucleus while residual amounts were present in the cytoplasm. The loss of function AHb3 mutant exhibited reduced root length and fresh weight. AHb3 knockout lines also displayed enhanced susceptibility towards the S. sclerotiorum. Interestingly, these lines displayed enhanced ROS accumulation upon pathogen challenge as suggested by DAB staining. Furthermore, enhanced/decreased NO accumulation in AHb3 knockout/overexpression lines upon treatment with multiple NO donors suggests a potent NO dioxygenase like activity for the protein. Taken together, our data indicate that AHb3 play a crucial role in regulating root length as well as in mediating defense response against S. sclerotiorum, possibly by modulating NO and ROS levels.

Functional characterization of a novel jasmonate ZIM-domain interactor (NINJA) from upland cotton (Gossypium hirsutum)

The jasmonic acid (JA) signalling pathway plays roles in plant development and defence against biotic and abiotic stresses. We isolated a cotton NINJA (novel interactor of JA ZIM-domain) gene, designated GhNINJA, which contains a 1305 bp open read frame. The GhNINJA gene encodes a 434 amino acid peptide. According to quantitative real-time PCR analysis, GhNINJA is preferentially expressed in roots, and its expression level is greatly induced by Verticillium dahliae infection. Through a virus-induced gene silencing technique, we developed GhNINJA-silenced cotton plants, which had significantly decreased expression of the target gene with an average expression of 6% of the control. The regenerating lateral root growth of silenced plants was largely inhibited compared to the control. Analysis by microscopy demonstrated that the cell length of the root differentiation zone in GhNINJA-silenced plants is significantly shorter than those of the control. Moreover, the silenced plants exhibited higher tolerance to V. dahliae infection compared to the control, which was linked to the increased expression of the defence marker genes PDF1.2 and PR4. Together, these data indicated that knockdown of GhNINJA represses the root growth and enhances the tolerance to V. dahliae. Therefore, GhNINJA gene can be used as a candidate gene to breed the new cultivars for improving cotton yield and disease resistance.

The Fusarium crown rot pathogen Fusarium pseudograminearum triggers a suite of transcriptional and metabolic changes in bread wheat (Triticum aestivum L.)

Background and Aims

Fusarium crown rot caused by the fungal pathogen Fusarium pseudograminearum is a disease of wheat and barley, bearing significant economic cost. Efforts to develop effective resistance to this disease have been hampered by the quantitative nature of resistance and a lack of understanding of the factors associated with resistance and susceptibility. Here, we aimed to dissect transcriptional responses triggered in wheat by F. pseudograminearum infection.

Methods

We used an RNA-seq approach to analyse host responses during a compatible interaction and identified >2700 wheat genes differentially regulated after inoculation with F. pseudograminearum . The production of a few key metabolites and plant hormones in the host during the interaction was also analysed.

Key Results

Analysis of gene ontology enrichment showed that a disproportionate number of genes involved in primary and secondary metabolism, signalling and transport were differentially expressed in infected seedlings. A number of genes encoding pathogen-responsive uridine-diphosphate glycosyltransferases (UGTs) potentially involved in detoxification of the Fusarium mycotoxin deoxynivalenol (DON) were differentially expressed. Using a F. pseudograminearum DON-non-producing mutant, DON was shown to play an important role in virulence during Fusarium crown rot. An over-representation of genes involved in the phenylalanine, tryptophan and tyrosine biosynthesis pathways was observed. This was confirmed through metabolite analyses that demonstrated tryptamine and serotonin levels are induced after F. pseudograminearum inoculation.

Conclusions

Overall, the observed host response in bread wheat to F. pseudograminearum during early infection exhibited enrichment of processes related to pathogen perception, defence signalling, transport and metabolism and deployment of chemical and enzymatic defences. Additional functional analyses of candidate genes should reveal their roles in disease resistance or susceptibility. Better understanding of host responses contributing to resistance and/or susceptibility will aid the development of future disease improvement strategies against this important plant pathogen.

The role of electrical and jasmonate signalling in the recognition of captured prey in the carnivorous sundew plant Drosera capensis

The carnivorous sundew plant (Drosera capensis) captures prey using sticky tentacles. We investigated the tentacle and trap reactions in response to the electrical and jasmonate signalling evoked by different stimuli to reveal how carnivorous sundews recognize digestible captured prey in their traps. We measured the electrical signals, phytohormone concentration, enzyme activities and Chla fluorescence in response to mechanical stimulation, wounding or insect feeding in local and systemic traps. Seven new proteins in the digestive fluid were identified using mass spectrometry. Mechanical stimuli and live prey induced a fast, localized tentacle-bending reaction and enzyme secretion at the place of application. By contrast, repeated wounding induced a nonlocalized convulsive tentacle movement and enzyme secretion in local but also in distant systemic traps. These differences can be explained in terms of the electrical signal propagation and jasmonate accumulation, which also had a significant impact on the photosynthesis in the traps. The electrical signals generated in response to wounding could partially mimic a mechanical stimulation of struggling prey and might trigger a false alarm, confirming that the botanical carnivory and plant defence mechanisms are related. To trigger the full enzyme activity, the traps must detect chemical stimuli from the captured prey.

Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation

Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P. minus has not been well-studied due to the limited genetic information. Hence, we performed Illumina paired-end RNA-seq for de novo reconstruction of P. minus leaf transcriptome to identify differentially expressed genes (DEGs) in response to MeJA elicitation. A total of 182,111 unique transcripts (UTs) were obtained by de novo assembly of 191.57 million paired-end clean reads using Trinity analysis pipeline. A total of 2374 UTs were identified to be significantly up-/down-regulated 24 h after MeJA treatment. These UTs comprising many genes related to plant secondary metabolite biosynthesis, defense and stress responses. To validate our sequencing results, we analyzed the expression of 21 selected DEGs by quantitative real-time PCR and found a good correlation between the two analyses. The single time-point analysis in this work not only provides a useful genomic resource for P. minus but also gives insights on molecular mechanisms of stress responses in P. minus.

Jasmonic Acid Enhances Al-Induced Root Growth Inhibition

Phytohormones such as ethylene and auxin are involved in the regulation of the aluminum (Al)-induced root growth inhibition. Although jasmonate (JA) has been reported to play a crucial role in the regulation of root growth and development in response to environmental stresses through interplay with ethylene and auxin, its role in the regulation of root growth response to Al stress is not yet known. In an attempt to elucidate the role of JA, we found that exogenous application of JA enhanced the Al-induced root growth inhibition. Furthermore, phenotype analysis with mutants defective in either JA biosynthesis or signaling suggests that JA is involved in the regulation of Al-induced root growth inhibition. The expression of the JA receptor CORONATINE INSENSITIVE1 (COI1) and the key JA signaling regulator MYC2 was up-regulated in response to Al stress in the root tips. This process together with COI1-mediated Al-induced root growth inhibition under Al stress was controlled by ethylene but not auxin. Transcriptomic analysis revealed that many responsive genes under Al stress were regulated by JA signaling. The differential responsive of microtubule organization-related genes between the wild-type and coi1-2 mutant is consistent with the changed depolymerization of cortical microtubules in coi1 under Al stress. In addition, ALMT-mediated malate exudation and thus Al exclusion from roots in response to Al stress was also regulated by COI1-mediated JA signaling. Together, this study suggests that root growth inhibition is regulated by COI1-mediated JA signaling independent from auxin signaling and provides novel insights into the phytohormone-mediated root growth inhibition in response to Al stress.

Jasmonates are induced by the PAMP flg22 but not the cell death-inducing elicitor Harpin in Vitis rupestris

Plants employ two layers of defence that differ with respect to cell death: pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). In our previous work, we have comparatively mapped the molecular events in a cell system derived from the wild American grape Vitis rupestris, where cell death-independent defence can be triggered by PAMP flg22, whereas the elicitor Harpin activates a cell death-related ETI-like response. Both defence responses overlapped with respect to early events, such as calcium influx, apoplastic alkalinisation, oxidative burst, mitogen-activated protein kinase (MAPK) signalling, activation of defence-related genes and accumulation of phytoalexins. However, timing and amplitude of early signals differed. In the current study, we address the role of jasmonates (JAs) as key signalling compounds in hypersensitive cell death. We find, in V. rupestris, that jasmonic acid and its bioactive conjugate jasmonoyl-isoleucine (JA-Ile) rapidly accumulate in response to flg22 but not in response to Harpin. However, Harpin can induce programmed cell death, whereas exogenous methyl jasmonate (MeJA) fails to do so, although both signals induce a similar response of defence genes. Also in a second cell line from V. vinifera cv. 'Pinot Noir', where Harpin cannot activate cell death and where flg22 fails to induce JA and JA-Ile, defence genes are activated in a similar manner. These findings indicate that the signal pathway culminating in cell death must act independently from the events culminating in the accumulation of toxic stilbenes.

Identification of Candidate Genes and Biosynthesis Pathways Related to Fertility Conversion by Wheat KTM3315A Transcriptome Profiling

The Aegilops kotschyi thermo-sensitive cytoplasmic male sterility (K-TCMS) system may facilitate hybrid wheat (Triticum aestivum L.) seed multiplication and production. The K-TCMS line is completely male sterile during the normal wheat-growing season, whereas its fertility can be restored in a high-temperature environment. To elucidate the molecular mechanisms responsible for male sterility/fertility conversion and candidate genes involved with pollen development in K-TCMS, we employed RNA-seq to sequence the transcriptomes of anthers from K-TCMS line KTM3315A during development under sterile and fertile conditions. We identified 16840 differentially expressed genes (DEGs) in different stages including15157 known genes (15135 nuclear genes and 22 plasmagenes) and 1683 novel genes. Bioinformatics analysis identified possible metabolic pathways involved with fertility based on KEGG pathway enrichment of the DEGs expressed in fertile and sterile plants. We found that most of the genes encoding key enzyme in the phenylpropanoid biosynthesis and jasmonate biosynthesis pathways were significant upregulated in uninucleate, binuclate or trinucleate stage, which both interact with MYB transcription factors, and that link between all play essential roles in fertility conversion. The relevant DEGs were verified by quantitative RT-PCR. Thus, we suggested that phenylpropanoid biosynthesis and jasmonate biosynthesis pathways were involved in fertility conversion of K-TCMS wheat. This will provide a new perspective and an effective foundation for the research of molecular mechanisms of fertility conversion of CMS wheat. Fertility conversion mechanism in thermo-sensitive cytoplasmic male sterile/fertile wheat involves the phenylpropanoid biosynthesis pathway, jasmonate biosynthesis pathway, and MYB transcription factors.

Monitoring of Crosstalk Between Jasmonate and Auxin in the Framework of Plant Stress Responses of Roots

Over the last few years, it became more and more evident that plant hormone action is to great parts determined through their sophisticated crosstalk, rather than by their isolated activities. Thus, the parallel analysis of interconnected phytohormones in only very small amounts of tissue developed to an important issue in the field of plant sciences. In the following, a highly sensitive and accurate method is described for the quantitative analysis of the plant hormones jasmonic acid and indole-3-acetic acid in the model plant Arabidopsis thaliana. The described methodology is, however, not limited to the analysis of Arabidopsis samples but can also be applied to other plant species. The presented method is optimized for the working up of as little as 20-50 mg of plant tissue. Thus, it is well suited for the analysis of plant hormone contents in plant tissue of only little biomass, such as roots. The presented protocol facilitates the implementation of the method into other laboratories that have access to appropriate laboratory equipment and comparable state-of-the-art gas chromatography-mass spectrometry (GC-MS) technology.

Identification of Root-Secreted Compounds Involved in the Communication Between Cucumber, the Beneficial Bacillus amyloliquefaciens, and the Soil-Borne Pathogen Fusarium oxysporum

Colonization of plant growth-promoting rhizobacteria (PGPR) is critical for exerting their beneficial effects on the plant. Root exudation is a major factor influencing the colonization of both PGPR and soil-borne pathogens within the root system. However, the tripartite interaction of PGPR, plant roots, and soil-borne pathogens is poorly understood. We screened root exudates for signals that mediate tripartite interactions in the rhizosphere. In a split-root system, we found that root colonization of PGPR strain Bacillus amyloliquefaciens SQR9 on cucumber root was significantly enhanced by preinoculation with SQR9 or the soil-borne pathogen Fusarium oxysporum f. sp. cucumerinum, whereas root colonization of F. oxysporum f. sp. cucumerinum was reduced upon preinoculation with SQR9 or F. oxysporum f. sp. cucumerinum. Root exudates from cucumbers preinoculated with SQR9 or F. oxysporum f. sp. cucumerinum were analyzed and 109 compounds were identified. Correlation analysis highlighted eight compounds that significantly correlated with root colonization of SQR9 or F. oxysporum f. sp. cucumerinum. After performing colonization experiments with these chemicals, raffinose and tryptophan were shown to positively affect the root colonization of F. oxysporum f. sp. cucumerinum and SQR9, respectively. These results indicate that cucumber roots colonized by F. oxysporum f. sp. cucumerinum or SQR9 increase root secretion of tryptophan to strengthen further colonization of SQR9. In contrast, these colonized cucumber roots reduce raffinose secretion to inhibit root colonization of F. oxysporum f. sp. cucumerinum.

Jasmonic Acid and Ethylene Signaling Pathways Regulate Glucosinolate Levels in Plants During Rhizobacteria-Induced Systemic Resistance Against a Leaf-Chewing Herbivore

Beneficial soil microbes can promote plant growth and induce systemic resistance (ISR) in aboveground tissues against pathogens and herbivorous insects. Despite the increasing interest in microbial-ISR against herbivores, the underlying molecular and chemical mechanisms of this phenomenon remain elusive. Using Arabidopsis thaliana and the rhizobacterium Pseudomonas simiae WCS417r (formerly known as P. fluorescens WCS417r), we here evaluate the role of the JA-regulated MYC2-branch and the JA/ET-regulated ORA59-branch in modulating rhizobacteria-ISR to Mamestra brassicae by combining gene transcriptional, phytochemical, and herbivore performance assays. Our data show a consistent negative effect of rhizobacteria-mediated ISR on the performance of M. brassicae. Functional JA- and ET-signaling pathways are required for this effect, as shown by investigating the knock-out mutants dde2-2 and ein2-1. Additionally, whereas herbivory mainly induces the MYC2-branch, rhizobacterial colonization alone or in combination with herbivore infestation induces the ORA59-branch of the JA signaling pathway. Rhizobacterial colonization enhances the synthesis of camalexin and aliphatic glucosinolates (GLS) compared to the control, while it suppresses the herbivore-induced levels of indole GLS. These changes are associated with modulation of the JA-/ET-signaling pathways. Our data show that the colonization of plant roots by rhizobacteria modulates plant-insect interactions by prioritizing the JA/ET-regulated ORA59-branch over the JA-regulated MYC2-branch. This study elucidates how microbial plant symbionts can modulate the plant immune system to mount an effective defense response against herbivorous plant attackers.

Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray

The natural rubber of Para rubber tree, Hevea brasiliensis, is the main crop involved in industrial rubber production due to its superior quality. The Hevea bark is commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. The laticifer is well defined in the aspect of morphology; however, only some genes associated with its development have been reported. We successfully induced secondary laticifer in the jasmonic acid (JA)-treated and linolenic acid (LA)-treated Hevea bark but secondary laticifer is not observed in the ethephon (ET)-treated and untreated Hevea bark. In this study, we analysed 27,195 gene models using NimbleGen microarrays based on the Hevea draft genome. 491 filtered differentially expressed (FDE) transcripts that are common to both JA- and LA-treated bark samples but not ET-treated bark samples were identified. In the Eukaryotic Orthologous Group (KOG) analysis, 491 FDE transcripts belong to different functional categories that reflect the diverse processes and pathways involved in laticifer differentiation. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) and KOG analysis, the profile of the FDE transcripts suggest that JA- and LA-treated bark samples have a sufficient molecular basis for secondary laticifer differentiation, especially regarding secondary metabolites metabolism. FDE genes in this category are from the cytochrome (CYP) P450 family, ATP-binding cassette (ABC) transporter family, short-chain dehydrogenase/reductase (SDR) family, or cinnamyl alcohol dehydrogenase (CAD) family. The data includes many genes involved in cell division, cell wall synthesis, and cell differentiation. The most abundant transcript in FDE list was SDR65C, reflecting its importance in laticifer differentiation. Using the Basic Local Alignment Search Tool (BLAST) as part of annotation and functional prediction, several characterised as well as uncharacterized transcription factors and genes were found in the dataset. Hence, the further characterization of these genes is necessary to unveil their role in laticifer differentiation. This study provides a platform for the further characterization and identification of the key genes involved in secondary laticifer differentiation.

A pivotal role of the jasmonic acid signal pathway in mediating radiation-induced bystander effects in Arabidopsis thaliana

Although radiation-induced bystander effects (RIBE) in Arabidopsis thaliana have been well demonstrated in vivo, little is known about their underlying mechanisms, particularly with regard to the participating signaling molecules and signaling pathways. In higher plants, jasmonic acid (JA) and its bioactive derivatives are well accepted as systemic signal transducers that are produced in response to various environmental stresses. It is therefore speculated that the JA signal pathway might play a potential role in mediating radiation-induced bystander signaling of root-to-shoot. In the present study, pretreatment of seedlings with Salicylhydroxamic acid, an inhibitor of lipoxigenase (LOX) in JA biosynthesis, significantly suppressed RIBE-mediated expression of the AtRAD54 gene. After root irradiation, the aerial parts of A. thaliana mutants deficient in JA biosynthesis (aos) and signaling cascades (jar1-1) showed suppressed induction of the AtRAD54 and AtRAD51 genes and TSI and 180-bp repeats, which have been extensively used as endpoints of bystander genetic and epigenetic effects in plants. These results suggest an involvement of the JA signal pathway in the RIBE of plants. Using the root micro-grafting technique, the JA signal pathway was shown to participate in both the generation of bystander signals in irradiated root cells and radiation responses in the bystander aerial parts of plants. The over-accumulation of endogenous JA in mutant fatty acid oxygenation up-regulated 2 (fou2), in which mutation of the Two Pore Channel 1 (TPC1) gene up-regulates expression of the LOX and allene oxide synthase (AOS) genes, inhibited RIBE-mediated expression of the AtRAD54 gene, but up-regulated expression of the AtKU70 and AtLIG4 genes in the non-homologous end joining (NHEJ) pathway. Considering that NHEJ is employed by plants with increased DNA damage, the switch from HR to NHEJ suggests that over-accumulation of endogenous JA might enhance the radiosensitivity of plants in terms of RIBE.

Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes

Drought stress has adverse impacts on plant production and productivity. MicroRNAs (miRNAs) are one class of noncoding RNAs regulating gene expression post-transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue-specific miRNAs responsible to drought stress, which are understudied in tomato. For this purpose, root and upground tissues of two different drought-responsive tomato genotypes (Lycopersicon esculentum as sensitive and L. esculentum var. cerasiforme as tolerant) were subjected to stress with 5% polyethylene glycol for 7 days. A total of 699 conserved miRNAs belonging to 578 families were determined and 688 miRNAs were significantly differentially expressed between different treatments, tissues and genotypes. Using degradome sequencing, 44 target genes were identified associated with 36 miRNA families. Drought-related miRNAs and their targets were enriched functionally by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Totally, 53 miRNAs targeted 23 key drought stress- and tissue development-related genes, including DRP (dehydration-responsive protein), GTs (glycosyltransferases), ERF (ethylene responsive factor), PSII (photosystem II) protein, HD-ZIP (homeodomain-leucine zipper), MYB and NAC-domain transcription factors. miR160, miR165, miR166, miR171, miR398, miR408, miR827, miR9472, miR9476 and miR9552 were the key miRNAs functioning in regulation of these genes and involving in tomato response to drought stress. Additionally, plant hormone signal transduction pathway genes were differentially regulated by miR169, miR172, miR393, miR5641, miR5658 and miR7997 in both tissues of both sensitive and tolerant genotypes. These results provide new insight into the regulatory role of miRNAs in drought response with plant hormone signal transduction and drought-tolerant tomato breeding.