Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Arabidopsis Flowers Unlocked the Mechanism of Jasmonate Signaling

The Arabidopsis male-sterile phenotype has been a wonderful model for jasmonate action in plants. It has allowed us to identify transcription factors that control gene expression during stamen and pollen maturation and provided for the discovery of the JAZ repressor proteins and the mechanism of jasmonate signaling. More recently, it has revealed intriguing details of the spatial localization of jasmonate synthesis and perception in stamen tissues. The extensive and thoughtful application of protein–protein interaction assays to identify JAZ-interacting partners has led to a much richer appreciation of the mechanisms by which jasmonate integrates with the actions of other hormones to regulate plant growth and physiological responses. This integration is strikingly evident in stamen and pollen development in Arabidopsis, which requires the actions of many hormones. Just as importantly, it is now evident that jasmonate has very different actions during flower development and reproduction in other plant species. This integration and diversity of action indicates that many exciting discoveries remain to be made in this area of jasmonate hormone signaling and response.

De novo Assembly of the Pokeweed Genome Provides Insight Into Pokeweed Antiviral Protein (PAP) Gene Expression

Ribosome-inactivating proteins (RIPs) are RNA glycosidases thought to function in defense against pathogens. These enzymes remove purine bases from RNAs, including rRNA; the latter activity decreases protein synthesis in vitro, which is hypothesized to limit pathogen proliferation by causing host cell death. Pokeweed antiviral protein (PAP) is a RIP synthesized by the American pokeweed plant (Phytolacca americana). PAP inhibits virus infection when expressed in crop plants, yet little is known about the function of PAP in pokeweed due to a lack of genomic tools for this non-model species. In this work, we de novo assembled the pokeweed genome and annotated protein-coding genes. Sequencing comprised paired-end reads from a short-insert library of 83X coverage, and our draft assembly (N50 = 42.5 Kb) accounted for 74% of the measured pokeweed genome size of 1.3 Gb. We obtained 29,773 genes, 73% of which contained known protein domains, and identified several PAP isoforms. Within the gene models of each PAP isoform, a long 5' UTR intron was discovered, which was validated by RT-PCR and sequencing. Presence of the intron stimulated reporter gene expression in tobacco. To gain further understanding of PAP regulation, we complemented this genomic resource with expression profiles of pokeweed plants subjected to stress treatments [jasmonic acid (JA), salicylic acid, polyethylene glycol, and wounding]. Cluster analysis of the top differentially expressed genes indicated that some PAP isoforms shared expression patterns with genes involved in terpenoid biosynthesis, JA-mediated signaling, and metabolism of amino acids and carbohydrates. The newly sequenced promoters of all PAP isoforms contained cis-regulatory elements associated with diverse biotic and abiotic stresses. These elements mediated response to JA in tobacco, based on reporter constructs containing promoter truncations of PAP-I, the most abundant isoform. Taken together, this first genomic resource for the Phytolaccaceae plant family provides new insight into the regulation and function of PAP in pokeweed.

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

Approximately 29% of all vascular plant species are unable to establish an arbuscular mycorrhizal (AM) symbiosis. Despite this, AM fungi (Rhizophagus spp.) are enriched in the root microbiome of the nonhost Arabidopsis thaliana, and Arabidopsis roots become colonized when AM networks nurtured by host plants are available. Here, we investigated the nonhost-AM fungus interaction by analyzing transcriptional changes in Rhizophagus, Arabidopsis and the host plant Medicago truncatula while growing in the same mycorrhizal network. In early interaction stages, Rhizophagus activated the Arabidopsis strigolactone biosynthesis genes CCD7 and CCD8, suggesting that detection of AM fungi is not completely impaired. However, in colonized Arabidopsis roots, fungal nutrient transporter genes GintPT, GintAMT2, GintMST2 and GintMST4, essential for AM symbiosis, were not activated. RNA-seq transcriptome analysis pointed to activation of costly defenses in colonized Arabidopsis roots. Moreover, Rhizophagus colonization caused a 50% reduction in shoot biomass, but also led to enhanced systemic immunity against Botrytis cinerea. This suggests that early signaling between AM fungi and Arabidopsis is not completely impaired and that incompatibility appears at later interaction stages. Moreover, Rhizophagus-mediated defenses coincide with reduced Arabidopsis growth, but also with systemic disease resistance, highlighting the multifunctional role of AM fungi in host and nonhost interactions.

Characterization of Jasmonoyl-Isoleucine (JA-Ile) Hormonal Catabolic Pathways in Rice upon Wounding and Salt Stress

BACKGROUND

Jasmonate (JA) signaling and functions have been established in rice development and response to a range of biotic or abiotic stress conditions. However, information on the molecular actors and mechanisms underlying turnover of the bioactive jasmonoyl-isoleucine (JA-Ile) is very limited in this plant species.

RESULTS

Here we explored two gene families in rice in which some members were described previously in Arabidopsis to encode enzymes metabolizing JA-Ile hormone, namely cytochrome P450 of the CYP94 subfamily (CYP94, 20 members) and amidohydrolases (AH, 9 members). The CYP94D subclade, of unknown function, was most represented in the rice genome with about 10 genes. We used phylogeny and gene expression analysis to narrow the study to candidate members that could mediate JA-Ile catabolism upon leaf wounding used as mimic of insect chewing or seedling exposure to salt, two stresses triggering jasmonate metabolism and signaling. Both treatments induced specific transcriptional changes, along with accumulation of JA-Ile and a complex array of oxidized jasmonate catabolites, with some of these responses being abolished in the JASMONATE RESISTANT 1 (jar1) mutant. However, upon response to salt, a lower dependence on JAR1 was evidenced. Dynamics of CYP94B5, CYP94C2, CYP94C4 and AH7 transcripts matched best the accumulation of JA-Ile catabolites. To gain direct insight into JA-Ile metabolizing activities, recombinant expression of some selected genes was undertaken in yeast and bacteria. CYP94B5 was demonstrated to catalyze C12-hydroxylation of JA-Ile, whereas similarly to its Arabidopsis bi-functional homolog IAR3, AH8 performed cleavage of JA-Ile and auxin-alanine conjugates.

CONCLUSIONS

Our data shed light on two rice gene families encoding enzymes related to hormone homeostasis. Expression data along with JA profiling and functional analysis identifies likely actors of JA-Ile catabolism in rice seedlings. This knowledge will now enable to better understand the metabolic fate of JA-Ile and engineer optimized JA signaling under stress conditions.

Interplay between Jasmonic Acid, Phosphate Signaling and the Regulation of Glycerolipid Homeostasis in Arabidopsis

Jasmonic acid (JA) biosynthesis and signaling are activated in Arabidopsis cultivated in phosphate (Pi) deprived conditions. This activation occurs mainly in photosynthetic tissues and is less important in roots. In leaves, the enhanced biosynthesis of JA coincides with membrane glycerolipid remodeling triggered by the lack of Pi. We addressed the possible role of JA on the dynamics and magnitude of glycerolipid remodeling in response to Pi deprivation and resupply. Based on combined analyses of gene expression, JA biosynthesis and glycerolipid remodeling in wild-type Arabidopsis and in the coi1-16 mutant, JA signaling seems important in the determination of the basal levels of phosphatidylcholine, phosphatidic acid (PA), monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol. JA impact on MGDG steady state level and fluctuations seem contradictory. In the coi1-16 mutant, the steady state level of MGDG is higher, possibly due to a higher level of PA in the mutant, activating MGD1, and to an increased expression of MGD3. These results support a possible impact of JA in limiting the overall content of this lipid. Concerning lipid variations, upon Pi deprivation, JA seems rather associated with a specific MGDG increase. Following Pi resupply, whereas the expression of glycerolipid remodeling genes returns to basal level, JA biosynthesis and signaling genes are still upregulated, likely due to a JA-induced positive feedback remaining active. Distinct impacts on enzymes synthesizing MGDG, that is, downregulating MGD3, possibly activating MGD1 expression and limiting the activation of MGD1 via PA, might allow JA playing a role in a sophisticated fine tuning of galactolipid variations.

Proteomic Analysis of MeJa-Induced Defense Responses in Rice against Wounding

The role of jasmonates in defense priming has been widely recognized. Priming is a physiological process by which a plant exposed to low doses of biotic or abiotic elicitors activates faster and/or stronger defense responses when subsequently challenged by a stress. In this work, we investigated the impact of MeJA-induced defense responses to mechanical wounding in rice (Oryza sativa). The proteome reprogramming of plants treated with MeJA, wounding or MeJA+wounding has been in-depth analyzed by using a combination of high throughput profiling techniques and bioinformatics tools. Gene Ontology analysis identified protein classes as defense/immunity proteins, hydrolases and oxidoreductases differentially enriched by the three treatments, although with different amplitude. Remarkably, proteins involved in photosynthesis or oxidative stress were significantly affected upon wounding in MeJA-primed plants. Although these identified proteins had been previously shown to play a role in defense responses, our study revealed that they are specifically associated with MeJA-priming. Additionally, we also showed that at the phenotypic level MeJA protects plants from oxidative stress and photosynthetic damage induced by wounding. Taken together, our results add novel insight into the molecular actors and physiological mechanisms orchestrated by MeJA in enhancing rice plants defenses after wounding.

A Jasmonate Signaling Network Activates Root Stem Cells and Promotes Regeneration

Plants are sessile and have to cope with environmentally induced damage through modification of growth and defense pathways. How tissue regeneration is triggered in such responses and whether this involves stem cell activation is an open question. The stress hormone jasmonate (JA) plays well-established roles in wounding and defense responses. JA also affects growth, which is hitherto interpreted as a trade-off between growth and defense. Here, we describe a molecular network triggered by wound-induced JA that promotes stem cell activation and regeneration. JA regulates organizer cell activity in the root stem cell niche through the RBR-SCR network and stress response protein ERF115. Moreover, JA-induced ERF109 transcription stimulates CYCD6;1 expression, functions upstream of ERF115, and promotes regeneration. Soil penetration and response to nematode herbivory induce and require this JA-mediated regeneration response. Therefore, the JA tissue damage response pathway induces stem cell activation and regeneration and activates growth after environmental stress.

The Arabidopsis thaliana transcription factor MYB59 regulates calcium signalling during plant growth and stress response

Transcription factor MYB59 is involved in plant growth and stress responses by acting as negative regulator of Ca signalling and homeostasis. The Arabidopsis thaliana transcription factor MYB59 is induced by cadmium (Cd) and plays a key role in the regulation of cell cycle progression and root elongation, but its mechanism of action is poorly understood. We investigated the expression of MYB59 and differences between wild-type plants, the myb59 mutant and MYB59-overexpressing lines (obtained by transformation in the mutant genotype) during plant growth and in response to various forms of stress. We also compared the transcriptomes of wild-type and myb59 mutant plants to determine putative MYB59 targets. The myb59 mutant has longer roots, smaller leaves and smaller cells than wild-type plants and responds differently to stress in germination assay. Transcriptomic analysis revealed the upregulation in the myb59 mutant of multiple genes involved in calcium (Ca) homeostasis and signalling, including those encoding calmodulin-like proteins and Ca transporters. Notably, MYB59 was strongly induced by Ca deficiency, and the myb59 mutant was characterized by higher levels of cytosolic Ca in root cells and showed a modest alteration of Ca transient frequency in guard cells, associated with the absence of Ca-induced stomatal closure. These results indicate that MYB59 negatively regulates Ca homeostasis and signalling during Ca deficiency, thus controlling plant growth and stress responses.

Mining the natural genetic variation in Arabidopsis thaliana for adaptation to sequential abiotic and biotic stresses

In this genome-wide association study, we obtained novel insights into the genetic basis of the effect of herbivory or drought stress on the level of resistance against the fungus Botrytis cinerea. In nature, plants function in complex environments where they encounter different biotic and abiotic stresses individually, sequentially or simultaneously. The adaptive response to a single stress does not always reflect how plants respond to such a stress in combination with other stresses. To identify genetic factors that contribute to the plant's ability to swiftly adapt to different stresses, we investigated the response of Arabidopsis thaliana to infection by the necrotrophic fungus B. cinerea when preceded by Pieris rapae herbivory or drought stress. Using 346 natural A. thaliana accessions, we found natural genetic variation in the level of resistance against single B. cinerea infection. When preceded by herbivory or drought stress, the level of B. cinerea resistance was differentially influenced in the 346 accessions. To study the genetic factors contributing to the differential adaptation of A. thaliana to B. cinerea infection under multi-stress conditions, we performed a genome-wide association study supported by quantitative trait loci mapping and fine mapping with full genome sequences of 164 accessions. This yielded several genes previously associated with defense to B. cinerea and additional candidate genes with putative roles in the plant's adaptive response to a combination of herbivory, drought and B. cinerea infection.

RNA-Seq analysis reveals transcript diversity and active genes after common cutworm (Spodoptera litura Fabricius) attack in resistant and susceptible wild soybean lines

BACKGROUND

Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

RESULTS

The transcriptomes of two wild accessions (W11 and W99) with different resistance to CCW were analyzed at early- and late-induction time points. After induction, the susceptible accession W11 differentially expressed 1268 and 508 genes at the early and late time points, respectively. Compared with W11, the resistant accession W99 differentially expressed 1270 genes at the early time point and many more genes (2308) at the late time point. In total, 3836 non-redundant genes were identified in both lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) in W99 at the late time point were mostly associated with specific processes and pathways. Among the non-redundant genes, 146 genes were commonly up-regulated in the treatment condition compared with the control condition at the early- and late-induction time points in both accessions used in this experiment. Approximately 40% of the common DEGs were related to secondary metabolism, disease resistance, and signal transduction based on their putative function. Excluding the common DEGs, W99 expressed more unique DEGs than W11. Further analysis of the 3836 DEGs revealed that the induction of CCW not only up-regulated defense-related genes, including 37 jasmonic acid (JA)-related genes, 171 plant-pathogen-related genes, and 17 genes encoding protease inhibitors, but also down-regulated growth-related genes, including 35 photosynthesis-related genes, 48 nutrition metabolism genes, and 28 auxin metabolism genes. Therefore, representative defense-related and growth-related genes were chosen for binding site prediction via co-expression of transcription factors (TFs) and spatial expression pattern analyses. In total, 53 binding sites of 28 TFs were identified based on 3 defense-related genes and 3 growth-related genes. Phosphate transporter PT1, which is a representative growth-related gene, was transformed into soybean, and the transgenic soybean plants were susceptible to CCW.

CONCLUSIONS

In summary, we described transcriptome reprograming after herbivore induction in wild soybean, identified the susceptibility of growth-related genes, and provided new resources for the breeding of herbivore-resistant cultivated soybeans.

The Transcription Factor MYB59 Regulates K+/NO3 - Translocation in the Arabidopsis Response to Low K+ Stress

Potassium and nitrogen are essential nutrients for plant growth and development. Plants can sense potassium nitrate (K⁺/NO₃ ^-) levels in soils, and accordingly they adjust root-to-shoot K⁺/NO₃ ^- transport to balance the distribution of these ions between roots and shoots. In this study, we show that the transcription factorMYB59 maintains this balance by regulating the transcription of the Arabidopsis (Arabidopsis thaliana) Nitrate Transporter1.5 (NRT1.5)/ Nitrate Transporter/Peptide Transporter Family7.3 (NPF7.3) in response to low K⁺ (LK) stress. The myb59 mutant showed a yellow-shoot sensitive phenotype when grown on LK medium. Both the transcript and protein levels of NPF7.3 were remarkably reduced in the myb59 mutant. LK stress repressed transcript levels of both MYB59 and NPF7.3 The npf7.3 and myb59 mutants, as well as the npf7.3 myb59 double mutant, showed similar LK-sensitive phenotypes. Ion content analyses indicated that root-to-shoot K⁺/NO₃ ^- transport was significantly reduced in these mutants under LK conditions. Moreover, chromatin immunoprecipitation and electrophoresis mobility shift assay assays confirmed that MYB59 bound directly to the NPF7.3 promoter. Expression of NPF7.3 in root vasculature driven by the PHOSPHATE 1 promoter rescued the sensitive phenotype of both npf7.3 and myb59 mutants. Together, these data demonstrate that MYB59 responds to LK stress and directs root-to-shoot K⁺/NO₃ ^- transport by regulating the expression of NPF7.3 in Arabidopsis roots.

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

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

An EDS1 heterodimer signalling surface enforces timely reprogramming of immunity genes in Arabidopsis

Plant intracellular NLR receptors recognise pathogen interference to trigger immunity but how NLRs signal is not known. Enhanced disease susceptibility1 (EDS1) heterodimers are recruited by Toll-interleukin1-receptor domain NLRs (TNLs) to transcriptionally mobilise resistance pathways. By interrogating the Arabidopsis EDS1 ɑ-helical EP-domain we identify positively charged residues lining a cavity that are essential for TNL immunity signalling, beyond heterodimer formation. Mutating a single, conserved surface arginine (R493) disables TNL immunity to an oomycete pathogen and to bacteria producing the virulence factor, coronatine. Plants expressing a weakly active EDS1^R493A variant have delayed transcriptional reprogramming, with severe consequences for resistance and countering bacterial coronatine repression of early immunity genes. The same EP-domain surface is utilised by a non-TNL receptor RPS2 for bacterial immunity, indicating that the EDS1 EP-domain signals in resistance conferred by different NLR receptor types. These data provide a unique structural insight to early downstream signalling in NLR receptor immunity.

AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis

Dynamic environmental changes such as extreme temperature, water scarcity and high salinity affect plant growth, survival, and reproduction. Plants have evolved sophisticated regulatory mechanisms to adapt to these unfavorable conditions, many of which interface with plant hormone signaling pathways. Abiotic stresses alter the production and distribution of phytohormones that in turn mediate stress responses at least in part through hormone- and stress-responsive transcription factors. Among these, the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factors (AP2/ERFs) have emerged as key regulators of various stress responses, in which they also respond to hormones with improved plant survival during stress conditions. Apart from participation in specific stresses, AP2/ERFs are involved in a wide range of stress tolerance, enabling them to form an interconnected stress regulatory network. Additionally, many AP2/ERFs respond to the plant hormones abscisic acid (ABA) and ethylene (ET) to help activate ABA and ET dependent and independent stress-responsive genes. While some AP2/ERFs are implicated in growth and developmental processes mediated by gibberellins (GAs), cytokinins (CTK), and brassinosteroids (BRs). The involvement of AP2/ERFs in hormone signaling adds the complexity of stress regulatory network. In this review, we summarize recent studies on AP2/ERF transcription factors in hormonal and abiotic stress responses with an emphasis on selected family members in Arabidopsis. In addition, we leverage publically available Arabidopsis gene networks and transcriptome data to investigate AP2/ERF regulatory networks, providing context and important clues about the roles of diverse AP2/ERFs in controlling hormone and stress responses.

MYC2 Regulates the Termination of Jasmonate Signaling via an Autoregulatory Negative Feedback Loop

In tomato (Solanum lycopersicum), as in other plants, the immunity hormone jasmonate (JA) triggers genome-wide transcriptional changes in response to pathogen and insect attack. These changes are largely regulated by the basic helix-loop-helix (bHLH) transcription factor MYC2. The function of MYC2 depends on its physical interaction with the MED25 subunit of the Mediator transcriptional coactivator complex. Although much has been learned about the MYC2-dependent transcriptional activation of JA-responsive genes, relatively less studied is the termination of JA-mediated transcriptional responses and the underlying mechanisms. Here, we report an unexpected function of MYC2 in regulating the termination of JA signaling through activating a small group of JA-inducible bHLH proteins, termed MYC2-TARGETED BHLH1 (MTB1), MTB2, and MTB3. MTB proteins negatively regulate JA-mediated transcriptional responses via their antagonistic effects on the functionality of the MYC2-MED25 transcriptional activation complex. MTB proteins impair the formation of the MYC2-MED25 complex and compete with MYC2 to bind to its target gene promoters. Therefore, MYC2 and MTB proteins form an autoregulatory negative feedback circuit to terminate JA signaling in a highly organized manner. We provide examples demonstrating that gene editing tools such as CRISPR/Cas9 open up new avenues to exploit MTB genes for crop protection.

Overexpression of Arabidopsis OPR3 in Hexaploid Wheat (Triticum aestivum L.) Alters Plant Development and Freezing Tolerance

Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid (JA) in wheat growth, development, and responses to environmental stresses, we have generated transgenic bread wheat plants overexpressing Arabidopsis 12-OXOPHYTODIENOATE REDUCTASE 3 (AtOPR3), one of the key genes of the JA biosynthesis pathway. Analysis of transgenic plants showed that AtOPR3 overexpression affects wheat development, including germination, growth, flowering time, senescence, and alters tolerance to environmental stresses. Transgenic wheat plants with high AtOPR3 expression levels have increased basal levels of JA, and up-regulated expression of ALLENE OXIDE SYNTHASE, a jasmonate biosynthesis pathway gene that is known to be regulated by a positive feedback loop that maintains and boosts JA levels. Transgenic wheat plants with high AtOPR3 expression levels are characterized by delayed germination, slower growth, late flowering and senescence, and improved tolerance to short-term freezing. The work demonstrates that genetic modification of the jasmonate pathway is a suitable tool for the modulation of developmental traits and stress responses in wheat.

Combining QTL mapping with transcriptome and metabolome profiling reveals a possible role for ABA signaling in resistance against the cabbage whitefly in cabbage

Whiteflies are among the world's most significant agricultural pests and chemical insecticides are extensively used to reduce crop damage to acceptable levels. However, nearly all insecticides pose a threat to the environment and alternative control methods, such as breeding of crop varieties that are inherently insect-resistant, are needed. Previously, a strong source of plant-age dependent resistance to the cabbage whitefly (Aleyrodes proletella) has been identified in the modern white cabbage (Brassica oleracea var. capitata) variety Rivera. However, nothing is known about the molecular mechanisms or the genes involved in this resistance. In the present study, a multidisciplinary approach combining transcriptome and metabolome profiling with genetic mapping was used to identify the molecular players of whitefly resistance in cabbage. Transcriptome profiles of young (susceptible) and older (resistant) Rivera plants were analyzed using RNA sequencing. While many genes involved in general processes were differentially expressed between both ages, several defense-related processes were overrepresented in the transcriptome profile of older plants. Hormone measurements revealed that jasmonic acid (JA) levels decreased upon whitefly infestation at both plant ages. Interestingly, abscisic acid (ABA) levels showed contrasting effects in response to whitefly infestation: ABA levels were reduced in young plants but induced in older plants upon whitefly feeding. Auxin levels were significantly lower in older plants compared with young plants, independent of whitefly presence, while glucosinolate levels were higher. Additionally, whitefly performance was monitored in an F2 population derived from a cross between Rivera and the susceptible white cabbage variety Christmas Drumhead. Significant QTL intervals were mapped on chromosome 2 and 9 for oviposition rate and whitefly adult survival, respectively. Several genes that were higher expressed in older plants and located in the identified QTL intervals were orthologous to Arabidopsis genes that have been related to ABA signaling, suggesting a role for ABA in the regulation of resistance towards whiteflies. Our results show that combining different omics approaches is a useful strategy to identify candidate genes underlying insect resistance.

Transcriptome Analysis of Gene Expression Patterns Potentially Associated with Premature Senescence in Nicotiana tabacum L

Senescence affects the remobilization of nutrients and adaption of the plant to the environment. Combined stresses can result in premature senescence in plants which exist in the field. In this study, transcriptomic analysis was performed on mature leaves and leaves in three stages of premature senescence to understand the molecular mechanism. With progressive premature senescence, a declining chlorophyll (chl) content and an increasing malonaldehyde (MDA) content were observed, while plasmolysis and cell nucleus pyknosis occurred, mitochondria melted, thylakoid lamellae were dilated, starch grains in chloroplast decreased, and osmiophilic granules increased gradually. Moreover, in total 69 common differentially expressed genes (DEGs) in three stages of premature senescing leaves were found, which were significantly enriched in summarized Gene Ontology (GO) terms of membrane-bounded organelle, regulation of cellular component synthesis and metabolic and biosynthetic processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the plant hormone signal transduction pathway was significantly enriched. The common DEGs and four senescence-related pathways, including plant hormone signal transduction, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, and regulation of autophagy were selected to be discussed further. This work aimed to provide potential genes signaling and modulating premature senescence as well as the possible dynamic network of gene expression patterns for further study.

Genome-wide identification, classification and expression of lipoxygenase gene family in pepper

KEY MESSAGE

Lipoxygenases mediate important biological processes. Through comparative genomics, domain-scan analysis, sequence analysis, phylogenetic analysis, homology modelling and transcriptional analysis the lipoxygenase gene family of pepper (Capsicum annuum) has been identified. Lipoxygenases (LOXs) are non-heme, iron-containing dioxygenases playing a pivotal role in diverse biological processes in plants, including defence and development. Here, we exploited the recent sequencing of the pepper genome to investigate the LOX gene family in pepper. Two LOX classes are recognized, the 9- and 13-LOXs that oxygenate lipids at the 9th and 13th carbon atom, respectively. Using two main in-silico approaches, we identified a total of eight LOXs in pepper. Phylogenetic analysis classified four LOXs (CaLOX1, CaLOX3, CaLOX4 and CaLOX5) as 9-LOXs and four (CaLOX2, CaLOX6, CaLOX7 and CaLOX8) as 13-LOXs. Furthermore, sequence similarity/identity and subcellular localization analysis strengthen the classification predicted by phylogenetic analysis. Pivotal amino acids together with all domains and motifs are highly conserved in all pepper LOXs. Expression of 13-LOXs appeared to be more dynamic compared to 9-LOXs both in response to exogenous JA application and to thrips feeding. Bioinformatic and expression analyses predict the putative functions of two 13-LOXs, CaLOX6 and CaLOX7, in the biosynthesis of Green Leaf Volatiles, involved in indirect defence. The data are discussed in the context of LOX families in solanaceous plants and plants of other families.

Genome-wide association study reveals novel players in defense hormone crosstalk in Arabidopsis

Jasmonic acid (JA) regulates plant defenses against necrotrophic pathogens and insect herbivores. Salicylic acid (SA) and abscisic acid (ABA) can antagonize JA-regulated defenses, thereby modulating pathogen or insect resistance. We performed a genome-wide association (GWA) study on natural genetic variation in Arabidopsis thaliana for the effect of SA and ABA on the JA pathway. We treated 349 Arabidopsis accessions with methyl JA (MeJA), or a combination of MeJA and either SA or ABA, after which expression of the JA-responsive marker gene PLANT DEFENSIN1.2 (PDF1.2) was quantified as a readout for GWA analysis. Both hormones antagonized MeJA-induced PDF1.2 in the majority of the accessions but with a large variation in magnitude. GWA mapping of the SA- and ABA-affected PDF1.2 expression data revealed loci associated with crosstalk. GLYI4 (encoding a glyoxalase) and ARR11 (encoding an Arabidopsis response regulator involved in cytokinin signalling) were confirmed by T-DNA insertion mutant analysis to affect SA-JA crosstalk and resistance against the necrotroph Botrytis cinerea. In addition, At1g16310 (encoding a cation efflux family protein) was confirmed to affect ABA-JA crosstalk and susceptibility to Mamestra brassicae herbivory. Collectively, this GWA study identified novel players in JA hormone crosstalk with potential roles in the regulation of pathogen or insect resistance.

Assessing Flux Distribution Associated with Metabolic Specialization of Glandular Trichomes

Many aromatic plants accumulate mixtures of secondary (or specialized) metabolites in anatomical structures called glandular trichomes (GTs). Different GT types may also synthesize different mixtures of secreted metabolites, and this contributes to the enormous chemical diversity reported to occur across species. Over the past two decades, significant progress has been made in characterizing the genes and enzymes that are responsible for the unique metabolic capabilities of GTs in different lineages of flowering plants. Less is known about the processes that regulate flux distribution through precursor pathways toward metabolic end-products. We discuss here the results from a meta-analysis of genome-scale models that were developed to capture the unique metabolic capabilities of different GT types.

Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng

Ginseng (Panax ginseng C.A. Meyer) is one of the best-selling herbal medicines, with ginsenosides as its main pharmacologically active constituents. Although extensive chemical and pharmaceutical studies of these compounds have been performed, genome-wide studies of the basic helix-loop-helix (bHLH) transcription factors of ginseng are still limited. The bHLH transcription factor family is one of the largest transcription factor families found in eukaryotic organisms, and these proteins are involved in a myriad of regulatory processes. In our study, 169 bHLH transcription factor genes were identified in the genome of P. ginseng, and phylogenetic analysis indicated that these PGbHLHs could be classified into 24 subfamilies. A total of 21 RNA-seq data sets, including two sequencing libraries for jasmonate (JA)-responsive and 19 reported libraries for organ-specific expression analyses were constructed. Through a combination of gene-specific expression patterns and chemical contents, 6 PGbHLH genes from 4 subfamilies were revealed to be potentially involved in the regulation of ginsenoside biosynthesis. These 6 PGbHLHs, which had distinct target genes, were further divided into two groups depending on the absence of MYC-N structure. Our results would provide a foundation for understanding the molecular basis and regulatory mechanisms of bHLH transcription factor action in P. ginseng.

A Framework for Engineering Stress Resilient Plants Using Genetic Feedback Control and Regulatory Network Rewiring

Crop disease leads to significant waste worldwide, both pre- and postharvest, with subsequent economic and sustainability consequences. Disease outcome is determined both by the plants' response to the pathogen and by the ability of the pathogen to suppress defense responses and manipulate the plant to enhance colonization. The defense response of a plant is characterized by significant transcriptional reprogramming mediated by underlying gene regulatory networks, and components of these networks are often targeted by attacking pathogens. Here, using gene expression data from Botrytis cinerea-infected Arabidopsis plants, we develop a systematic approach for mitigating the effects of pathogen-induced network perturbations, using the tools of synthetic biology. We employ network inference and system identification techniques to build an accurate model of an Arabidopsis defense subnetwork that contains key genes determining susceptibility of the plant to the pathogen attack. Once validated against time-series data, we use this model to design and test perturbation mitigation strategies based on the use of genetic feedback control. We show how a synthetic feedback controller can be designed to attenuate the effect of external perturbations on the transcription factor CHE in our subnetwork. We investigate and compare two approaches for implementing such a controller biologically-direct implementation of the genetic feedback controller, and rewiring the regulatory regions of multiple genes-to achieve the network motif required to implement the controller. Our results highlight the potential of combining feedback control theory with synthetic biology for engineering plants with enhanced resilience to environmental stress.

Thrips advisor: exploiting thrips-induced defences to combat pests on crops

Plants have developed diverse defence mechanisms to ward off herbivorous pests. However, agriculture still faces estimated crop yield losses ranging from 25% to 40% annually. These losses arise not only because of direct feeding damage, but also because many pests serve as vectors of plant viruses. Herbivorous thrips (Thysanoptera) are important pests of vegetable and ornamental crops worldwide, and encompass virtually all general problems of pests: they are highly polyphagous, hard to control because of their complex lifestyle, and they are vectors of destructive viruses. Currently, control management of thrips mainly relies on the use of chemical pesticides. However, thrips rapidly develop resistance to these pesticides. With the rising demand for more sustainable, safer, and healthier food production systems, we urgently need to pinpoint the gaps in knowledge of plant defences against thrips to enable the future development of novel control methods. In this review, we summarize the current, rather scarce, knowledge of thrips-induced plant responses and the role of phytohormonal signalling and chemical defences in these responses. We describe concrete opportunities for breeding resistance against pests such as thrips as a prototype approach for next-generation resistance breeding.

Combinatorial Transcriptional Control of Plant Specialized Metabolism

Plants produce countless specialized compounds of diverse chemical nature and biological activities. Their biosynthesis often exclusively occurs either in response to environmental stresses or is limited to dedicated anatomical structures. In both scenarios, regulation of biosynthesis appears to be mainly controlled at the transcriptional level, which is generally dependent on a combined interplay of DNA-related mechanisms and the activity of transcription factors that may act in a combinatorial manner. How environmental and developmental cues are integrated into a coordinated cell type-specific stress response has only partially been unraveled so far. Building on the available examples from (metabolic) gene expression, here we propose theoretical models of how this integration of signals may occur at the level of transcriptional control.

Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis

Plants use diverse mechanisms influenced by vast regulatory networks of indefinite scale to adapt to their environment. These regulatory networks have an unknown potential for epistasis between genes within and across networks. To test for epistasis within an adaptive trait genetic network, we generated and tested 47 Arabidopsis thaliana double mutant combinations for 20 transcription factors, which all influence the accumulation of aliphatic glucosinolates, the defense metabolites that control fitness. The epistatic combinations were used to test if there is more or less epistasis depending on gene membership within the same or different phenotypic subnetworks. Extensive epistasis was observed between the transcription factors, regardless of subnetwork membership. Metabolite accumulation displayed antagonistic epistasis, suggesting the presence of a buffering mechanism. Epistasis affecting enzymatic estimated activity was highly conditional on the tissue and environment and shifted between both antagonistic and synergistic forms. Transcriptional analysis showed that epistasis shifts depend on how the trait is measured. Because the 47 combinations described here represent a small sampling of the potential epistatic combinations in this genetic network, there is potential for significantly more epistasis. Additionally, the main effect of the individual gene was not predictive of the epistatic effects, suggesting that there is a need for further studies.

Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists

Below ground, microbe-associated molecular patterns (MAMPs) of root-associated microbiota can trigger costly defenses at the expense of plant growth. However, beneficial rhizobacteria, such as Pseudomonas simiae WCS417, promote plant growth and induce systemic resistance without being warded off by local root immune responses. To investigate early root responses that facilitate WCS417 to exert its plant-beneficial functions, we performed time series RNA-Seq of Arabidopsis roots in response to live WCS417 and compared it with MAMPs flg22⁴¹⁷ (from WCS417), flg22^Pa (from pathogenic Pseudomonas aeruginosa) and fungal chitin. The MAMP transcriptional responses differed in timing, but displayed a large overlap in gene identity. MAMP-upregulated genes are enriched for genes with functions in immunity, while downregulated genes are enriched for genes related to growth and development. Although 74% of the transcriptional changes inflicted by live WCS417 overlapped with the flg22⁴¹⁷ profile, WCS417 actively suppressed more than half of the MAMP-triggered transcriptional responses, possibly to allow the establishment of a mutually beneficial interaction with the host root. Interestingly, the sector of the flg22⁴¹⁷ -repressed transcriptional network that is not affected by WCS417 has a strong auxin signature. Using auxin response mutant tir1afb2afb3, we demonstrate a dual role for auxin signaling in finely balancing growth-promoting and defense-eliciting activities of beneficial microbes in plant roots.

Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets

Statistical and machine learning (ML)-based methods have recently advanced in construction of gene regulatory network (GRNs) based on high-throughput biological datasets. GRNs underlie almost all cellular phenomena; hence, comprehensive GRN maps are essential tools to elucidate gene function, thereby facilitating the identification and prioritization of candidate genes for functional analysis. High-throughput gene expression datasets have yielded various statistical and ML-based algorithms to infer causal relationship between genes and decipher GRNs. This review summarizes the recent advancements in the computational inference of GRNs, based on large-scale transcriptome sequencing datasets of model plants and crops. We highlight strategies to select contextual genes for GRN inference, and statistical and ML-based methods for inferring GRNs based on transcriptome datasets from plants. Furthermore, we discuss the challenges and opportunities for the elucidation of GRNs based on large-scale datasets obtained from emerging transcriptomic applications, such as from population-scale, single-cell level, and life-course transcriptome analyses.