Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Transcriptome analysis of the role of autophagy in plant response to heat stress

Autophagy plays a critical role in plant heat tolerance in part by targeting heat-induced nonnative proteins for degradation. Autophagy also regulates metabolism, signaling and other processes and it is less understood how the broad function of autophagy affects plant heat stress responses. To address this issue, we performed transcriptome profiling of Arabidopsis wild-type and autophagy-deficient atg5 mutant in response to heat stress. A large number of differentially expressed genes (DEGs) were identified between wild-type and atg5 mutant even under normal conditions. These DEGs are involved not only in metabolism, hormone signaling, stress responses but also in regulation of nucleotide processing and DNA repair. Intriguingly, we found that heat treatment resulted in more robust changes in gene expression in wild-type than in the atg5 mutant plants. The dampening effect of autophagy deficiency on heat-regulated gene expression was associated with already altered expression of many heat-regulated DEGs prior to heat stress in the atg5 mutant. Altered expression of a large number of genes involved in metabolism and signaling in the autophagy mutant prior to heat stress may affect plant response to heat stress. Furthermore, autophagy played a positive role in the expression of defense- and stress-related genes during the early stage of heat stress responses but had little effect on heat-induced expression of heat shock genes. Taken together, these results indicate that the broad role of autophagy in metabolism, cellular homeostasis and other processes can also potentially affect plant heat stress responses and heat tolerance.

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean

Throughout the growing season, crops experience a multitude of short periods of various abiotic stresses. These stress events have long-term impacts on plant performance and yield. It is imperative to improve our understanding of the genes and biological processes underlying plant stress tolerance to mitigate end of season yield loss. The majority of studies examining transcriptional changes induced by stress focus on single stress events. Few studies have been performed in model or crop species to examine transcriptional responses of plants exposed to repeated or sequential stress exposure, which better reflect field conditions. In this study, we examine the transcriptional profile of soybean plants exposed to iron deficiency stress followed by phosphate deficiency stress (-Fe-Pi). Comparing this response to previous studies, we identified a core suite of genes conserved across all repeated stress exposures (-Fe-Pi, -Fe-Fe, -Pi-Pi). Additionally, we determined transcriptional response to sequential stress exposure (-Fe-Pi) involves genes usually associated with reproduction, not stress responses. These findings highlight the plasticity of the plant transcriptome and the complexity of unraveling stress response pathways.

Regulation of Sixth Seminal Root Formation by Jasmonate in Triticum aestivum L

A well-developed root system is an important characteristic of crop plants, which largely determines their productivity, especially under conditions of water and nutrients deficiency. Being Poaceous, wheat has more than one seminal root. The number of grown seminal roots varies in different wheat accessions and is regulated by environmental factors. Currently, the molecular mechanisms determining the number of germinated seminal roots remain poorly understood. The analysis of the root system development in germinating seeds of genetically modified hexaploid wheat plants with altered activity of jasmonate biosynthesis pathway and seeds exogenously treated with methyl jasmonate revealed the role of jasmonates in the regulation of sixth seminal root development. This regulatory effect strongly depends on the jasmonate concentration and the duration of the exposure to this hormone. The maximum stimulatory effect of exogenously applied methyl jasmonate on the formation of the sixth seminal root was achieved at 200 μM concentration after 48 h of treatment. Further increase in concentration and exposure time does not increase the stimulating effect. While 95% of non-transgenic plants under non-stress conditions possess five or fewer seminal roots, the number of plants with developed sixth seminal root reaches up to 100% when selected transgenic lines are treated with methyl jasmonate.

PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

BACKGROUND

Valsa canker is a serious disease in the stem of Malus sieversii, caused by Valsa mali. However, little is known about the global response mechanism in M. sieversii to V. mali infection.

RESULTS

Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen V. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8139 were DETs. Total 1336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of V. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage.

CONCLUSIONS

The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to V. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen V. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

Heat-Induced Oxidation of the Nuclei and Cytosol

The concept that heat stress (HS) causes a large accumulation of reactive oxygen species (ROS) is widely accepted. However, the intracellular compartmentation of ROS accumulation has been poorly characterized. We therefore used redox-sensitive green fluorescent protein (roGFP2) to provide compartment-specific information on heat-induced redox changes of the nuclei and cytosol of Arabidopsis leaf epidermal and stomatal guard cells. We show that HS causes a large increase in the degree of oxidation of both compartments, causing large shifts in the glutathione redox potentials of the cells. Heat-induced increases in the levels of the marker transcripts, heat shock protein (HSP)101, and ascorbate peroxidase (APX)2 were maximal after 15 min of the onset of the heat treatment. RNAseq analysis of the transcript profiles of the control and heat-treated seedlings revealed large changes in transcripts encoding HSPs, mitochondrial proteins, transcription factors, and other nuclear localized components. We conclude that HS causes extensive oxidation of the nucleus as well as the cytosol. We propose that the heat-induced changes in the nuclear redox state are central to both genetic and epigenetic control of plant responses to HS.

Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane

Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3'H1, C3'H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.

Multiple levels of crosstalk in hormone networks regulating plant defense

Plant hormones are essential for regulating the interactions between plants and their complex biotic and abiotic environments. Each hormone initiates a specific molecular pathway and these different hormone pathways are integrated in a complex network of synergistic, antagonistic and additive interactions. This inter-pathway communication is called hormone crosstalk. By influencing the immune network topology, hormone crosstalk is essential for tailoring plant responses to diverse microbes and insects in diverse environmental and internal contexts. Crosstalk provides robustness to the immune system but also drives specificity of induced defense responses against the plethora of biotic interactors. Recent advances in dry-lab and wet-lab techniques have greatly enhanced our understanding of the broad-scale effects of hormone crosstalk on immune network functioning and have revealed underlying principles of crosstalk mechanisms. Molecular studies have demonstrated that hormone crosstalk is modulated at multiple levels of regulation, such as by affecting protein stability, gene transcription and hormone homeostasis. These new insights into hormone crosstalk regulation of plant defense are reviewed here, with a focus on crosstalk acting on the jasmonic acid pathway in Arabidopsis thaliana, highlighting the transcription factors MYC2 and ORA59 as major targets for modulation by other hormones.

Architecture and Dynamics of the Wounding-Induced Gene Regulatory Network During the Oolong Tea Manufacturing Process (Camellia sinensis)

Understanding extensive transcriptional reprogramming events mediated by wounding during the oolong tea manufacturing process is essential for improving oolong tea quality. To improve our comprehension of the architecture of the wounding-induced gene regulatory network, we systematically analyzed the high-resolution transcriptomic and metabolomic data from wounding-treated (after turnover stage) tea leaves at 11 time points over a 220-min period. The results indicated that wounding activates a burst of transcriptional activity within 10 min and that the temporal expression patterns over time could be partitioned into 18 specific clusters with distinct biological processes. The transcription factor (TF) activity linked to the TF binding motif participated in specific biological processes within different clusters. A chronological model of the wounding-induced gene regulatory network provides insight into the dynamic transcriptional regulation event after wounding treatment (the turnover stage). Time series data of wounding-induced volatiles reveal the scientific significance of resting for a while after wounding treatment during the actual manufacturing process of oolong tea. Integrating information-rich expression data with information on volatiles allowed us to identify many high-confidence TFs participating in aroma formation regulation after wounding treatment by using weighted gene co-expression network analysis (WGCNA). Collectively, our research revealed the complexity of the wounding-induced gene regulatory network and described wounding-mediated dynamic transcriptional reprogramming events, serving as a valuable theoretical basis for the quality formation of oolong tea during the post-harvest manufacturing process.

Priming by Timing: Arabidopsis thaliana Adjusts Its Priming Response to Lepidoptera Eggs to the Time of Larval Hatching

Plants can respond to eggs laid by herbivorous insects on their leaves by preparing (priming) their defense against the hatching larvae. Egg-mediated priming of defense is known for several plant species, including Brassicaceae. However, it is unknown yet for how long the eggs need to remain on a plant until a primed defense state is reached, which is ecologically manifested by reduced performance of the hatching larvae. To address this question, we used Arabidopsis thaliana, which carried eggs of the butterfly Pieris brassicae for 1-6 days prior to exposure to larval feeding. Our results show that larvae gained less biomass the longer the eggs had previously been on the plant. The strongest priming effect was obtained when eggs had been on the plant for 5 or 6 days, i.e., for (almost) the entire development time of the Pieris embryo inside the egg until larval hatching. Transcript levels of priming-responsive genes, levels of jasmonic acid-isoleucine (JA-Ile), and of the egg-inducible phytoalexin camalexin increased with the egg exposure time. Larval performance studies on mutant plants revealed that camalexin is dispensable for anti-herbivore defense against P. brassicae larvae, whereas JA-Ile - in concert with egg-induced salicylic acid (SA) - seems to be important for signaling egg-mediated primed defense. Thus, A. thaliana adjusts the kinetics of its egg-primed response to the time point of larval hatching. Hence, the plant is optimally prepared just in time prior to larval hatching.

Breaking Bad News: Dynamic Molecular Mechanisms of Wound Response in Plants

Recognition and repair of damaged tissue are an integral part of life. The failure of cells and tissues to appropriately respond to damage can lead to severe dysfunction and disease. Therefore, it is essential that we understand the molecular pathways of wound recognition and response. In this review, we aim to provide a broad overview of the molecular mechanisms underlying the fate of damaged cells and damage recognition in plants. Damaged cells release the so-called damage associated molecular patterns to warn the surrounding tissue. Local signaling through calcium (Ca2+), reactive oxygen species (ROS), and hormones, such as jasmonic acid, activates defense gene expression and local reinforcement of cell walls to seal off the wound and prevent evaporation and pathogen colonization. Depending on the severity of damage, Ca2+, ROS, and electrical signals can also spread throughout the plant to elicit a systemic defense response. Special emphasis is placed on the spatiotemporal dimension in order to obtain a mechanistic understanding of wound signaling in plants.

Ménage à Trois: Unraveling the Mechanisms Regulating Plant-Microbe-Arthropod Interactions

Plant-microbe-arthropod (PMA) three-way interactions have important implications for plant health. However, our poor understanding of the underlying regulatory mechanisms hampers their biotechnological applications. To this end, we searched for potential common patterns in plant responses regarding taxonomic groups or lifestyles. We found that most signaling modules regulating two-way interactions also operate in three-way interactions. Furthermore, the relative contribution of signaling modules to the final plant response cannot be directly inferred from two-way interactions. Moreover, our analyses show that three-way interactions often result in the activation of additional pathways, as well as in changes in the speed or intensity of defense activation. Thus, detailed, basic knowledge of plant-microbe-arthropod regulation will be essential for the design of environmentally friendly crop management strategies.

High-resolution temporal transcriptome sequencing unravels ERF and WRKY as the master players in the regulatory networks underlying sesame responses to waterlogging and recovery

Major crops are generally sensitive to waterlogging, but our limited understanding of the waterlogging gene regulatory network hinders the efforts to develop waterlogging-tolerant cultivars. We generated high-resolution temporal transcriptome data from root of two contrasting sesame genotypes over a 48 h period waterlogging and drainage treatments. Three distinct chronological transcriptional phases were identified, including the early-waterlogging, late-waterlogging and drainage responses. We identified 47 genes representing the core waterlogging-responsive genes. Waterlogging/drainage-induced transcriptional changes were mainly driven by ERF and WRKY transcription factors (TF). The major difference between the two genotypes resides in the early transcriptional phase. A chronological transcriptional network model predicting putative causal regulations between TFs and downstream waterlogging-responsive genes was constructed and some interactions were validated through yeast one-hybrid assay. Overall, this study unveils the architecture and dynamic regulation of the waterlogging/drainage response in a non-model crop and helps formulate new hypotheses on stress sensing, signaling and sophisticated adaptive responses.

OsJAZ9 overexpression modulates jasmonic acid biosynthesis and potassium deficiency responses in rice

Enhanced bioactive JA (JA-Ile) accumulation in OsJAZ9 overexpressing rice helps plants tolerate K deficiency. Potassium (K) represents up to 10% of the plant's total dry biomass, and its deficiency makes plants highly susceptible to both abiotic and biotic stresses. K shortage results in the inhibition of root and shoots growth, but the underlying mechanism of this response is unclear. Our RNA-Seq and qPCR analysis suggested leading roles for JA pathway genes under K deficiency in rice. Notably, K deficiency and JA application produced similar phenotypic and transcriptional responses. Here, we integrated molecular, physiological and morphological studies to analyze the role of OsJAZ9 in JA homeostasis and K deficiency responses. We raised OsJAZ9 over-expression, knockdown, transcriptional reporter, translational reporter and C-terminal deleted translational reporter lines in rice to establish the role of JA signaling in K ion homeostasis. JA profiling revealed significantly increased JA-Ile levels in OsJAZ9 OE lines under K deficiency. Furthermore, we established that OsJAZ9 overexpression and knockdown result in K deficiency tolerance and sensitivity, respectively, by modulating various K transporters and root system architecture. Our data provide evidence on the crucial roles of OsJAZ9 for improving K deficiency tolerance in rice by altering JA levels and JA responses.

Effects of exogenous methyl jasmonate on the synthesis of endogenous jasmonates and the regulation of photosynthesis in citrus

Methyl jasmonate (MeJA) is an airborne signaling phytohormone that can induce changes in endogenous jasmonates (JAs) and cause photosynthetic responses. However, the response of these two aspects of citrus plants at different MeJA concentrations is still unclear. Four MeJA concentrations were used in two citrus varieties, Huangguogan (C. reticulata × C. sinensis) and Shiranuhi [C. reticulata × (C. reticulata × C. sinensis)], to investigate the effects of MeJA dose on the endogenous JAs pathway and photosynthetic capacity. We observed that MeJA acted in a dose-dependent manner, and its stimulation in citrus leaves showed a bidirectional character at different concentrations. This work demonstrates that MeJA at only a concentration of 2.2 mM or less contributed to the activation of magnesium protoporphyrin IX methyltransferase (ChlM, EC 2.1.1.11) and protochlorophyllide oxidoreductase (POR, EC 1.3.1.11) and the simultaneous accumulation of Chl a and Chl b, which in turn contributed to an improved photosynthetic capacity and PSII photochemistry efficiency of citrus. Meanwhile, the inhibition of endogenous JAs synthesis by exogenous MeJA was observed. This was achieved by reducing the ratio of monogalactosyl diacylglycerol (MGDG) to diagalactosyl diacylglycerol (DGDG) and inhibiting the activities of key enzymes in JAs synthesis, especially 12-oxo-phytodienoic acid reductase (OPR, EC 1.3.1.42). Another noteworthy finding is that there may exist a JA-independent pathway that could regulate 12-oxo-phytodienoic acid (OPDA) synthesis. This study jointly analyzed the internal hormone regulation mechanism and the external physiological response, as well as revealed the effects of exogenous MeJA on promoting the photosynthesis and inhibiting the endogenous JAs synthesis.

Viral Perturbation of Alternative Splicing of a Host Transcript Benefits Infection

Pathogens disturb alternative splicing patterns of infected eukaryotic hosts. However, in plants it is unknown if this is incidental to infection or represents a pathogen-induced remodeling of host gene expression needed to support infection. Here, we compared changes in transcription and protein accumulation with changes in transcript splicing patterns in maize (Zea mays) infected with the globally important pathogen sugarcane mosaic virus (SCMV). Our results suggested that changes in alternative splicing play a major role in determining virus-induced proteomic changes. Focusing on maize phytoene synthase1 (ZmPSY1), which encodes the key regulatory enzyme in carotenoid biosynthesis, we found that although SCMV infection decreases total ZmPSY1 transcript accumulation, the proportion of splice variant T001 increases by later infection stages so that ZmPSY1 protein levels are maintained. We determined that ZmPSY1 has two leaf-specific transcripts, T001 and T003, distinguished by differences between the respective 3'-untranslated regions (UTRs). The shorter 3'-UTR of T001 makes it the more efficient mRNA. Nonsense ZmPSY1 mutants or virus-induced silencing of ZmPSY1 expression suppressed SCMV accumulation, attenuated symptoms, and decreased chloroplast damage. Thus, ZmPSY1 acts as a proviral host factor that is required for virus accumulation and pathogenesis. Taken together, our findings reveal that SCMV infection-modulated alternative splicing ensures that ZmPSY1 synthesis is sustained during infection, which supports efficient virus infection.

Identification, genomic organization, and expression profiles of single C2H2 zinc finger transcription factors in tomato (Solanum lycopersicum)

C2H2 zinc finger proteins (ZFPs) play essential roles in leaf morphogenesis and floral development, as well as heat stress response and trichome formation, which activate or inhibit gene transcription mainly through interactions with nucleic acids, such as single-strand DNA, RNA binding or RNA/DNA bidirectional binding, and protein interaction. Single C2H2 ZFPs is the subfamily of ZFPs, but little of single C2H2 ZFP family is known in tomato. In this study, we identified 30 single ZFP genes in tomato using bioinformatics-based methods. Gene structures, phylogeny, conserved motifs, cis-element of promoter, chromosomal localization, gene duplication, and expression patterns of these single C2H2 ZFP genes were analyzed. Sequence analysis showed that most single C2H2 ZFP genes possessed only one exon, except for SlC1-liZFP1 and SlC1-liZFP2. These single C2H2 ZFP genes were asymmetrically distributed on 10 chromosomes, excluding 2 and 12 chromosomes. In addition, 24 of these genes were predicated to have experienced segmental duplication. Cis-element prediction indicated that many important elements were located in the putative promoter regions, like light and gibberellic acid (GA)-responsive elements. The expression profiles of these genes in different tissues and various hormones and stress treatment were further analyzed. Many genes were lowly expressed in all tissues, whereas some were specifically expressed in certain tissues, like SlC1-liZFP2 in young leaves, and SlC1-liZFP15 in fruits. Furthermore, these genes could also be induced by several hormones and stresses, including IAA, ETH, GA, cold, and drought. This study sets a good foundation for further characterizing the biological roles of single C2H2 ZFP genes in tomato.

Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana

BACKGROUND

Plants have adapted to survive under adverse conditions or exploit favorable conditions in response to their environment as sessile creatures. In a way of plant adaptation, plant hormones have been evolved to efficiently use limited resources. Plant hormones including auxin, jasmonic acid, salicylic acid, and ethylene have been studied to reveal their role in plant adaptation against their environment by phenotypic observation with experimental design such as mutation on hormone receptors and treatment / non-treatment of plant hormones along with other environmental conditions. With the development of Next Generation Sequencing (NGS) technology, it became possible to score the total gene expression of the sampled plants and estimate the degree of effect of plant hormones in gene expression. This allowed us to infer the signaling pathway through plant hormones, which greatly stimulated the study of functional genomics using mutants. Due to the continued development of NGS technology and analytical techniques, many plant hormone-related studies have produced and accumulated NGS-based data, especially RNAseq data have been stored in the sequence read archive represented by NCBI, EBI, and DDBJ.

DESCRIPTION

Here, hormone treatment RNAseq data of Arabidopsis (Col0), wild-type genotype, were collected with mock, SA, and MeJA treatments. The genes affected by hormones were identified through a machine learning approach. The degree of expression of the affected gene was quantified, visualized in boxplot using d3 (data-driven-document), and the database was built by Django.

CONCLUSION

Using this database, we created a web application ( http://pgl.gnu.ac.kr/hormoneDB/ ) that lists hormone-related or hormone-affected genes and visualizes the boxplot of the gene expression of selected genes. This web application eventually aids the functional genomics researchers who want to gather the cases of the gene responses by the hormones.

Network-based approaches for understanding gene regulation and function in plants

Expression reprogramming directed by transcription factors is a primary gene regulation underlying most aspects of the biology of any organism. Our views of how gene regulation is coordinated are dramatically changing thanks to the advent and constant improvement of high-throughput profiling and transcriptional network inference methods: from activities of individual genes to functional interactions across genes. These technical and analytical advances can reveal the topology of transcriptional networks in which hundreds of genes are hierarchically regulated by multiple transcription factors at systems level. Here we review the state of the art of experimental and computational methods used in plant biology research to obtain large-scale datasets and model transcriptional networks. Examples of direct use of these network models and perspectives on their limitations and future directions are also discussed.

MYC2-Activated TRICHOME BIREFRINGENCE-LIKE37 Acetylates Cell Walls and Enhances Herbivore Resistance

O-Acetylation of polysaccharides predominantly modifies plant cell walls by changing the physicochemical properties and, consequently, the structure and function of the cell wall. Expression regulation and specific function of cell wall-acetylating enzymes remain to be fully understood. In this report, we cloned a previously identified stunted growth mutant named sucrose uncoupled1 (sun1) in Arabidopsis (Arabidopsis thaliana). SUN1 encodes a member of the TRICHOME BIREFRINGEN-LIKE family, AtTBL37 AtTBL37 is highly expressed in fast-growing plant tissues and encodes a Golgi apparatus-localized protein that regulates secondary cell wall thickening and acetylation. In sun1, jasmonate signaling and expression of downstream chemical defense genes, including VEGETATIVE STORAGE PROTEIN1 and BRANCHED-CHAIN AMINOTRANSFERASE4, are increased but, unexpectedly, sun1 is more susceptible to insect feeding. The central transcription factor in jasmonate signaling, MYC2, binds to and induces AtTBL37 expression. MYC2 also promotes the expression of many other TBLs Moreover, MYC activity enhances cell wall acetylation. Overexpression of AtTBL37 in the myc2-2 background reduces herbivore feeding. Our study highlights the role of O-acetylation in controlling plant cell wall properties, plant development, and herbivore defense.

MYC2, MYC3, and MYC4 function additively in wounding-induced jasmonic acid biosynthesis and catabolism

Jasmonic acid (JA) plays a critical role in plant defenses against insects and necrotrophic fungi. Wounding or lepidopteran insect feeding rapidly induces a burst of JA in plants, which usually reaches peak values within 1 to 2 h. The induced JA is converted to JA-Ile and perceived by the COI1-JAZ co-receptor, leading to activation of the transcription factors MYC2 and its homologs, which further induce JA-responsive genes. Although much is known about JA biosynthesis and catabolism enzymes and JA signaling, how JA biosynthesis and catabolism are regulated remain unclear. Here, we show that in Arabidopsis thaliana MYC2 functions additively with MYC3 and MYC4 to regulate wounding-induced JA accumulation by directly binding to the promoters of genes function in JA biosynthesis and catabolism to promote their transcription. MYC2 also controls the transcription of JAV1 and JAM1, which are key factors controlling JA biosynthesis and catabolism, respectively. In addition, we also found that MYC2 could bind to the MYC2 promoter and self-inhibit its own expression. This work illustrates the central role of MYC2/3/4 in controlling wounding-induced JA accumulation by regulating the transcription of genes involved in JA biosynthesis and catabolism.

RcMYB84 and RcMYB123 mediate jasmonate-induced defense responses against Botrytis cinerea in rose (Rosa chinensis)

Jasmonates (JAs) are important for pathogen resistance in many plants, but the role of these phytohormones in fungal pathogen resistance in rose is unclear. Here, we determined that exogenous application of methyl jasmonate increased resistance to the important fungal pathogen Botrytis cinerea in Rosa chinensis 'Old blush', whereas silencing the JA biosynthetic pathway gene Allene Oxide Synthase (AOS) and JA co-receptor gene CORONATINE INSENSITIVE 1 (COI1) suppressed this response. Transcriptome profiling identified various MYB transcription factor genes that responded to both JA and B. cinerea treatment. Silencing Ri-RcMYB84/Ri-RcMYB123 increased the susceptibility of rose plants to B. cinerea and inhibited the protective effects of JA treatment, confirming the crucial roles of these genes in JA-induced responses to B. cinerea. JAZ1, a key repressor of JA signaling, directly interacts with RcMYB84 and RcMYB123 to deplete their free pools. The JAZ1-RcMYB84 complex binds to the RcMYB123 promoter via the CAACTG motifs to block its transcription. Upon JA treatment, the expression of RcMYB123 is de-repressed, and free forms of RcMYB84 and RcMYB123 are released due to JAZ1 degradation, thereby activating the defense responses of plants to B. cinerea. These findings shed light on the molecular mechanisms underlying JA-induced pathogen resistance in roses.

Coronatine is more potent than jasmonates in regulating Arabidopsis circadian clock

Recent studies establish a crucial role of the circadian clock in regulating plant defense against pathogens. Whether pathogens modulate host circadian clock as a potential strategy to suppress host innate immunity is not well understood. Coronatine is a toxin produced by the bacterial pathogen Pseudomonas syringae that is known to counteract Arabidopsis defense through mimicking defense signaling molecules, jasmonates (JAs). We report here that COR preferentially suppresses expression of clock-related genes in high throughput gene expression studies, compared with the plant-derived JA molecule methyl jasmonate (MJ). COR treatment dampens the amplitude and lengthens the period of all four reporters tested while MJ and another JA agonist JA-isoleucine (JA-Ile) only affect some reporters. COR, MJ, and JA-Ile act through the canonical JA receptor COI1 in clock regulation. These data support a stronger role of the pathogen-derived molecule COR than plant-derived JA molecules in regulating Arabidopsis clock. Further study shall reveal mechanisms underlying COR regulation of host circadian clock.

Stress- and pathway-specific impacts of impaired jasmonoyl-isoleucine (JA-Ile) catabolism on defense signalling and biotic stress resistance

Jasmonate synthesis and signalling are essential for plant defense upregulation upon herbivore or microbial attacks. Stress-induced accumulation of jasmonoyl-isoleucine (JA-Ile), the bioactive hormonal form triggering transcriptional changes, is dynamic and transient because of the existence of potent removal mechanisms. Two JA-Ile turnover pathways operate in Arabidopsis, consisting in cytochrome P450 (CYP94)-mediated oxidation and deconjugation by the amidohydrolases IAR3/ILL6. Understanding their impacts was previously blurred by gene redundancy and compensation mechanisms. Here we address the consequences of blocking these pathways on jasmonate homeostasis and defenses in double-2ah, triple-3cyp mutants, and a quintuple-5ko line deficient in all known JA-Ile-degrading activities. These lines reacted differently to either mechanical wounding/insect attack or fungal infection. Both pathways contributed additively to JA-Ile removal upon wounding, but their impairement had opposite impacts on insect larvae feeding. By contrast, only the ah pathway was essential for JA-Ile turnover upon infection by Botrytis, yet only 3cyp was more fungus-resistant. Despite building-up extreme JA-Ile levels, 5ko displayed near-wild-type resistance in both bioassays. Molecular analysis indicated that restrained JA-Ile catabolism resulted in enhanced defense/resistance only when genes encoding negative regulators were not simultaneously overstimulated. This occurred in discrete stress- and pathway-specific combinations, providing a framework for future defense-enhancing strategies.

Exogenous Melatonin Enhances Rice Plant Resistance Against Xanthomonas oryzae pv. oryzae

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae, is one of the most serious diseases of rice. In this study we found that exogenous melatonin can increase rice resistance to BB. Treatment of rice plants with exogenous melatonin (20 µg/ml) increased nitrate reductase, nitric oxide synthase, and peroxidase activity, enabling high intracellular concentrations of melatonin, nitric oxide, and H₂O₂. The expression of NPR1, a key regulator in the salicylic acid signaling pathway, was upregulated more than 10-fold when the plants were challenged with melatonin. Similarly, the messenger RNA level of PDF1.2, a jasmonic acid-induced defense marker, was 15 times higher in the treated plants than in the control plants. Moreover, three pathogenesis-related proteins, PR1b, PR8a, and PR9, were upregulated 20-fold in the presence of melatonin. The application of melatonin (100 µg/ml) to soil-grown rice reduced the incidence of BB by 86.21%. Taken together, these results not only provide a better understanding of melatonin-mediated innate immunity to X. oryzae pv. oryzae in rice but also represent a promising cultivation strategy to protect rice against X. oryzae pv. oryzae infection.

Knockdown of GmVQ58 encoding a VQ motif-containing protein enhances soybean resistance to the common cutworm (Spodoptera litura Fabricius)

Plants have evolved complex defense mechanisms to withstand insect attack. Identification of plant endogenous insect resistance genes is of great significance for understanding plant-herbivore interactions and improving crop insect resistance. Soybean (Glycine max (L.) Merr.) is an important crop that is often attacked by the common cutworm (CCW) (Spodoptera litura Fabricius). In this study, based on our transcriptomic data, the gene GmVQ58, encoding a FxxxVQxxTG (VQ) motif-containing protein, was cloned and characterized. This gene showed the highest expression in the leaves and roots and was up-regulated significantly after CCW attack. Constitutive expression of GmVQ58 rescued the susceptibility of an Arabidopsis mutant to CCW, and interference of GmVQ58 in soybean hairy roots enhanced the resistance to CCW. Furthermore, GmVQ58 was localized to the nucleus and physically interacted with the transcription factor GmWRKY32. The expression of two defense-related genes, GmN:IFR and GmVSPβ, was up-regulated in GmVQ58-RNAi lines. Additionally, the promoter region of GmVQ58 was likely selected during domestication, resulting in different expression patterns in cultivated soybeans relative to wild soybeans. These results suggest that silencing GmVQ58 confers soybean resistance to CCW.

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.

Gossypium hirsutum Salt Tolerance Is Enhanced by Overexpression of G. arboreum JAZ1

Gossypium arboreum possesses many favorable traits including robust defense against biotic and abiotic stress although it has been withdrawn from the market because of lower yield and fiber quality compared to G. hirsutum (upland cotton). It is therefore important to explore and utilize the beneficial genes of G. arboretum for G. hirsutum cultivar breeding. Here, the function of G. arboreum JAZ1 in tolerance to salt stress was determined through loss-of-function analysis. GaJAZ1can interact with GaMYC2 to repress expression of downstream genes whose promoters contain a G-box cis element, affecting plant tolerance to salinity stress. The experimental data from NaCl treatments and a 2 year continuous field trial with natural saline-alkaline soil showed that the ectopically overexpressed GaJAZ1 significantly increased salt tolerance in upland cotton compared to the wild type, showing higher growth vigor with taller plants, increased fresh weight, and more bolls, which is due to reprogrammed expression of tolerance-related genes and promotion of root development. High-throughput RNA sequencing of GaJAZ1 transgenic and wild-type plants showed many differentially expressed genes involved in JA signaling and biosynthesis, salt stress-related genes, and hormone-related genes, suggesting that overexpressing GaJAZ1 can reprogram the expression of defense-related genes in G. hirsutum plants to increase tolerance to salt stress. The research provides a foundation to explore and utilize favorable genes from Gossypium species for upland cotton cultivar breeding.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

Foliar herbivory by caterpillars and aphids differentially affects phytohormonal signalling in roots and plant defence to a root herbivore

Plant-mediated interactions are an important force in insect ecology. Through such interactions, herbivores feeding on leaves can affect root feeders. However, the mechanisms regulating the effects of above-ground herbivory on below-ground herbivores are poorly understood. Here, we investigated the performance of cabbage root fly larvae (Delia radicum) on cabbage plants (Brassica oleracea) previously exposed to above ground herbivores belonging to two feeding guilds: leaf chewing diamondback moth caterpillars (Plutella xylostella) or phloem-feeding cabbage aphids (Brevicoryne brassicae). Our study focusses on root-herbivore performance and defence signalling in primary roots by quantifying phytohormones and gene expression. We show that leaf herbivory by caterpillars, but not by aphids, strongly attenuates root herbivore performance. Above-ground herbivory causes changes in primary roots in terms of gene transcripts and metabolites involved in plant defence. Feeding by below-ground herbivores strongly induces the jasmonate pathway in primary roots. Caterpillars feeding on leaves cause a slight induction of the primary root jasmonate pathway and interact with plant defence signalling in response to root herbivores. In conclusion, feeding by a leaf chewer and a phloem feeder differentially affects root-herbivore performance, root-herbivore-induced phytohormonal signalling, and secondary metabolites.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

Genome-wide and expression pattern analysis of JAZ family involved in stress responses and postharvest processing treatments in Camellia sinensis

The JASMONATE-ZIM DOMAIN (JAZ) family genes are key repressors in the jasmonic acid signal transduction pathway. Recently, the JAZ gene family has been systematically characterized in many plants. However, this gene family has not been explored in the tea plant. In this study, 13 CsJAZ genes were identified in the tea plant genome. Phylogenetic analysis showed that the JAZ proteins from tea and other plants clustered into 11 sub-groups. The CsJAZ gene transcriptional regulatory network predictive and expression pattern analyses suggest that these genes play vital roles in abiotic stress responses, phytohormone crosstalk and growth and development of the tea plant. In addition, the CsJAZ gene expression profiles were associated with tea postharvest processing. Our work provides a comprehensive understanding of the CsJAZ family and will help elucidate their contributions to tea quality during tea postharvest processing.

Pheophorbide a May Regulate Jasmonate Signaling during Dark-Induced Senescence

Chlorophyll degradation is one of the most visible signs of leaf senescence. During senescence, chlorophyll is degraded in the multistep pheophorbide a oxygenase (PAO)/phyllobilin pathway. This pathway is tightly regulated at the transcriptional level, allowing coordinated and efficient remobilization of nitrogen toward sink organs. Using a combination of transcriptome and metabolite analyses during dark-induced senescence of Arabidopsis (Arabidopsis thaliana) mutants deficient in key steps of the PAO/phyllobilin pathway, we show an unanticipated role for one of the pathway intermediates, i.e. pheophorbide a Both jasmonic acid-related gene expression and jasmonic acid precursors specifically accumulated in pao1, a mutant deficient in PAO. We propose that pheophorbide a, the last intact porphyrin intermediate of chlorophyll degradation and a unique pathway "bottleneck," has been recruited as a signaling molecule of chloroplast metabolic status. Our work challenges the assumption that chlorophyll breakdown is merely a result of senescence, and proposes that the flux of pheophorbide a through the pathway acts in a feed-forward loop that remodels the nuclear transcriptome and controls the pace of chlorophyll degradation in senescing leaves.

Jasmonic acid alleviates cadmium toxicity in Arabidopsis via suppression of cadmium uptake and translocation

Jasmonic acid (JA) is thought to be involved in plant responses to cadmium (Cd) stress, but the underlying molecular mechanisms are poorly understood. Here, we show that Cd treatment rapidly induces the expression of genes promoting endogenous JA synthesis, and subsequently increases the JA concentration in Arabidopsis roots. Furthermore, exogenous methyl jasmonate (MeJA) alleviates Cd-generated chlorosis of new leaves by decreasing the Cd concentration in root cell sap and shoot, and decreasing the expression of the AtIRT1, AtHMA2 and AtHMA4 genes promoting Cd uptake and long-distance translocation, respectively. In contrast, mutation of a key JA synthesis gene, AtAOS, greatly enhances the expression of AtIRT1, AtHMA2 and AtHMA4, increases Cd concentration in both roots and shoots, and confers increased sensitivity to Cd. Exogenous MeJA recovers the enhanced Cd-sensitivity of the ataos mutant, but not of atcoi1, a JA receptor mutant. In addition, exogenous MeJA reduces NO levels in Cd-stressed Arabidopsis root tips. Taken together, our results suggest that Cd-induced JA acts via the JA signaling pathway and its effects on NO levels to positively restrict Cd accumulation and alleviates Cd toxicity in Arabidopsis via suppression of the expression of genes promoting Cd uptake and long-distance translocation.

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3′–5′ ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.

Systematic identification of genes associated with plant growth-defense tradeoffs under JA signaling in Arabidopsis

Co-expression and regulatory networks yield important insights into the growth-defense tradeoffs mechanism under jasmonic acid (JA) signals in Arabidopsis. Elevated defense is commonly associated with growth inhibition. However, a comprehensive atlas of the genes associated with the plant growth-defense tradeoffs under JA signaling is lacking. To gain an insight into the dynamic architecture of growth-defense tradeoffs, a coexpression network analysis was employed on publicly available high-resolution transcriptomes of Arabidopsis treated with coronatine (COR), a mimic of jasmonoyl-l-isoleucine. The genes involved in JA-mediated growth-defense tradeoffs were systematically revealed. Promoter enrichment analysis revealed the core regulatory module in which the genes underwent rapid activation, sustained upregulation after COR treatment, and mediated the growth-defense tradeoffs. Several transcription factors (TFs), including RAP2.6L, MYB44, WRKY40, and WRKY18, were identified as instantly activated components associated with pathogen and insect resistance. JA might rapidly activate RAV1 and KAN1 to repress brassinosteroid (BR) response genes, upregulate KAN1, the C2H2 TF families ZF2, ZF3, ZAT6, and STZ/ZAT10 to repress the biosynthesis, transport, and signaling of auxin to arrest growth. Independent datasets and preserved analyses validated the reproducibility of the results. Our study provided a comprehensive snapshot of genes that respond to JA signals and provided valuable resources for functional studies on the genetic modification of breeding population that exhibit robust growth and defense simultaneously.

Interplay between Plant Cell Walls and Jasmonate Production

Plant cell walls are sophisticated carbohydrate-rich structures representing the immediate contact surface with the extracellular environment, often serving as the first barrier against biotic and abiotic stresses. Notably, a variety of perturbations in plant cell walls result in upregulated jasmonate (JA) production, a phytohormone with essential roles in defense and growth responses. Hence, cell wall-derived signals can initiate intracellular JA-mediated responses and the elucidation of the underlying signaling pathways could provide novel insights into cell wall maintenance and remodeling, as well as advance our understanding on how is JA biosynthesis initiated. This Mini Review will describe current knowledge about cell wall-derived damage signals and their effects on JA biosynthesis, as well as provide future perspectives.

Jasmonic Acid Is Required for Plant Acclimation to a Combination of High Light and Heat Stress

In the field, plants experience high light (HL) intensities that are often accompanied by elevated temperatures. Such conditions are a serious threat to agriculture production, because photosynthesis is highly sensitive to both HL intensities and high-temperature stress. One of the potential cellular targets of HL and heat stress (HS) combination is PSII because its degree of photoinhibition depends on the balance between the rate of PSII damage (induced by light stress), and the rate of PSII repair (impaired under HS). Here, we studied the responses of Arabidopsis (Arabidopsis thaliana) plants to a combination of HL and HS (HL+HS) conditions. Combined HL+HS was accompanied by irreversible damage to PSII, decreased D1 (PsbA) protein levels, and an enhanced transcriptional response indicative of PSII repair activation. We further identified several unique aspects of this stress combination that included enhanced accumulation of jasmonic acid (JA) and JA-Ile, elevated expression of over 2,200 different transcripts that are unique to the stress combination (including many that are JA-associated), and distinctive structural changes to chloroplasts. A mutant deficient in JA biosynthesis (allene oxide synthase) displayed enhanced sensitivity to combined HL+HS and further analysis revealed that JA is required for regulating several transcriptional responses unique to the stress combination. Our study reveals that JA plays an important role in the acclimation of plants to a combination of HL+HS.

Amelioration of heavy metal stress by endophytic Bacillus amyloliquefaciens RWL-1 in rice by regulating metabolic changes: potential for bacterial bioremediation

This study aimed to investigate the bioremediation efficiency of phytohormone-producing endophytic Bacillus amyloliquefaciens RWL-1 isolated from rice seeds. In this study, we tested RWL-1 against various heavy metals (Cu, Cr, Pb, and Cd). Among the tested heavy metals, RWL-1 showed the highest tolerance for Cu stress and we observed alterations in growth kinetics with various Cu concentrations (1, 2.5, and 5 mM). We confirmed the biosorption potential of RWL-1 by scanning electron microscopy coupled with energy-dispersive X-ray spectrometry showing that Cu ions were adsorbed on RWL-1 cell surfaces. We further tested RWL-1 for its plant growth promoting and stress reliance efficiency in response to a dose-dependent increase in soil Cu (1, 2.5, and 5 mM). The RWL-1 inoculation significantly increased seedling biomass and growth attributes compared with non-inoculated control seedlings with and without Cu stress. Moreover, RWL-1 inoculation significantly promoted a physiochemical response in seedlings with and without Cu stress by reducing Cu uptake, improving carbohydrate levels (glucose, sucrose, fructose, and raffinose), enhancing amino acids regulation, and augmenting antioxidant levels (POD, PPO, and GHS). Levels of stress-responsive phytohormones such as abscisic acid (ABA) and jasmonic acid were significantly reduced in RWL-1-inoculated seedlings as compared with non-inoculated control seedlings under normal condition and same levels of Cu stress. In conclusion, the inoculation of B. amyloliquefaciens RWL-1 can significantly improve plant growth in Cu-contaminated soil and reduce metal accumulation, thus making plants safer for consumption. This approach could be tremendously helpful for safe and sustainable agriculture in heavy metal-contaminated areas.

A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels

Mechanical stimuli, such as wind, rain, and touch affect plant development, growth, pest resistance, and ultimately reproductive success. Using water spray to simulate rain, we demonstrate that jasmonic acid (JA) signaling plays a key role in early gene-expression changes, well before it leads to developmental changes in flowering and plant architecture. The JA-activated transcription factors MYC2/MYC3/MYC4 modulate transiently induced expression of 266 genes, most of which peak within 30 min, and control 52% of genes induced >100-fold. Chromatin immunoprecipitation-sequencing analysis indicates that MYC2 dynamically binds >1,300 promoters and trans-activation assays show that MYC2 activates these promoters. By mining our multiomic datasets, we identified a core MYC2/MYC3/MYC4-dependent "regulon" of 82 genes containing many previously unknown MYC2 targets, including transcription factors bHLH19 and ERF109 bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/MYC3/MYC4 initiate a hierarchical network of downstream transcription factors. Finally, we also reveal that rapid water spray-induced accumulation of JA and JA-isoleucine is directly controlled by MYC2/MYC3/MYC4 through a positive amplification loop that regulates JA-biosynthesis genes.

Transcription Factors Associated with Leaf Senescence in Crops

Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables. Different crops present a delay in leaf senescence with an important impact on grain yield trough the maintenance of the photosynthetic leaf area during the reproductive stage. Additionally, because of the temporal gap between the onset and phenotypic detection of the senescence process, candidate genes are key tools to enable the early detection of this process. In this sense and given the importance of some transcription factors as hub genes in senescence pathways, we present a comprehensive review on senescence-associated transcription factors, in model plant species and in agronomic relevant crops. This review will contribute to the knowledge of leaf senescence process in crops, thus providing a valuable tool to assist molecular crop breeding.

Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis

Hevea brasiliensis remains the primary crop commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. Here, we described the transcriptional events related to jasmonic acid (JA)- and linolenic acid (LA)-induced secondary laticifer differentiation (SLD) in H. brasiliensis clone RRIM 600 based on RNA-seq approach. Histochemical approach proved that JA- and LA-treated samples resulted in SLD in H. brasiliensis when compared to ethephon and untreated control. RNA-seq data resulted in 86,614 unigenes, of which 2,664 genes were differentially expressed in JA and LA-induced secondary laticifer harvested from H. brasiliensis bark samples. Among these, 450 genes were unique to JA and LA as they were not differentially expressed in ethephon-treated samples compared with the untreated samples. Most transcription factors from the JA- and LA-specific dataset were classified under MYB, APETALA2/ethylene response factor (AP2/ERF), and basic-helix-loop-helix (bHLH) gene families that were involved in tissue developmental pathways, and we proposed that Bel5-GA2 oxidase 1-KNOTTED-like homeobox complex are likely involved in JA- and LA-induced SLD in H. brasiliensis. We also discovered alternative spliced transcripts, putative novel transcripts, and cis-natural antisense transcript pairs related to SLD event. This study has advanced understanding on the transcriptional regulatory network of SLD in H. brasiliensis.

Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data

Determining where transcription factors (TFs) bind in genomes provides insight into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances in high-throughput profiling of regulatory DNA have yielded large amounts of information about chromatin accessibility. Interpreting the functional significance of these data sets requires knowledge of which regulators are likely to bind these regions. This can be achieved by using information about TF-binding preferences, or motifs, to identify TF-binding events that are likely to be functional. Although different approaches exist to map motifs to DNA sequences, a systematic evaluation of these tools in plants is missing. Here, we compare four motif-mapping tools widely used in the Arabidopsis (Arabidopsis thaliana) research community and evaluate their performance using chromatin immunoprecipitation data sets for 40 TFs. Downstream gene regulatory network (GRN) reconstruction was found to be sensitive to the motif mapper used. We further show that the low recall of Find Individual Motif Occurrences, one of the most frequently used motif-mapping tools, can be overcome by using an Ensemble approach, which combines results from different mapping tools. Several examples are provided demonstrating how the Ensemble approach extends our view on transcriptional control for TFs active in different biological processes. Finally, a protocol is presented to effectively derive more complete cell type-specific GRNs through the integrative analysis of open chromatin regions, known binding site information, and expression data sets. This approach will pave the way to increase our understanding of GRNs in different cellular conditions.

A DAO1-Mediated Circuit Controls Auxin and Jasmonate Crosstalk Robustness during Adventitious Root Initiation in Arabidopsis

Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.

The stereoisomeric Bacillus subtilis HN09 metabolite 3,4-dihydroxy-3-methyl-2-pentanone induces disease resistance in Arabidopsis via different signalling pathways

BACKGROUND

Plant immune responses can be induced by plant growth-promoting rhizobacteria (PGPRs), but the exact compounds that induce resistance are poorly understood. Here, we identified the novel natural elicitor 3,4-dihydroxy-3-methyl-2-pentanone from the PGPR Bacillus subtilis HN09, which dominates HN09-induced systemic resistance (ISR).

RESULTS

The HN09 strain, as a rhizobacterium that promotes plant growth, can induce systemic resistance of Arabidopsis thaliana plants against Pseudomonas syringae pv. tomato DC3000, and the underlying role of its metabolite 3,4-dihydroxy-3-methyl-2-pentanone in this induced resistance mechanism was explored in this study. The stereoisomers of 3,4-dihydroxy-3-methyl-2-pentanone exhibited differential bioactivity of resistance induction in A. thaliana. B16, a 1:1 mixture of the threo-isomers (3R,4S) and (3S,4R), was significantly superior to B17, a similar mixture of the erythro-isomers (3R,4R) and (3S,4S). Moreover, B16 induced more expeditious and stronger callose deposition than B17 when challenged with the pathogen DC3000. RT-qPCR and RNA-seq results showed that B16 and B17 induced systemic resistance via JA/ET and SA signalling pathways. B16 and B17 activated different but overlapping signalling pathways, and these compounds have the same chemical structure but subtle differences in stereo configuration.

CONCLUSIONS

Our results indicate that 3,4-dihydroxy-3-methyl-2-pentanone is an excellent immune elicitor in plants. This compound is of great importance to the systemic resistance induced by HN09. Its threo-isomers (3R,4S) and (3S,4R) are much better than erythro-isomers (3R,4R) and (3S,4S). This process involves SA and JA/ET signalling pathways.

Unraveling the Genetic Elements Involved in Shoot and Root Growth Regulation by Jasmonate in Rice Using a Genome-Wide Association Study

BACKGROUND

Due to their sessile life style, plant survival is dependent on the ability to build up fast and highly adapted responses to environmental stresses by modulating defense response and organ growth. The phytohormone jasmonate plays an essential role in regulating these plant responses to stress.

RESULTS

To assess variation of plant growth responses and identify genetic determinants associated to JA treatment, we conducted a genome-wide association study (GWAS) using an original panel of Vietnamese rice accessions. The phenotyping results showed a high natural genetic variability of the 155 tested rice accessions in response to JA for shoot and root growth. The level of growth inhibition by JA is different according to the rice varieties tested. We conducted genome-wide association study and identified 28 significant associations for root length (RTL), shoot length (SHL), root weight (RTW), shoot weight (SHW) and total weight (TTW) in response to JA treatment. Three common QTLs were found for RTL, RTW and SHL. Among a list of 560 candidate genes found to co-locate with the QTLs, a transcriptome analysis from public database for the JA response allows us to identify 232 regulated genes including several JA-responsive transcription factors known to play a role in stress response.

CONCLUSION

Our genome-wide association study shows that common and specific genetic elements are associated with inhibition of shoot and root growth under JA treatment suggesting the involvement of a complex JA-dependent genetic control of rice growth inhibition at the whole plant level. Besides, numerous candidate genes associated to stress and JA response are co-located with the association loci, providing useful information for future studies on genetics and breeding to optimize the growth-defense trade-off in rice.

Plant Networks as Traits and Hypotheses: Moving Beyond Description

Biology relies on the central thesis that the genes in an organism encode molecular mechanisms that combine with stimuli and raw materials from the environment to create a final phenotypic expression representative of the genomic programming. While conceptually simple, the genotype-to-phenotype linkage in a eukaryotic organism relies on the interactions of thousands of genes and an environment with a potentially unknowable level of complexity. Modern biology has moved to the use of networks in systems biology to try to simplify this complexity to decode how an organism's genome works. Previously, biological networks were basic ways to organize, simplify, and analyze data. However, recent advances are allowing networks to move beyond description and become phenotypes or hypotheses in their own right. This review discusses these efforts, like mapping responses across biological scales, including relationships among cellular entities, and the direct use of networks as traits or hypotheses.

SPX4 Acts on PHR1-Dependent and -Independent Regulation of Shoot Phosphorus Status in Arabidopsis

Phosphorus (P) is an essential macronutrient for all living organisms and limits plant growth. Four proteins comprising a single SYG1/Pho81/XPR1 (SPX) domain, SPX1 to SPX4, are putative phosphate-dependent inhibitors of Arabidopsis (Arabidopsis thaliana) PHOSPHATE STARVATION RESPONSE1 (PHR1), the master transcriptional activator of phosphate starvation responses. This work demonstrated that SPX4 functions as a negative regulator not only of PHR1-dependent but also of PHR1-independent responses in P-replete plants. Transcriptomes of P-limited spx4 revealed that, unlike SPX1 and SPX2, SPX4 modulates the shoot phosphate starvation response but not short-term recovery after phosphate resupply. In roots, transcriptional regulation of P status is SPX4 independent. Genes misregulated in spx4 shoots intersect with both PHR1-dependent and PHOSPHATE2-dependent signaling networks associated with plant development, senescence, and ion/metabolite transport. Gene regulatory network analyses suggested that SPX4 interacts with transcription factors other than PHR1, such as SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 and ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN55, known regulators of shoot development. Transient expression studies in protoplasts indicated that PHR1 retention in the cytosol by SPX4 occurs in a dose- and P-status-dependent manner. Using a luciferase reporter in vivo, SPX4 expression kinetics and stability revealed that SPX4 is a short-lived protein with P-status-dependent turnover. SPX4 protein levels were quickly restored by phosphate resupply to P-limited plants. Unlike its monocot ortholog, AtSPX4 was not stabilized by the phosphate analog phosphite, implying that intracellular P status is sensed by its SPX domain via phosphate-rich metabolite signals.

The Future of Digital Sequence Information for Plant Genetic Resources for Food and Agriculture

The recent debates on the legal status of "digital sequence information" (DSI) at the international level could have extensive consequences for the future of agriculture and food security. A large majority of recent advances in biology, medicine, or agriculture were achieved by sharing and mining of freely accessible sequencing data. It is most probably because of the tremendous success of modern genomics and advances of synthetic biology that concerns were raised about possible fair and equitable ways of sharing data. The DSI concept is relatively new, and all concerned parties agreed upon the need for a clear definition. For example, the extent to which DSI understanding is limited only to genetic sequence data has to be clarified. In this paper, I focus on a subset of DSI essential to humankind: the DSI originating from plant genetic resources for food and agriculture (PGRFA). Two international agreements shape the conservation and use of plant genetic resources: the Convention on Biodiversity and the International Treaty for Plant Genetic Resources for Food and Agriculture. In an attempt to mobilize DSI users and producers involved in research, breeding, and conservation, I describe here how the increasing amount of genomic data, information, and studies interact with the existing legal framework at the global level. Using possible scenarios, I will emphasize the complexity of the issues surrounding DSI for PGRFA and propose potential ways forward for developing an inclusive governance and fair use of these genetic resources.