In Dormant Red Rice Seeds, the Inhibition of Early Seedling Growth, but Not of Germination, Requires Extracellular ABA

The phytohormone abscisic acid (ABA) inhibits seed germination and seedling growth and is required for the inception of dormancy. Xanthoxal (also known as xanthoxin) is the first specific biosynthetic precursor of ABA. In this study, a modified method to produce xanthoxal is described. I tested the ability of either xanthoxal or ABA to reinstate dormancy in dormant red rice seeds whose dormancy was broken by fluridone (an inhibitor of the synthesis of carotenoids and, subsequently, ABA). Xanthoxal was shown to have a stronger inhibitory effect on germination than ABA when exogenously provided. Although this could indicate an additional effect of xanthoxal above that expected if xanthoxal were simply converted to ABA in the seed, alternative hypotheses cannot be excluded. One alternative is that exogenous xanthoxal may be trapped inside the cells to a greater extent than exogenous ABA, resulting in an intracellular level of ABA higher than that reached with a direct application of ABA. As a further alternative, exogenous xanthoxal may interfere with ABA action in the apoplast. In this study, following germination, early seedling growth was delayed only if ABA was applied. This suggests that inhibition of early seedling growth, but not of germination, requires extracellular ABA.

Differential Contributions of MYCs to Insect Defense Reveals Flavonoids Alleviating Growth Inhibition Caused by Wounding in Arabidopsis

In Arabidopsis, basic helix-loop-helix transcription factors (TFs) MYC2, MYC3, and MYC4 are involved in many biological processes, such as defense against insects. We found that despite functional redundancy, MYC-related mutants displayed different resistance to cotton bollworm (Helicoverpa armigera). To screen out the most likely genes involved in defense against insects, we analyzed the correlation of gene expression with cotton bollworm resistance in wild-type (WT) and MYC-related mutants. In total, the expression of 94 genes in untreated plants and 545 genes in wounded plants were strongly correlated with insect resistance, and these genes were defined as MGAIs (MYC-related genes against insects). MYC3 had the greatest impact on the total expression of MGAIs. Gene ontology (GO) analysis revealed that besides the biosynthesis pathway of glucosinolates (GLSs), MGAIs, which are well-known defense compounds, were also enriched in flavonoid biosynthesis. Moreover, MYC3 dominantly affected the gene expression of flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) revealed that AAE18, which is involved in activating auxin precursor 2,4-dichlorophenoxybutyric acid (2,4-DB) and two other auxin response genes, was highly co-expressed with flavonoid biosynthesis genes. With wounding treatment, the WT plants exhibited better growth performance than chalcone synthase (CHS), which was defective in flavonoid biosynthesis. The data demonstrated dominant contributions of MYC3 to cotton bollworm resistance and imply that flavonoids might alleviate the growth inhibition caused by wounding in Arabidopsis.

Unravelling the Metabolic Reconfiguration of the Post-Challenge Primed State in Sorghum bicolor Responding to Colletotrichum sublineolum Infection

Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of priming events is still limited. A non-targeted metabolomics approach was used to investigate metabolic changes in plant growth-promoting rhizobacteria (PGPR)-primed Sorghum bicolor seedlings infected with the anthracnose-causing fungal pathogen, Colletotrichum sublineolum, with a focus on the post-challenge primed state phase. At the 4-leaf growth stage, the plants were treated with a strain of Paenibacillus alvei at 10⁸ cfu mL⁻¹. Following a 24 h PGPR application, the plants were inoculated with a C. sublineolum spore suspension (10⁶ spores mL⁻¹), and the infection monitored over time: 1, 3, 5, 7 and 9 days post-inoculation. Non-infected plants served as negative controls. Intracellular metabolites from both inoculated and non-inoculated plants were extracted with 80% methanol-water. The extracts were chromatographically and spectrometrically analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to high-definition mass spectrometry. The acquired multidimensional data were processed to create data matrices for chemometric modelling. The computed models indicated time-related metabolic perturbations that reflect primed responses to the fungal infection. Evaluation of orthogonal projection to latent structure-discriminant analysis (OPLS-DA) loading shared and unique structures (SUS)-plots uncovered the differential stronger defence responses against the fungal infection observed in primed plants. These involved enhanced levels of amino acids (tyrosine, tryptophan), phytohormones (jasmonic acid and salicylic acid conjugates, and zeatin), and defence-related components of the lipidome. Furthermore, other defence responses in both naïve and primed plants were characterised by a complex mobilisation of phenolic compounds and de novo biosynthesis of the flavones, apigenin and luteolin and the 3-deoxyanthocyanidin phytoalexins, apigeninidin and luteolinidin, as well as some related conjugates.

Metabolomics in Plant Priming Research: The Way Forward?

A new era of plant biochemistry at the systems level is emerging, providing detailed descriptions of biochemical phenomena at the cellular and organismal level. This new era is marked by the advent of metabolomics—the qualitative and quantitative investigation of the entire metabolome (in a dynamic equilibrium) of a biological system. This field has developed as an indispensable methodological approach to study cellular biochemistry at a global level. For protection and survival in a constantly-changing environment, plants rely on a complex and multi-layered innate immune system. This involves surveillance of ‘self’ and ‘non-self,’ molecule-based systemic signalling and metabolic adaptations involving primary and secondary metabolites as well as epigenetic modulation mechanisms. Establishment of a pre-conditioned or primed state can sensitise or enhance aspects of innate immunity for faster and stronger responses. Comprehensive elucidation of the molecular and biochemical processes associated with the phenotypic defence state is vital for a better understanding of the molecular mechanisms that define the metabolism of plant–pathogen interactions. Such insights are essential for translational research and applications. Thus, this review highlights the prospects of metabolomics and addresses current challenges that hinder the realisation of the full potential of the field. Such limitations include partial coverage of the metabolome and maximising the value of metabolomics data (extraction of information and interpretation). Furthermore, the review points out key features that characterise both the plant innate immune system and enhancement of the latter, thus underlining insights from metabolomic studies in plant priming. Future perspectives in this inspiring area are included, with the aim of stimulating further studies leading to a better understanding of plant immunity at the metabolome level.

Metabolomics-guided investigations of unintended effects of the expression of the hydroxycinnamoyl quinate hydroxycinnamoyltransferase (hqt1) gene from Cynara cardunculus var. scolymus in Nicotiana tabacum cell cultures

Chlorogenic acids (CGAs) are phenolic compounds biosynthesized in the phenylpropanoid pathway, with hydroxycinnamoyl quinate hydroxycinnamoyltransferase (HQT) as the key enzyme. Variation of CGAs has been noted in different plants, with globe artichoke (Cynara cardunculus var. scolymus L.) producing high amounts and a diverse spectrum of CGAs in its leaves. In the current study, the effect of overexpression of the hqt1 transgene from globe artichoke in tobacco was evaluated at the metabolome level. Here, metabolomic approaches based on ultra-high performance liquid chromatography coupled to mass spectrometry, together with chemometric models such as principal component analysis and orthogonal partial least square discriminant analysis, were employed to evaluate altered metabolic changes due to hqt1 overexpression. CGA profiles (caffeoylquinic acids: 3-CQA, 4-CQA and 5-CQA; p-coumaroylquinic acids: 4-pCoQA and 5-pCoQA; and 4,5-di-caffeoylquinic acid) of transgenic tobacco cell cultures were detected at lower concentrations than in the wild type. Interestingly, the cells were found to rather accumulate, as an unintended effect, abscisic acid - and benzoic acid derivatives. The results suggest that insertion of hqt1 in tobacco, and overexpression in undifferentiated cells, led to rechannelling of the phenylpropanoid pathway to accumulate benzoic acids. These findings proved to be contrary to the results shown elsewhere in leaf tissues, thus indicating differential metabolic control and regulation in the undifferentiated cell culture system.

Defence signalling marker gene responses to hormonal elicitation differ between roots and shoots

Phytohormones such as jasmonic acid (JA), salicylic acid (SA), ethylene (ET) and abscisic acid (ABA) play a key role in regulation of plant immune responses to different attackers. Extensive research over recent years has led to the identification of molecular markers for specific hormonal-regulated defence pathways. However, most of our current knowledge on the regulation of plant immunity derives from studies focused on above-ground organs, mainly on the model plant Arabidopsis thaliana. Therefore, it is unclear whether the paradigms based on experiments on above-ground organs are entirely transferable to roots. Here, we used the non-model plant Brassica rapa to study the regulation dynamics of hormonal-related marker genes in both roots and shoots. These markers were identified in Arabidopsis shoots after elicitation of the JA-, SA-, ET- or ABA-signalling pathways, and are commonly used to study induced responses. We assessed whether the regulation of those genes by hormonal elicitation differs between roots and shoots. To discern whether the differences in marker gene expression between roots and shoots are related to differences in hormone production or to differential responsiveness, we also measured actual hormone content in the treated tissue after elicitation. Our results show that some of the widely used markers did not show specific responsiveness to single hormone applications in B. rapa. We further found that hormonal elicitation led to different response patterns of the molecular markers in shoots and roots. Our results suggest that the regulation of some hormonal-related marker genes in B. rapa is organ specific and differs from the Arabidopsis-derived paradigms.

The Active Jasmonate JA-Ile Regulates a Specific Subset of Plant Jasmonate-Mediated Resistance to Herbivores in Nature

The jasmonate hormones are essential regulators of plant defense against herbivores and include several dozen derivatives of the oxylipin jasmonic acid (JA). Among these, the conjugate jasmonoyl isoleucine (JA-Ile) has been shown to interact directly with the jasmonate co-receptor complex to regulate responses to jasmonate signaling. However, functional studies indicate that some aspects of jasmonate-mediated defense are not regulated by JA-Ile. Thus, it is not clear whether JA-Ile is best characterized as the master jasmonate regulator of defense, or if it regulates more specific aspects. We investigated possible functions of JA-Ile in anti-herbivore resistance of the wild tobacco Nicotiana attenuata, a model system for plant-herbivore interactions. We first analyzed the soluble and volatile secondary metabolomes of irJAR4xirJAR6, asLOX3, and WT plants, as well as an RNAi line targeting the jasmonate co-receptor CORONATINE INSENSITIVE 1 (irCOI1), following a standardized herbivory treatment. irJAR4xirJAR6 were the most similar to WT plants, having a ca. 60% overlap in differentially regulated metabolites with either asLOX3 or irCOI1. In contrast, while at least 25 volatiles differed between irCOI1 or asLOX3 and WT plants, there were few or no differences in herbivore-induced volatile emission between irJAR4xirJAR6 and WT plants, in glasshouse- or field-collected samples. We then measured the susceptibility of jasmonate-deficient vs. JA-Ile-deficient plants in nature, in comparison to wild-type (WT) controls, and found that JA-Ile-deficient plants (irJAR4xirJAR6) are much better defended even than a mildly jasmonate-deficient line (asLOX3). The differences among lines could be attributed to differences in damage from specific herbivores, which appeared to prefer either one or the other jasmonate-deficient phenotype. We further investigated the elicitation of one herbivore-induced volatile known to be jasmonate-regulated and to mediate resistance to herbivores: (E)-α-bergamotene. We found that JA was a more potent elicitor of (E)-α-bergamotene emission than was JA-Ile, and when treated with JA, irJAR4xirJAR6 plants emitted 20- to 40-fold as much (E)-α-bergamotene than WT. We conclude that JA-Ile regulates specific aspects of herbivore resistance in N. attenuata. This specificity may allow plants flexibility in their responses to herbivores and in managing trade-offs between resistance, vs. growth and reproduction, over the course of ontogeny.

A Maize Inbred Exhibits Resistance Against Western Corn Rootwoorm, Diabrotica virgifera virgifera

Insect resistance against root herbivores like the western corn rootworm (WCR, Diabrotica virgifera virgifera) is not well understood in non-transgenic maize. We studied the responses of two American maize inbreds, Mp708 and Tx601, to WCR infestation using biomechanical, molecular, biochemical analyses, and laser ablation tomography. Previous studies performed on several inbreds indicated that these two maize genotypes differed in resistance to pests including fall armyworm (Spodoptera frugiperda) and WCR. Our data confirmed that Mp708 shows resistance against WCR, and demonstrates that the resistance mechanism is based in a multi-trait phenotype that includes increased resistance to cutting in nodal roots, stable root growth during insect infestation, constitutive and induced expression of known herbivore-defense genes, including ribosomal inhibitor protein 2 (rip2), terpene synthase 23 (tps23) and maize insect resistance cysteine protease-1 (mir1), as well high constitutive levels of jasmonic acid and production of (E)-β-caryophyllene. In contrast, Tx601 is susceptible to WCR. These findings will facilitate the use of Mp708 as a model to explore the wide variety of mechanisms and traits involved in plant defense responses and resistance to herbivory by insects with several different feeding habits.

Exploring Omics data from designed experiments using analysis of variance multiblock Orthogonal Partial Least Squares

Many experimental factors may have an impact on chemical or biological systems. A thorough investigation of the potential effects and interactions between the factors is made possible by rationally planning the trials using systematic procedures, i.e. design of experiments. However, assessing factors' influences remains often a challenging task when dealing with hundreds to thousands of correlated variables, whereas only a limited number of samples is available. In that context, most of the existing strategies involve the ANOVA-based partitioning of sources of variation and the separate analysis of ANOVA submatrices using multivariate methods, to account for both the intrinsic characteristics of the data and the study design. However, these approaches lack the ability to summarise the data using a single model and remain somewhat limited for detecting and interpreting subtle perturbations hidden in complex Omics datasets. In the present work, a supervised multiblock algorithm based on the Orthogonal Partial Least Squares (OPLS) framework, is proposed for the joint analysis of ANOVA submatrices. This strategy has several advantages: (i) the evaluation of a unique multiblock model accounting for all sources of variation; (ii) the computation of a robust estimator (goodness of fit) for assessing the ANOVA decomposition reliability; (iii) the investigation of an effect-to-residuals ratio to quickly evaluate the relative importance of each effect and (iv) an easy interpretation of the model with appropriate outputs. Case studies from metabolomics and transcriptomics, highlighting the ability of the method to handle Omics data obtained from fixed-effects full factorial designs, are proposed for illustration purposes. Signal variations are easily related to main effects or interaction terms, while relevant biochemical information can be derived from the models.

Hormone profiling

Phytohormones are low molecular weight compounds that are produced by plants to regulate growth and development and also in response to biotic and abiotic stresses. The quantitative analysis of these molecules, which is essential for a better understanding of their physiological functions, is still particularly challenging due to their very low abundance in plant tissues. In this chapter, a rapid, sensitive, and accurate method for the quantification of acidic plant hormones is described. A fast and simple extraction procedure without purification or derivatization was devised, followed by optimized ultrahigh pressure liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis. The analytical procedure was validated in terms of selectivity, sensitivity, linearity, precision, recovery, and matrix effects. This protocol facilitates the high-throughput analysis of the main plant hormones and is applicable as a routine tool for a wide range of research fields such as plant-pathogen interactions, mutant screening, or plant development.

Salicyloyl-aspartate synthesized by the acetyl-amido synthetase GH3.5 is a potential activator of plant immunity in Arabidopsis

Salicylic acid (SA) plays a critical role in plant immunity responses against pathogen infection, especially in the establishment of systemic acquired resistance. Whether other forms of salicylates also function in plant immunity has not been explored. Our previous study has revealed that salicyloyl-aspartate (SA-Asp), the only reported endogenous SA-amino acid conjugate in plants, was highly accumulated in the Arabidopsis activation-tagged mutant gh3.5-1D after pathogen infection. In this study, we dissected SA-Asp production in Arabidopsis. In vitro biochemical experiments showed that the GH3.5 protein could catalyze the conjugation of SA with aspartic acid to form SA-Asp. SA-Asp is not converted into free SA and likely acts as a mobile molecule in plants. SA-Asp could induce pathogenesis-related (PR) gene expression and increase disease resistance to pathogenic Pseudomonas syringae. Our current study also supports the notion that GH3.5 is a multifunction enzyme in plant hormone metabolism.

AtMYB44 positively modulates disease resistance to Pseudomonas syringae through the salicylic acid signalling pathway in Arabidopsis

Plant MYB transcription factors are implicated in resistance to biotic and abiotic stresses. Here, we demonstrate that an R2-R3 MYB transcription factor, AtMYB44, plays a role in the plant defence response to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (PstDC3000). The expression of AtMYB44 was upregulated upon pathogen infection and treatments with defence-related phytohormones. Transgenic plants overexpressing AtMYB44 (35S-Ms) exhibited greater levels of PR1 gene expression, cell death, callose deposition and hydrogen peroxide (H2O2) accumulation in leaves infected with PstDC3000. Consequently, 35S-M lines displayed enhanced resistance to PstDC3000. In contrast, the atmyb44 T-DNA insertion mutant was more susceptible to PstDC3000 and exhibited decreased PR1 gene expression upon infection. Using double mutants constructed via crosses of 35S-M lines with NahG transgenic plants and nonexpressor of pathogenesis-related genes1 mutant (npr1-1), we demonstrated that the enhanced PR1 gene expression and PstDC3000 resistance in 35S-M plants occur mainly through the salicylic acid signalling pathway.

Induced resistance in maize is based on organ-specific defence responses

To obtain further insight into the intricate inter-play between maize (Zea mays) and the fungal pathogen Colletotrichum graminicola, the local and systemic molecular and chemical defence responses of maize leaves and roots were simultaneously investigated and compared. Similar gene expression and hormonal patterns were detected in both above- and below-ground organs; however, roots responded more rapidly and accumulated higher levels of defence-related hormones than leaves. Leaf and root infection with C. graminicola triggered systemic resistance in the foliage against the same fungus. This systemic defence response was associated with systemic transcriptional adaptations, and elevated levels of salicylic acid and abscisic acid. Metabolomic profiling revealed significant differences in the composition of secondary metabolites in leaves and roots, indicating that these organs employ distinct chemical defence systems. In addition, higher basal levels of antimicrobial flavonoids suggest an enhanced basal defensive state of roots. Our findings reveal tissue-specific local and systemic antifungal defence mechanisms in maize.

A non-targeted approach for extended liquid chromatography-mass spectrometry profiling of free and esterified jasmonates after wounding

Upon wounding or herbivory, plants quickly react by activating various defense mechanisms. A major part of these defenses is thought to be regulated by the jasmonate pathway through the induction of jasmonic acid and its biologically active jasmonoyl-isoleucine conjugate. Yet, these well-known phytohormones are only two among the numerous compounds that compose the jasmonate family. Here, we describe a method based on ultrahigh-pressure liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry that can potentially profile the full range of known free and esterified jasmonates in a non-targeted manner. The developed approach is illustrated by the analysis of Arabidopsis thaliana leaves after mechanical wounding.

Role of phytohormones in insect-specific plant reactions

The capacity to perceive and respond is integral to biological immune systems, but to what extent can plants specifically recognize and respond to insects? Recent findings suggest that plants possess surveillance systems that are able to detect general patterns of cellular damage as well as highly specific herbivore-associated cues. The jasmonate (JA) pathway has emerged as the major signaling cassette that integrates information perceived at the plant-insect interface into broad-spectrum defense responses. Specificity can be achieved via JA-independent processes and spatio-temporal changes of JA-modulating hormones, including ethylene (ET), salicylic acid (SA), abscisic acid (ABA), auxin, cytokinins (CK), brassinosteroids (BR) and gibberellins (GB). The identification of receptors and ligands and an integrative view of hormone-mediated response systems are crucial to understand specificity in plant immunity to herbivores.

Expression of a bacterial feedback-insensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase of the shikimate pathway in Arabidopsis elucidates potential metabolic bottlenecks between primary and secondary metabolism

The shikimate pathway of plants mediates the conversion of primary carbon metabolites via chorismate into the three aromatic amino acids and to numerous secondary metabolites derived from them. However, the regulation of the shikimate pathway is still far from being understood. We hypothesized that 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme regulating flux through the shikimate pathway. To test this hypothesis, we expressed a mutant bacterial AroG gene encoding a feedback-insensitive DAHPS in transgenic Arabidopsis plants. The plants were subjected to detailed analysis of primary metabolism, using GC-MS, as well as secondary metabolism, using LC-MS. Our results exposed a major effect of bacterial AroG expression on the levels of shikimate intermediate metabolites, phenylalanine, tryptophan and broad classes of secondary metabolite, such as phenylpropanoids, glucosinolates, auxin and other hormone conjugates. We propose that DAHPS is a key regulatory enzyme of the shikimate pathway. Moreover, our results shed light on additional potential metabolic bottlenecks bridging plant primary and secondary metabolism.

Detection, characterization and quantification of salicylic acid conjugates in plant extracts by ESI tandem mass spectrometric techniques

An approach for the detection and characterization of SA derivatives in plant samples is presented based on liquid chromatography coupled to electrospray ionization (ESI) tandem mass spectrometric techniques. Precursor ion scan methods using an ESI triple quadrupole spectrometer for samples from plants challenged with the virulent Pseudomonas syringae pv tomato DC3000 allowed us to detect two potential SA derivatives. The criterion used to consider a potential SA derivative is based on the detection of analytes in the precursor ion scan chromatogram upon selecting m/z 137 and m/z 93 that correspond to the salicylate and its main product ion, respectively. Product ion spectra of the newly-detected analytes as well as accurate m/z determinations using an ESI Q-time-of-flight instrument were registered as means of characterization and strongly suggest that glucosylated forms of SA at the carboxylic and at the phenol functional groups are present in plant samples. The specific synthesis and subsequent chromatography of salicylic glucosyl ester (SGE) and glucosyl salicylate (SAG) standards confirmed the chemical identity of both peaks that were obtained applying different tandem mass spectrometric techniques and accurate m/z determinations. A multiple reaction monitoring method has been developed and applied to plant samples. The advantages of this LC-ESI-MS/MS methods with respect to the traditional analysis of glucosyl conjugates are also discussed. Preliminary results revealed that SA and the glucosyl conjugates are accumulated in Arabidopsis thaliana in a time dependent manner, accordingly to the up-regulation of SA-dependent defenses following P. syringae infection. This technique applied to plant hormones or fragment ions may be useful to obtain chemical family members of plant metabolites and help identify their contribution in the signaling of plant defenses.

Plants: biofactories for a sustainable future?

Depletion of oil reserves and the associated effects on climate change have prompted a re-examination of the use of plant biomass as a sustainable source of organic carbon for the large-scale production of chemicals and materials. While initial emphasis has been placed on biofuel production from edible plant sugars, the drive to reduce the competition between crop usage for food and non-food applications has prompted massive research efforts to access the less digestible saccharides in cell walls (lignocellulosics). This in turn has prompted an examination of the use of other plant-derived metabolites for the production of chemicals spanning the high-value speciality sectors through to platform intermediates required for bulk production. The associated science of biorefining, whereby all plant biomass can be used efficiently to derive such chemicals, is now rapidly developing around the world. However, it is clear that the heterogeneity and distribution of organic carbon between valuable products and waste streams are suboptimal. As an alternative, we now propose the use of synthetic biology approaches to 're-construct' plant feedstocks for optimal processing of biomass for non-food applications. Promising themes identified include re-engineering polysaccharides, deriving artificial organelles, and the reprogramming of plant signalling and secondary metabolism.