JASMONATE-INSENSITIVE1 encodes a MYC transcription factor essential to discriminate between different jasmonate-regulated defense responses in Arabidopsis

Methyl Jasmonate Induced Oxidative Stress and Accumulation of Secondary Metabolites in Plant Cell and Organ Cultures

Recently, plant secondary metabolites are considered as important sources of pharmaceuticals, food additives, flavours, cosmetics, and other industrial products. The accumulation of secondary metabolites in plant cell and organ cultures often occurs when cultures are subjected to varied kinds of stresses including elicitors or signal molecules. Application of exogenous jasmonic acid (JA) and methyl jasmonate (MJ) is responsible for the induction of reactive oxygen species (ROS) and subsequent defence mechanisms in cultured cells and organs. It is also responsible for the induction of signal transduction, the expression of many defence genes followed by the accumulation of secondary metabolites. In this review, the application of exogenous MJ elicitation strategies on the induction of defence mechanism and secondary metabolite accumulation in cell and organ cultures is introduced and discussed. The information presented here is useful for efficient large-scale production of plant secondary metabolites by the plant cell and organ cultures.

Comparative Transcriptome Analysis Reveals Key Pathways and Hub Genes in Rapeseed During the Early Stage of Plasmodiophora brassicae Infection

Rapeseed (Brassica napus L., AACC, 2n = 38) is one of the most important oil crops around the world. With intensified rapeseed cultivation, the incidence and severity of clubroot infected by Plasmodiophora brassicae Wor. (P. brassicae) has increased very fast, which seriously impedes the development of rapeseed industry. Therefore, it is very important and timely to investigate the mechanisms and genes regulating clubroot resistance (CR) in rapeseed. In this study, comparative transcriptome analysis was carried out on two rapeseed accessions of R- (resistant) and S- (susceptible) line. Three thousand one hundred seventy-one and 714 differentially expressed genes (DEGs) were detected in the R- and S-line compared with the control groups, respectively. The results indicated that the CR difference between the R- and S-line had already shown during the early stage of P. brassicae infection and the change of gene expression pattern of R-line exhibited a more intense defensive response than that of S-line. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of 2,163 relative-DEGs, identified between the R- and S-line, revealed that genes participated in plant hormone signal transduction, fatty acid metabolism, and glucosinolate biosynthesis were involved in regulation of CR. Further, 12 hub genes were identified from all relative-DEGs with the help of weighted gene co-expression network analysis. Haplotype analysis indicated that the natural variations in the coding regions of some hub genes also made contributed to CR. This study not only provides valuable information for CR molecular mechanisms, but also has applied implications for CR breeding in rapeseed.

The transcriptome of Pinus pinaster under Fusarium circinatum challenge

BACKGROUND

Fusarium circinatum, the causal agent of pitch canker disease, poses a serious threat to several Pinus species affecting plantations and nurseries. Although Pinus pinaster has shown moderate resistance to F. circinatum, the molecular mechanisms of defense in this host are still unknown. Phytohormones produced by the plant and by the pathogen are known to play a crucial role in determining the outcome of plant-pathogen interactions. Therefore, the aim of this study was to determine the role of phytohormones in F. circinatum virulence, that compromise host resistance.

RESULTS

A high quality P. pinaster de novo transcriptome assembly was generated, represented by 24,375 sequences from which 17,593 were full length genes, and utilized to determine the expression profiles of both organisms during the infection process at 3, 5 and 10 days post-inoculation using a dual RNA-sequencing approach. The moderate resistance shown by Pinus pinaster at the early time points may be explained by the expression profiles pertaining to early recognition of the pathogen, the induction of pathogenesis-related proteins and the activation of complex phytohormone signaling pathways that involves crosstalk between salicylic acid, jasmonic acid, ethylene and possibly auxins. Moreover, the expression of F. circinatum genes related to hormone biosynthesis suggests manipulation of the host phytohormone balance to its own benefit.

CONCLUSIONS

We hypothesize three key steps of host manipulation: perturbing ethylene homeostasis by fungal expression of genes related to ethylene biosynthesis, blocking jasmonic acid signaling by coronatine insensitive 1 (COI1) suppression, and preventing salicylic acid biosynthesis from the chorismate pathway by the synthesis of isochorismatase family hydrolase (ICSH) genes. These results warrant further testing in F. circinatum mutants to confirm the mechanism behind perturbing host phytohormone homeostasis.

Hydrogen sulfide acts downstream of jasmonic acid to inhibit stomatal development in Arabidopsis

Main conclusion: Jasmonic acid (JA) negatively regulates stomatal development by promoting LCD expression and hydrogen sulfide (H₂S) biosynthesis. H₂S inhibits the initiation of stomata formation and acts upstream of SPEECHLESS. Abstract: Stomatal development is strictly regulated by endogenous signals and environmental cues. We recently revealed that jasmonic acid (JA) negatively regulates stomatal development in Arabidopsis thaliana cotyledons (Han et al., Plant Physiol 176:2871-2885, 2018), but the underlying molecular mechanism remains largely unknown. Here, we uncovered a role for H₂S in regulating stomatal development. The H₂S scavenger hypotaurine reversed the JA-induced repression of stomatal development in the epidermis of wild-type Arabidopsis. The H₂S-deficient mutant lcd displayed increased stomatal density and stomatal index values, which were rescued by treatment with sodium hydrosulfide (NaHS; an H₂S donor) but not JA, suggesting that JA-mediated repression of stomatal development is dependent on H₂S biosynthesis. The high stomatal density of JA-deficient mutants was rescued by exogenous NaHS treatment. Further analysis indicated that JA positively regulates LCD expression, L-cysteine desulfhydrases (L-CDes) activity, and endogenous H₂S content. Furthermore, H₂S represses the expression of stomate-associated genes and functions downstream of stomate-related signaling pathway components TOO MANY MOUTHS (TMM) and STOMATAL DENSITY AND DISTRIBUTION1 (SDD1) and upstream of SPEECHLESS (SPCH). Therefore, H₂S acts downstream of JA signaling to regulate stomatal development in Arabidopsis cotyledons.

Combined transcriptome and metabolome analysis identifies defence responses in spider mite-infested pepper (Capsicum annuum)

Plants regulate responses towards herbivory through fine-tuning of defence-related hormone production, expression of defence genes, and production of secondary metabolites. Jasmonic acid (JA) plays a key role in plant-herbivorous arthropod interactions. To understand how pepper (Capsicum annuum) responds to herbivory, leaf transcriptomes and metabolomes of two genotypes different in their susceptibility to spider mites were studied. Mites induced both JA and salicylic acid (SA) signalling. However, mite infestation and exogenous JA resulted in distinct transcriptome profiles. Compared with JA, mites induced fewer differentially expressed genes involved in metabolic processes (except for genes involved in the phenylpropanoid pathway) and lipid metabolic processes. Furthermore, pathogen-related defence responses including WRKY transcription factors were more strongly induced upon mite infestation, probably as a result of induced SA signalling. Untargeted analysis of secondary metabolites confirmed that JA treatment induced larger changes in metabolism than spider mite infestation, resulting in higher terpenoid and flavonoid production. The more resistant genotype exhibited a larger increase in endogenous JA and volatile and non-volatile secondary metabolites upon infestation, which could explain its stronger defence. Reasoning that in JA-SA antagonizing crosstalk, SA defences are prioritized over JA defences, we hypothesize that lack of SA-mediated repression of JA-induced defences could result in gain of resistance towards spider mites in pepper.

JAZ4 is involved in plant defense, growth, and development in Arabidopsis

Jasmonate zim-domain (JAZ) proteins comprise a family of transcriptional repressors that modulate jasmonate (JA) responses. JAZ proteins form a co-receptor complex with the F-box protein coronatine insensitive1 (COI1) that recognizes both jasmonoyl-l-isoleucine (JA-Ile) and the bacterial-produced phytotoxin coronatine (COR). Although several JAZ family members have been placed in this pathway, the role of JAZ4 in this model remains elusive. In this study, we observed that the jaz4-1 mutant of Arabidopsis is hyper-susceptible to Pseudomonas syringae pv. tomato (Pst) DC3000, while Arabidopsis lines overexpressing a JAZ4 protein lacking the Jas domain (JAZ4∆Jas) have enhanced resistance to this bacterium. Our results show that the Jas domain of JAZ4 is required for its physical interaction with COI1, MYC2 or MYC3, but not with the repressor complex adaptor protein NINJA. Furthermore, JAZ4 degradation is induced by COR in a proteasome- and Jas domain-dependent manner. Phenotypic evaluations revealed that expression of JAZ4∆Jas results in early flowering and increased length of root, hypocotyl, and petiole when compared with Col-0 and jaz4-1 plants, although JAZ4∆Jas lines remain sensitive to MeJA- and COR-induced root and hypocotyl growth inhibition. Additionally, jaz4-1 mutant plants have increased anthocyanin accumulation and late flowering compared with Col-0, while JAZ4∆Jas lines showed no alteration in anthocyanin production. These findings suggest that JAZ4 participates in the canonical JA signaling pathway leading to plant defense response in addition to COI1/MYC-independent functions in plant growth and development, supporting the notion that JAZ4-mediated signaling may have distinct branches.

Combined transcriptome and metabolome analysis identifies defence responses in spider mite-infested pepper (Capsicum annuum)

Plants regulate responses towards herbivory through fine-tuning of defence-related hormone production, expression of defence genes, and production of secondary metabolites. Jasmonic acid (JA) plays a key role in plant-herbivorous arthropod interactions. To understand how pepper (Capsicum annuum) responds to herbivory, leaf transcriptomes and metabolomes of two genotypes different in their susceptibility to spider mites were studied. Mites induced both JA and salicylic acid (SA) signalling. However, mite infestation and exogenous JA resulted in distinct transcriptome profiles. Compared with JA, mites induced fewer differentially expressed genes involved in metabolic processes (except for genes involved in the phenylpropanoid pathway) and lipid metabolic processes. Furthermore, pathogen-related defence responses including WRKY transcription factors were more strongly induced upon mite infestation, probably as a result of induced SA signalling. Untargeted analysis of secondary metabolites confirmed that JA treatment induced larger changes in metabolism than spider mite infestation, resulting in higher terpenoid and flavonoid production. The more resistant genotype exhibited a larger increase in endogenous JA and volatile and non-volatile secondary metabolites upon infestation, which could explain its stronger defence. Reasoning that in JA-SA antagonizing crosstalk, SA defences are prioritized over JA defences, we hypothesize that lack of SA-mediated repression of JA-induced defences could result in gain of resistance towards spider mites in pepper.

A Jasmonate-Activated MYC2-Dof2.1-MYC2 Transcriptional Loop Promotes Leaf Senescence in Arabidopsis

DNA binding-with-one-finger (Dof) proteins are plant-specific transcription factors closely associated with a variety of physiological processes. Here, we show that the Dof protein family in Arabidopsis (Arabidopsis thaliana) functions in leaf senescence. Disruption of Dof2 1, a jasmonate (JA)-inducible gene, led to a marked reduction in promotion of leaf senescence and inhibition of root development as well as dark-induced and age-dependent leaf senescence, while overexpression of Dof2 1 promoted these processes. Additionally, the dof2 1 knockout mutant showed almost no change in the transcriptome in the absence of JA; in the presence of JA, expression of many senescence-associated genes, including MYC2, which encodes a central regulator of JA responses, was induced to a lesser extent in the dof2 1 mutant than in the wild type. Furthermore, direct activation of the MYC2 promoter by Dof2.1, along with the results of epistasis analysis, indicated that Dof2.1 enhances leaf senescence mainly by promoting MYC2 expression. Interestingly, MYC2 was also identified as a transcriptional activator responsible for JA-inducible expression of Dof2 1 Based on these results, we propose that Dof2.1 acts as an enhancer of JA-induced leaf senescence through the MYC2-Dof2.1-MYC2 feedforward transcriptional loop.

Ring/U-Box Protein AtUSR1 Functions in Promoting Leaf Senescence Through JA Signaling Pathway in Arabidopsis

Leaf senescence is regulated by a large number of internal and environmental factors. Here, we report that AtUSR1 (U-box Senescence Related 1) which encodes a plant Ring/U-box protein, is involved in age-dependent and dark-induced leaf senescence in Arabidopsis. Expression of AtUSR1 gene in leaves was up-regulated in darkness and during aging. Plants of usr1, an AtUSR1 gene knock-down mutant, showed a significant delay in age-dependent and dark-induced leaf senescence and the delayed senescence phenotype was rescued when the AtUSR1 gene was transferred back to the mutant plants. Meanwhile, overexpression of AtUSR1 caused accelerated leaf senescence. Furthermore, the role of AtUSR1 in regulating leaf senescence is related to MYC2-mediuated jasmonic acid (JA) signaling pathway. MeJA treatments promoted the accumulation of AtUSR1 transcripts and this expression activation was dependent on the function of MYC2, a key transcription factor in JA signaling. Dual-luciferase assay results indicated that MYC2 promoted the expression of AtUSR1. Overexpression of AtUSR1 in myc2 mutant plants showed precocious senescence, while myc2 mutation alone caused a delay in leaf senescence, suggesting that AtUSR1 functions downstream to MYC2 in the JA signaling pathway in promoting leaf senescence.

Directing Trophic Divergence in Plant-Pathogen Interactions: Antagonistic Phytohormones With NO Doubt?

A fundamental process culminating in the mechanisms of plant-pathogen interactions is the regulation of trophic divergence into biotrophic, hemibiotrophic, and necrotrophic interactions. Plant hormones, of almost all types, play significant roles in this regulatory apparatus. In plant-pathogen interactions, two classical mechanisms underlying hormone-dependent trophic divergence are long recognized. While salicylic acid dominates in the execution of host defense response against biotrophic and early-stage hemibiotrophic pathogens, jasmonic acid, and ethylene are key players facilitating host defense response against necrotrophic and later-stage hemibiotrophic pathogens. Evidence increasingly suggests that trophic divergence appears to be modulated by more complex signaling networks. Acting antagonistically or agonistically, other hormones such as auxins, cytokinins, abscisic acid, gibberellins, brassinosteroids, and strigolactones, as well as nitric oxide, are emerging candidates in the regulation of trophic divergence. In this review, the latest advances in the dynamic regulation of trophic divergence are summarized, emphasizing common and contrasting hormonal and nitric oxide signaling strategies deployed in plant-pathogen interactions.

Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves

BACKGROUND

Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes.

RESULTS

Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H₂O₂ production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA.

CONCLUSION

Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

Background

MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the crosstalk between Jasmonic acid regulatory pathway and light signaling in Arabidopsis, but such kinds of studies are rare in wheat, especially in photo-thermo-sensitive genic male sterile (PTGMS) wheat line.

Results

27 non-redundant MYC gene copies, which belonged to 11 TaMYC genes, were identified in the whole genome of wheat (Chinese Spring). These gene copies were distributed on 13 different chromosomes, respectively. Based on the results of phylogenetic analysis, 27 TaMYC gene copies were clustered into group I, group III, and group IV. The identified TaMYC genes copies contained different numbers of light, stress, and hormone-responsive regulatory elements in their 1500 base pair promoter regions. Besides, we found that TaMYC3 was expressed highly in stem, TaMYC5 and TaMYC9 were expressed specially in glume, and the rest of TaMYC genes were expressed in all tissues (root, stem, leaf, pistil, stamen, and glume) of the PTGMS line BS366. Moreover, we found that TaMYC3, TaMYC7, TaMYC9, and TaMYC10 were highly sensitive to methyl jasmonate (MeJA), and other TaMYC genes responded at different levels. Furthermore, we confirmed the expression profiles of TaMYC family members under different light quality and plant hormone stimuli, and abiotic stresses. Finally, we predicted the wheat microRNAs that could interact with TaMYC family members, and built up a network to show their integrative relationships.

Conclusions

This study analyzed the size and composition of the MYC gene family in wheat, and investigated stress-responsive and light quality induced expression profiles of each TaMYC gene in the PTGMS wheat line BS366. In conclusion, we obtained lots of important information of TaMYC family, and the results of this study was supposed to contribute novel insights and gene and microRNA resources for wheat breeding, especially for the improvement of PTGMS wheat lines.

A novel Arabidopsis pathosystem reveals cooperation of multiple hormonal response-pathways in host resistance against the global crop destroyer Macrophomina phaseolina

Dubbed as a "global destroyer of crops", the soil-borne fungus Macrophomina phaseolina (Mp) infects more than 500 plant species including many economically important cash crops. Host defenses against infection by this pathogen are poorly understood. We established interactions between Mp and Arabidopsis thaliana (Arabidopsis) as a model system to quantitatively assess host factors affecting the outcome of Mp infections. Using agar plate-based infection assays with different Arabidopsis genotypes, we found signaling mechanisms dependent on the plant hormones ethylene, jasmonic acid and salicylic acid to control host defense against this pathogen. By profiling host transcripts in Mp-infected roots of the wild-type Arabidopsis accession Col-0 and ein2/jar1, an ethylene/jasmonic acid-signaling deficient mutant that exhibits enhanced susceptibility to this pathogen, we identified hundreds of genes potentially contributing to a diverse array of defense responses, which seem coordinated by complex interplay between multiple hormonal response-pathways. Our results establish Mp/Arabidopsis interactions as a useful model pathosystem, allowing for application of the vast genomics-related resources of this versatile model plant to the systematic investigation of previously understudied host defenses against a major crop plant pathogen.

Interruption of Jasmonic Acid Biosynthesis Causes Differential Responses in the Roots and Shoots of Maize Seedlings against Salt Stress

Jasmonates (JAs) together with jasmonic acid and its offshoots are lipid-derived endogenous hormones that play key roles in both developmental processes and different defense responses in plants. JAs have been studied intensively in the past decades for their substantial roles in plant defense comebacks against diverse environmental stresses among model plants. However, the role of this phytohormone has been poorly investigated in the monocotyledonous species against abiotic stresses. In this study, a JA biosynthesis mutant opr7opr8 was used for the investigation of JA roles in the salt stress responses of maize seedlings, whose roots were exposed to 0 to 300 mM NaCl. Foliar stomatal observation showed that opr7opr8 had a larger stomatal aperture than wild type (WT) (B73) under salinity stress, indicating that JA positively regulates guard cell movement under salt stress. The results regarding chlorophyll content and leaf senescence showed that opr7opr8 exhibited delayed leaf senescence under salt stress as compared to WT, indicating that JA plays a role in salt-inducing cell death and subsequent leaf senescence. Moreover, the morphological parameters, including the length of the shoots and roots, and the fresh and dry weights of the shoots and roots, showed that after 7 days of salt treatment, opr7opr8 had heavier and longer shoots than WT but slighter and shorter roots than WT. In addition, ion analysis showed that opr7opr8 accumulated less sodium but more potassium in the leaves than WT but more sodium and less potassium in the roots than WT, suggesting that JA deficiency causes higher salt stress to the roots but less stress to the leaves of the seedlings. Reactive oxygen species (ROS) analysis showed that opr7opr8 produced less H₂O₂ than WT in the leaves but more H₂O₂ in the roots under salt treatment, and correspondingly, ROS-scavenging enzymes superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) showed a similar variation, i.e., opr7opr8 has lower enzymatic activities in the shoots but higher activities in the roots than WT under salt treatment. For osmotic adjustment, opr7opr8 produced less proline in the shoots at 100 and 300 mM NaCl treatments but more in the roots than the WT roots under all salt treatments. In addition, the gene expression for abscisic acid (ABA) biosynthesis under salt stress was investigated. Results showed that the expression levels of four key enzymes of ABA biosynthesis, ZEP1, NCED5, AO1, and VP10, were significantly downregulated in the shoots as compared to WT under salt treatment. Putting all the data together, we concluded that JA-deficiency in maize seedlings reduced the salt-stress responses in the shoots but exaggerated the responses in the roots. In addition, endogenous JA acted as a positive regulator for the transportation of sodium ions from the roots to the shoots because the mutant opr7opr8 had a higher level of sodium in the roots but a significantly lower level in the shoots than WT. Furthermore, JA may act as a positive regulator for ABA biosynthesis in the leaves under salt stress.

Plant Specialized Metabolism Regulated by Jasmonate Signaling

As sessile and autotrophic organisms, plants have evolved sophisticated pathways to produce a rich array of specialized metabolites, many of which are biologically active and function as defense substances in protecting plants from herbivores and pathogens. Upon stimuli, these structurally diverse small molecules may be synthesized or constitutively accumulated. Jasmonate acids (JAs) are the major defense phytohormone involved in transducing external signals (such as wounding) to activate defense reactions, including, in particular, the reprogramming of metabolic pathways that initiate and enhance the production of defense compounds against insect herbivores and pathogens. In this review, we summarize the progress of recent research on the control of specialized metabolic pathways in plants by JA signaling, with an emphasis on the molecular regulation of terpene and alkaloid biosynthesis. We also discuss the interplay between JA signaling and various signaling pathways during plant defense responses. These studies provide valuable data for breeding insect-proof crops and pave the way to engineering the production of valuable metabolites in future.

Jasmonate Signaling during Arabidopsis Stamen Maturation

The last stages of stamen development, collectively called stamen maturation, encompass pollen viability, filament elongation and anther dehiscence or opening. These processes are essential for male fertility in Arabidopsis and require the function of jasmonate signaling. There is a good understanding of jasmonate synthesis, perception and transcriptional outputs in Arabidopsis stamens. In addition, the spatiotemporal localization of jasmonate signaling components at the tissue and cellular levels has started to emerge in recent years. However, the ultimate cellular functions activated by jasmonate to promote stamen maturation remain unknown. The hormones auxin and gibberellin have been proposed to control the activation of jasmonate synthesis to promote stamen maturation, although we hypothesize that this action is rather indirect. In this review, we examine these different areas, attempt to clarify some confusing aspects found in the literature and raise testable hypothesis that may help to further understand how jasmonate controls male fertility in Arabidopsis.

Suppression of abscisic acid biosynthesis at the early infection stage of Verticillium longisporum in oilseed rape (Brassica napus)

Verticillium longisporum infects oilseed rape (Brassica napus) and Arabidopsis thaliana. To investigate the early response of oilseed rape to the fungal infection, we determined transcriptomic changes in oilseed rape roots at 6 days post-inoculation (dpi) by RNA-Seq analysis, in which non-infected roots served as a control. Strikingly, a subset of genes involved in abscisic acid (ABA) biosynthesis was found to be down-regulated and the ABA level was accordingly attenuated in 6 dpi oilseed rape as compared with the control. Gene expression analysis revealed that this was mainly attributed to the suppression of BnNCED3-mediated ABA biosynthesis, involving, for example, BnWRKY57. However, this down-regulation of ABA biosynthesis could not be observed in infected Arabidopsis roots. Arabidopsis ABA- defective mutants nced3 and aao3 displayed pronounced tolerance to the fungal infection with delayed and impeded symptom development, even though fungal colonization was not affected in both mutants. These data suggest that ABA appears to be required for full susceptibility of Arabidopsis to the fungal infection. Furthermore, we found that in both 6 dpi oilseed rape and the Arabidopsis nced3 mutant, the salicylic acid (SA) signalling pathway was induced while the jasmonic acid (JA)/ethylene (ET) signalling pathway was concomitantly mitigated. Following these data, we conclude that in oilseed rape the V. longisporum infection triggers a host-specific suppression of the NCED3-mediated ABA biosynthesis, consequently increasing plant tolerance to the fungal infection. We believe that this might be part of the virulence strategy of V. longisporum to initiate/establish a long-lasting compatible interaction with oilseed rape (coexistence), which appears to be different from the infection process in Arabidopsis.

The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity

Polycomb repressive complexes (PRCs) have been traditionally associated with the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional upregulation. Consistently, increased expression of these two transcription factors leads to the misregulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019, and ANAC055 overexpressers in several of their phenotypes, including increased aphid resistance, abscisic acid (ABA) sensitivity and drought tolerance. In addition, like the MYC2 and ANAC overexpressers, lhp1 displays reduced salicylic acid (SA) content caused by a deregulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress-responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine tuning the complex balance between developmental and stress-responsive processes.

PatJAZ6 Acts as a Repressor Regulating JA-Induced Biosynthesis of Patchouli Alcohol in Pogostemon Cablin

The JASMONATE ZIM DOMAIN (JAZ) proteins act as negative regulators in the jasmonic acid (JA) signaling pathways of plants, and these proteins have been reported to play key roles in plant secondary metabolism mediated by JA. In this study, we firstly isolated one JAZ from P. cablin, PatJAZ6, which was characterized and revealed based on multiple alignments and a phylogenic tree analysis. The result of subcellular localization indicated that the PatJAZ6 protein was located in the nucleus of plant protoplasts. The expression level of PatJAZ6 was significantly induced by the methyl jasmonate (MeJA). Furthermore, by means of yeast two-hybrid screening, we identified two transcription factors that interact with the PatJAZ6, the PatMYC2b1 and PatMYC2b2. Virus-induced gene silencing (VIGS) of PatJAZ6 caused a decrease in expression abundance, resulting in a significant increase in the accumulation of patchouli alcohol. Moreover, we overexpressed PatJAZ6 in P. cablin, which down-regulated the patchoulol synthase expression, and then suppressed the biosynthesis of patchouli alcohol. The results demonstrate that PatJAZ6 probably acts as a repressor in the regulation of patchouli alcohol biosynthesis, contributed to a model proposed for the potential JA signaling pathway in P. cablin.

Establishment of Actinorhizal Symbiosis in Response to Ethylene, Salicylic Acid, and Jasmonate

Phytohormones play a crucial role in regulating plant developmental processes. Among them, ethylene and jasmonate are known to be involved in plant defense responses to a wide range of biotic stresses as their levels increase with pathogen infection. In addition, these two phytohormones have been shown to inhibit plant nodulation in legumes. Here, exogenous salicylic acid (SA), jasmonate acid (JA), and ethephon (ET) were applied to the root system of Casuarina glauca plants before Frankia inoculation, in order to analyze their effects on the establishment of actinorhizal symbiosis. This protocol further describes how to identify putative ortholog genes involved in ethylene and jasmonate biosynthesis and/or signaling pathways in plant, using the Arabidopsis Information Resource (TAIR), Legume Information System (LIS), and Genevestigator databases. The expression of these genes in response to the bacterium Frankia was analyzed using the gene atlas for Casuarina-Frankia symbiosis (SESAM web site).

Metatranscriptomic Analysis of Multiple Environmental Stresses Identifies RAP2.4 Gene Associated with Arabidopsis Immunity to Botrytis cinerea

In this study, we aimed to identify common genetic components during stress response responsible for crosstalk among stresses, and to determine the role of differentially expressed genes in Arabidopsis-Botrytis cinerea interaction. Of 1,554 B. cinerea up-regulated genes, 24%, 1.4% and 14% were induced by biotic, abiotic and hormonal treatments, respectively. About 18%, 2.5% and 22% of B. cinerea down-regulated genes were also repressed by the same stress groups. Our transcriptomic analysis indicates that plant responses to all tested stresses can be mediated by commonly regulated genes; and protein-protein interaction network confirms the cross-interaction between proteins regulated by these genes. Upon challenges to individual or multiple stress(es), accumulation of signaling molecules (e.g. hormones) plays a major role in the activation of downstream defense responses. In silico gene analyses enabled us to assess the involvement of RAP2.4 (related to AP2.4) in plant immunity. Arabidopsis RAP2.4 was repressed by B. cinerea, and its mutants enhanced resistance to the same pathogen. To the best of our knowledge, this is the first report demonstrating the role of RAP2.4 in plant defense against B. cinerea. This research can provide a basis for breeding programs to increase tolerance and improve yield performance in crops.

Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

BACKGROUND

White rot is one of the most dangerous fungal diseases and can considerably affect grape berry production and quality. However, few studies have focused on this disease, and thus, finding candidate white rot resistance genes is of great importance for breeding resistant grapevine cultivars. Based on field observations and indoor experiments, the cultivars "Victoria" and "Zhuosexiang" showed significant differences in white rot resistance. For understanding the molecular mechanisms behind it, different phenotypes of grapevine leaves were used for RNA sequencing via Illumina and single-molecule real-time (SMRT) sequencing technology.

RESULTS

A transcript library containing 53,906 reads, including known and novel transcripts, was constructed following the full-length transcriptome sequencing of the two grapevine cultivars. Genes involved in salicylic acid (SA) and jasmonic acid (JA) synthesis pathways showed different expression levels. Furthermore, four key transcription factors (TFs), NPR1, TGA4, Pti6, and MYC2, all involved in the SA and JA signal pathways were identified, and the expression profile revealed the different regulation of the pathogenesis related protein1 (PR1) resistance gene, as mediated by the four TFs.

CONCLUSIONS

Full-length transcript sequencing can substantially improve the accuracy and integrity of gene prediction and gene function research in grapevine. Our results contribute to identify candidate resistance genes and improve our understanding of the genes and regulatory mechanisms involved in grapevine resistance to white rot.

Comparative gene expression profile analysis of ovules provides insights into Jatropha curcas L. ovule development

Jatropha curcas, an economically important biofuel feedstock with oil-rich seeds, has attracted considerable attention among researchers in recent years. Nevertheless, valuable information on the yield component of this plant, particularly regarding ovule development, remains scarce. In this study, transcriptome profiles of anther and ovule development were established to investigate the ovule development mechanism of J. curcas. In total, 64,325 unigenes with annotation were obtained, and 1723 differentially expressed genes (DEGs) were identified between different stages. The DEG analysis showed the participation of five transcription factor families (bHLH, WRKY, MYB, NAC and ERF), five hormone signaling pathways (auxin, gibberellic acid (GA), cytokinin, brassinosteroids (BR) and jasmonic acid (JA)), five MADS-box genes (AGAMOUS-2, AGAMOUS-1, AGL1, AGL11, and AGL14), SUP and SLK3 in ovule development. The role of GA and JA in ovule development was evident with increases in flower buds during ovule development: GA was increased approximately twofold, and JA was increased approximately sevenfold. In addition, the expression pattern analysis using qRT-PCR revealed that CRABS CLAW and AGAMOUS-2 were also involved in ovule development. The upregulation of BR signaling genes during ovule development might have been regulated by other phytohormone signaling pathways through crosstalk. This study provides a valuable framework for investigating the regulatory networks of ovule development in J. curcas.

MYC2 regulates ARR16, a component of cytokinin signaling pathways, in Arabidopsis seedling development

MYC2 is a basic helix-loop-helix transcription factor that acts as a repressor of blue light-mediated photomorphogenic growth; however, it promotes lateral root formation. MYC2 also regulates different phytohormone-signaling pathways in crucial manner. Arabidopsis response regulator 16 (ARR16) is a negative regulator of cytokinin signaling pathways. Here, we show that MYC2 directly binds to the E-box of ARR16 minimal promoter and negatively regulates its expression in a cytokinin-dependent manner. While ARR16 and MYC2 influence jasmonic acid and cytokinin signaling, the expression of ARR16 is regulated by cry1, GBF1, and HYH, the components of light signaling pathways. The transgenic studies show that the expression of ARR16 is regulated by MYC2 at various stages of development. The mutational studies reveal that ARR16 positively regulates the hypocotyl growth in blue light, and phenotypic analysis of atmyc2 arr16 double mutant further reveals that arr16 can suppress the short hypocotyl phenotype of atmyc2. Altogether, this work highlights MYC2-mediated transcriptional repression of ARR16 in Arabidopsis seedling development.

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.

Evolutionary Analysis of JAZ Proteins in Plants: An Approach in Search of the Ancestral Sequence

Jasmonates are phytohormones that regulate development, metabolism and immunity. Signal transduction is critical to activate jasmonate responses, but the evolution of some key regulators such as jasmonate-ZIM domain (JAZ) repressors is not clear. Here, we identified 1065 JAZ sequence proteins in 66 lower and higher plants and analyzed their evolution by bioinformatics methods. We found that the TIFY and Jas domains are highly conserved along the evolutionary scale. Furthermore, the canonical degron sequence LPIAR(R/K) of the Jas domain is conserved in lower and higher plants. It is noteworthy that degron sequences showed a large number of alternatives from gymnosperms to dicots. In addition, ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs are displayed in all plant lineages from liverworts to angiosperms. However, the cryptic MYC2-interacting domain (CMID) domain appeared in angiosperms for the first time. The phylogenetic analysis performed using the Maximum Likelihood method indicated that JAZ ortholog proteins are grouped according to their similarity and plant lineage. Moreover, ancestral JAZ sequences were constructed by PhyloBot software and showed specific changes in the TIFY and Jas domains during evolution from liverworts to dicots. Finally, we propose a model for the evolution of the ancestral sequences of the main eight JAZ protein subgroups. These findings contribute to the understanding of the JAZ family origin and expansion in land plants.

Expression of AoNHX1 increases salt tolerance of rice and Arabidopsis, and bHLH transcription factors regulate AtNHX1 and AtNHX6 in Arabidopsis

Expression of AoNHX1 from the mangrove Avicennia increases salt tolerance of rice and Arabidopsis, and specific bHLH transcription factors regulate AtNHX1 and AtNHX6 in Arabidopsis to mediate the salinity response. Improving crop plants to better tolerate soil salinity is a challenging task. Mangrove trees such as Avicennia officinalis have special adaptations to thrive in high salt conditions, which include subcellular compartmentalization of ions facilitated by specialized ion transporters. We identified and characterized two genes encoding Na⁺/H⁺ exchangers AoNHX1 and AoNHX6 from Avicennia. AoNHX1 was present in the tonoplast, while, AoNHX6 was localized to the ER and Golgi. Both NHXs were induced by NaCl treatment, with AoNHX1 showing high expression levels in the leaves and AoNHX6 in the seedling roots. Yeast deletion mutants (ena1-5Δ nha1Δ nhx1Δ and ena1-5Δ nha1Δ vnx1Δ) complemented with AoNHX1 and AoNHX6 showed increased tolerance to both NaCl and KCl. Expression of AoNHX1 and AoNHX6 in the corresponding Arabidopsis mutants conferred enhanced NaCl tolerance. The underlying molecular regulatory mechanism was investigated using AtNHX1 and AtNHX6 in Arabidopsis. We identified two basic helix-loop-helix (bHLH) transcription factors AtMYC2 and AtbHLH122 as the ABA-mediated upstream regulators of AtNHX1 and AtNHX6 by chromatin immunoprecipitation. Furthermore, expression of AtNHX1 and AtNHX6 transcripts was reduced in the atmyc2 and atbhlh122 mutants. Lastly, transgenic rice seedlings harboring pUBI::AoNHX1 showed enhanced salt tolerance, suggesting that this gene can be exploited for developing salt-tolerant crops.

The jasmonate-ZIM domain gene VqJAZ4 from the Chinese wild grape Vitis quinquangularis improves resistance to powdery mildew in Arabidopsis thaliana

Grape (Vitis vinifera L.) is one of the most widely cultivated and economically important fruits. Most cultivated varieties of grape are highly susceptible to fungal diseases, and one of the most pervasive is powdery mildew, caused by Uncinula necator. The jasmonate-ZIM domain (JAZ) family proteins are critical for plant responses to environmental stresses. Here, we report the characterization of VqJAZ4, a jasmonate-ZIM domain gene isolated from Vitis quinquangularis, a Chinese wild Vitis species that exhibits high tolerance to several kinds of fungi. Subcellular localization assay indicated that the VqJAZ4 protein is targeted to the nucleus. The VqJAZ4 gene was strongly induced by U. necator inoculation, as well as by the defense-related hormones methyl jasmonate (MeJA) and salicylic acid (SA). The upregulation of VqJAZ4 after inoculation was dependent on its promoter sequences. Expression of VqJAZ4 in Arabidopsis thaliana improved resistance to powdery mildew. Histochemical staining assays indicated that plants expressing VqJAZ4 displayed a larger number of dead cells and stronger reactive oxygen species (ROS) burst than non-transgenic control (NTC) plants. Expression analysis of several disease-related genes suggested that VqJAZ4 expression enhanced defense responses though SA and/or JA signaling pathways. We also found that VqJAZ4-expressing Arabidopsis showed increased susceptibility to Botrytis cinerea. Taken together, these results provide evidence that VqJAZ4 may play an important role in response to fungal pathogens in grape, and may represent a candidate for future grape molecular breeding for disease resistance.

Jasmonate-Related MYC Transcription Factors Are Functionally Conserved in Marchantia polymorpha

The lipid-derived phytohormone jasmonoyl-isoleucine regulates plant immunity, growth and development in vascular plants by activating genome-wide transcriptional reprogramming. In Arabidopsis (Arabidopsis thaliana), this process is largely orchestrated by the master regulator MYC2 and related transcription factors (TFs). However, the TFs activating this pathway in basal plant lineages are currently unknown. We report the functional conservation of MYC-related TFs between the eudicot Arabidopsis and the liverwort Marchantia polymorpha, a plant belonging to an early diverging lineage of land plants. Phylogenetic analysis suggests that MYC function first appeared in charophycean algae and therefore predates the evolutionary appearance of any other jasmonate pathway component. M. polymorpha possesses two functionally interchangeable MYC genes, one in females and one in males. Similar to AtMYC2, MpMYCs showed nuclear localization, interaction with JASMONATE-ZIM-DOMAIN PROTEIN repressors, and regulation by light. Phenotypic and molecular characterization of loss- and gain-of-function mutants demonstrated that MpMYCs are necessary and sufficient for activating the jasmonate pathway in M. polymorpha, but unlike their Arabidopsis orthologs, do not regulate fertility. Therefore, despite 450 million years of independent evolution, MYCs are functionally conserved between bryophytes and eudicots. Genetic conservation in an early diverging lineage suggests that MYC function existed in the common ancestor of land plants and evolved from a preexisting MYC function in charophycean algae.

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.

LEUNIG_HOMOLOG Mediates MYC2-Dependent Transcriptional Activation in Cooperation with the Coactivators HAC1 and MED25

Groucho/Thymidine uptake 1 (Gro/Tup1) family proteins are evolutionarily conserved transcriptional coregulators in eukaryotic cells. Despite their prominent function in transcriptional repression, little is known about their role in transcriptional activation and the underlying mechanism. Here, we report that the plant Gro/Tup1 family protein LEUNIG_HOMOLOG (LUH) activates MYELOCYTOMATOSIS2 (MYC2)-directed transcription of JAZ2 and LOX2 via the Mediator complex coactivator and the histone acetyltransferase HAC1. We show that the Mediator subunit MED25 physically recruits LUH to MYC2 target promoters that then links MYC2 with HAC1-dependent acetylation of Lys-9 of histone H3 (H3K9ac) to activate JAZ2 and LOX2 Moreover, LUH promotes hormone-dependent enhancement of protein interactions between MYC2 and its coactivators MED25 and HAC1. Our results demonstrate that LUH interacts with MED25 and HAC1 through its distinct domains, thus imposing a selective advantage by acting as a scaffold for MYC2 activation. Therefore, the function of LUH in regulating jasmonate signaling is distinct from the function of TOPLESS, another member of the Gro/Tup1 family that represses MYC2-dependent gene expression in the resting stage.

Arabidopsis FHY3 and FAR1 Regulate the Balance between Growth and Defense Responses under Shade Conditions

Increasing crop yield per unit of area can be achieved by increasing planting density. However, high-density planting could trigger shade avoidance responses, which cause exaggerated growth and increased susceptibility to various diseases. Previous studies have shown that the rapid elongation of plants under shade (i.e., reduced red to far-red ratios) is regulated by phytochromes and various phytohormones. However, the detailed molecular mechanisms governing the interaction among these signaling pathways are not well understood. Here, we report that loss-of-function mutants of FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), which encode two homologous transcription factors essential for phytochrome signaling, exhibit an exaggerated shade avoidance phenotype. We show that FHY3 and FAR1 repress plant growth through directly activating the expression of two atypical basic helix-loop-helix transcriptional cofactors, PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2, and that this process is antagonized by a group of JASMONATE ZIM-DOMAIN proteins, key repressors of the jasmonic acid (JA) signaling pathway, through physical interactions. Furthermore, we show that FHY3 interacts with MYC2, a key transcriptional regulator of JA responses, coordinately regulating JA-responsive defense gene expression. Our results unveil a previously unrecognized mechanism whereby plants balance their growth and defense responses through convergence of the phytochrome signaling pathway and JA signaling pathway under shade conditions.

Nodulation Induces Systemic Resistance of Medicago truncatula and Pisum sativum Against Erysiphe pisi and Primes for Powdery Mildew-Triggered Salicylic Acid Accumulation

Plants encounter beneficial and detrimental microorganisms both above- and belowground and the health status of the plant depends on the composition of this pan-microbiome. Beneficial microorganisms contribute to plant nutrition or systemically or locally protect plants against pathogens, thus facilitating adaptation to a variety of environments. Induced systemic resistance, caused by root-associated microbes, manifests as aboveground resistance against necrotrophic pathogens and is mediated by jasmonic acid/ethylene-dependent signaling. By contrast, systemic acquired resistance relies on salicylic acid (SA) signaling and confers resistance against secondary infection by (hemi)biotrophic pathogens. To investigate whether symbiotic rhizobia that are ubiquitously found in natural ecosystems are able to modulate resistance against biotrophs, we tested the impact of preestablished nodulation of Medicago truncatula and pea (Pisum sativum) plants against infection by the powdery mildew fungus Erysiphe pisi. We found that root symbiosis interfered with fungal penetration of M. truncatula and reduced asexual spore formation on pea leaves independently of symbiotic nitrogen fixation. Improved resistance of nodulated plants correlated with elevated levels of free SA and SA-dependent marker gene expression upon powdery mildew infection. Our results suggest that nodulation primes the plants systemically for E. pisi-triggered SA accumulation and defense gene expression, resulting in increased resistance.

RNA-seq of eight different poplar clones reveals conserved up-regulation of gene expression in response to insect herbivory

BACKGROUND

Herbivorous insects can have a profound impact on plant growth performance. In some years, canopy damage in poplar plantations exceeds 50% of the total leaf surface, thereby possibly compromising carbon fixation and biomass yield. To assess the transcriptional response of elite poplar clones to insect feeding and to test whether this response varies between different genotypes, we performed an RNA-sequencing experiment. We deeply sequenced the transcriptomes of eight elite clones belonging to three poplar species (Populus trichocarpa, P. nigra and P. maximowiczii), under Phratora vitellinae feeding and control conditions. This allowed us to precisely quantify transcript levels of about 24,000 expressed genes.

RESULTS

Our data reveal a striking overall up-regulation of gene expression under insect attack in all eight poplar clones studied. The up-regulated genes were markedly enriched for the biological process 'regulation of transcription' indicating a highly concerted restructuring of the transcriptome. A search for potential cis-regulatory elements (CREs) that may be involved in this process identified the G-box (CACGTG) as the most significant motif in the promoters of the induced genes. In line with the role of the G-box in jasmonate (JA)-mediated activation of gene expression by MYC2, several genes involved in JA biosynthesis and signaling were up-regulated in our dataset. A co-expression network analysis additionally highlighted WRKY transcription factors. Within the most prominent expression module, WRKYs were strongly overrepresented and occupied several network hubs. Finally, the insect-induced genes comprised several protein families known to be involved in plant defenses, e.g. cytochrome P450s, chitinases and protease inhibitors.

CONCLUSIONS

Our data represent a comprehensive characterization of the transcriptional response of selected elite poplar clones to insect herbivory. Our results suggest that the concerted up-regulation of gene expression is controlled by JA signaling and WRKY transcription factors, and activates several defense mechanisms. Our data highlight potential targets of selection and may thus contribute to breeding insect-resistant poplar clones.

Tackling Plant Phosphate Starvation by the Roots

Plant responses to phosphate deprivation encompass a wide range of strategies, varying from altering root system architecture, entering symbiotic interactions to excreting root exudates for phosphorous release, and recycling of internal phosphate. These processes are tightly controlled by a complex network of proteins that are specifically upregulated upon phosphate starvation. Although the different effects of phosphate starvation have been intensely studied, the full extent of its contribution to altered root system architecture remains unclear. In this review, we focus on the effect of phosphate starvation on the developmental processes that shape the plant root system and their underlying molecular pathways.

Effects of Jasmonate on Ethylene Function during the Development of Tomato Stamens

The phenotype of the tomato mutant jasmonate-insensitive1-1 (jai1-1) mutated in the JA-Ile co-receptor COI1 demonstrates JA function in flower development, since it is female-sterile. In addition, jai1-1 exhibits a premature anther dehydration and pollen release, being in contrast to a delayed anther dehiscence in the JA-insensitive Arabidopsis mutant coi1-1. The double mutant jai1-1 Never ripe (jai1-1 Nr), which is in addition insensitive to ethylene (ET), showed a rescue of the jai1-1 phenotype regarding pollen release. This suggests that JA inhibits a premature rise in ET to prevent premature stamen desiccation. To elucidate the interplay of JA and ET in more detail, stamen development in jai1-1 Nr was compared to wild type, jai1-1 and Nr regarding water content, pollen vitality, hormone levels, and accumulation of phenylpropanoids and transcripts encoding known JA- and ET-regulated genes. For the latter, RT-qPCR based on nanofluidic arrays was employed. The data showed that additional prominent phenotypic features of jai1-1, such as diminished water content and pollen vitality, and accumulation of phenylpropanoids were at least partially rescued by the ET-insensitivity. Hormone levels and accumulation of transcripts were not affected. The data revealed that strictly JA-regulated processes cannot be rescued by ET-insensitivity, thereby emphasizing a rather minor role of ET in JA-regulated stamen development.

Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon

Myelocytomatosis oncogenes (MYC) transcription factors (TFs) belong to basic helix-loop-helix (bHLH) TF family and have a special bHLH_MYC_N domain in the N-terminal region. Presently, there is no detailed and systematic analysis of MYC TFs in wheat, rice, and Brachypodium distachyon. In this study, 26 TaMYC, 7 OsMYC, and 7 BdMYC TFs were identified and their features were characterized. Firstly, they contain a JAZ interaction domain (JID) and a putative transcriptional activation domain (TAD) in the bHLH_MYC_N region and a BhlH region in the C-terminal region. In some cases, the bHLH region is followed by a leucine zipper region; secondly, they display tissue-specific expression patterns: wheat MYC genes are mainly expressed in leaves, rice MYC genes are highly expressed in stems, and B. distachyon MYC genes are mainly expressed in inflorescences. In addition, three types of cis-elements, including plant development/growth-related, hormone-related, and abiotic stresses-related were identified in different MYC gene promoters. In combination with the previous studies, these results indicate that MYC TFs mainly function in growth and development, as well as in response to stresses. This study laid a foundation for the further functional elucidation of MYC genes.

Co-orthologues of ribosome biogenesis factors in A. thaliana are differentially regulated by transcription factors

Different genes coding for one ribosome biogenesis factor are differentially expressed and are likely under the control of distinct transcription factors, which contributes to the regulatory space for ribosome maturation. Maturation of ribosomes including rRNA processing and modification, rRNA folding and ribosome protein association requires the function of many ribosome biogenesis factors (RBFs). Recent studies document plant-specific variations of the generally conserved process of ribosome biogenesis. For instance, distinct rRNA maturation pathways and intermediates have been identified, the existence of plant specific RBFs has been proposed and several RBFs are encoded by multiple genes. The latter in combination with the discussed ribosome heterogeneity points to a possible function of the different proteins representing one RBF in diversification of ribosomal compositions. Such factor-based regulation would require a differential regulation of their expression, may be even controlled by different transcription factors. We analyzed the expression profiles of genes coding for putative RBFs and transcription factors. Most of the genes coding for RBFs are expressed in a comparable manner, while different genes coding for a single RBF are often differentially expressed. Based on a selected set of genes we document a function of the transcription factors AtMYC1, AtMYC2, AtbHLH105 and AtMYB26 on the regulation of different RBFs. Moreover, on the example of the RBFs LSG1 and BRX1, both encoded by two genes, we give a first hint on a differential transcription factor dependence of expression. Consistent with this observation, the phenotypic analysis of RBF mutants suggests a relation between LSG1-1 and BRX1-1 expression and the transcription factor MYC1. In summary, we propose that the multiple genes coding for one RBF are required to enlarge the regulatory space for ribosome biogenesis.

Role of calreticulin in biotic and abiotic stress signalling and tolerance mechanisms in plants

Calreticulin (CRT) is calcium binding protein of endoplasmic reticulum (ER) which performs plethora of functions besides it's role as molecular chaperone. Among the three different isoforms of this protein, CRT3 is most closely related to primitive CRT gene of higher plants. Based on their distinct structural and functional organisation, the plant CRTs have been known to contain three different domains: N, P and the C domain. The domain organisation and various biochemical characterstics of plant and animal CRTs are common with the exception of some differences. In plant calreticulin, the important N-glycosylation site(s) are replaced by the glycan chain(s) and several consensus sequences for in vitro phosphorylation by protein kinase CK2 (casein kinase-2), are also present unlike the animal calreticulin. Biotic and abiotic stresses play a significant role in bringing down the crop production. The role of various phytohormones in defense against fungal pathogens is well documented. CRT3 has been reported to play important role in protecting the plants against fungal and bacterial pathogens and in maintaining plant innate immunity. There is remarkable crosstalk between CRT mediated signalling and biotic, abiotic stress, and phytohormone mediated signalling pathways The role of CRT mediated pathway in mitigating biotic and abiotic stress can be further explored in plants so as to strategically modify it for development of stress tolerant plants.

The plant Mediator complex and its role in jasmonate signaling

The Mediator complex is an essential, multisubunit transcriptional coactivator that is highly conserved in eukaryotes. Mediator interacts with gene-specific transcription factors, the RNA polymerase II transcriptional machinery, as well as several other factors involved in transcription, and acts as an integral hub to regulate various aspects of transcription. Recent studies of the plant Mediator complex have established that it functions in diverse aspects of plant development and fitness. Jasmonate (JA) is an oxylipin-derived plant hormone that regulates plant immunity and development. The basic helix-loop-helix transcription factor MYC2, which is a master regulator of JA signaling, orchestrates genome-wide transcriptional reprogramming of plant cells to coordinate defense- and growth-related processes. Here, we review the function of the plant Mediator complex in regulating JA signaling. We focus on the multifunctional Mediator subunit MED25, which emerges as an integrative hub for the transcriptional regulation of jasmonate signaling.

Jasmonate action in plant defense against insects

Herbivorous insects represent one of the major threats to sessile plants. To cope with herbivore challenges, plants have evolved sophisticated defense systems, in which the lipid-derived phytohormone jasmonate plays a crucial role. Perception of insect attack locally and systemically elicits rapid synthesis of jasmonate, which is perceived by the F-box protein COI1 to further recruit JAZ repressors for ubiquitination and degradation, thereby releasing transcription factors that subsequently activate plant defense against insect attack. Here, we review recent progress in understanding the molecular basis of jasmonate action in plant defense against insects.

Jasmonate and auxin perception: how plants keep F-boxes in check

Phytohormones regulate the plasticity of plant growth and development, and responses to biotic and abiotic stresses. Many hormone signal transduction cascades involve ubiquitination and subsequent degradation of proteins by the 26S proteasome. The conjugation of ubiquitin to a substrate is facilitated by the E1 activating, E2 conjugating, and the substrate-specifying E3 ligating enzymes. The most prevalent type of E3 ligase in plants is the Cullin-RING ligase (CRL)-type, with F-box proteins (FBPs) as the substrate recognition component. The activity of these SKP-Cullin-F-box (SCF) complexes needs to be tightly regulated in time and place. Here, we review the regulation of SCF function in plants on multiple levels, with a focus on the auxin and jasmonate SCF-type receptor complexes. We discuss in particular the relevance of protein-protein interactions and post-translational modifications as mechanisms to keep SCF functioning under control. Additionally, we highlight the unique property of SCFTIR1/AFB and SCFCOI1 to recognize substrates by forming co-receptor complexes. Finally, we explore how engineered selective agonists can be used to study and uncouple the outcomes of the complex auxin and jasmonate signaling networks that are governed by these FBPs.

Genome-Wide Identification and Characterization of JAZ Protein Family in Two Petunia Progenitors

Jasmonate ZIM-domain (JAZ) family proteins are the key repressors in the jasmonate signaling pathway and play crucial roles in plant development, defenses, and responses to stresses. However, our knowledge about the JAZ protein family in petunia is limited. This research respectively identified 12 and 16 JAZ proteins in two Petunia progenitors, Petunia axillaris and Petunia inflata. Phylogenetic analysis showed that the 28 proteins could be divided into four groups (Groups A–D) and further classified into six subgroups (A1, A2, B1, B3, C, and D1); members in the same subgroup shared some similarities in motif composition and sequence structure. The Ka/Ks ratios of seven paralogous pairs were less than one, suggesting the petunia JAZ family might have principally undergone purifying selection. Quantitative real-time PCR (qRT-PCR) analysis revealed that PaJAZ genes presented differential expression patterns during the development of flower bud and anther in petunia, and the expression of PaJAZ5, 9, 12 genes was generally up-regulated after MeJA treatment. Subcellular localization assays demonstrated that proteins PaJAZ5, 9, 12 were localized in nucleus. Yeast two hybrid (Y2H) elucidated most PaJAZ proteins (PaJAZ1-7, 9, 12) might interact with transcription factor MYC2. This study provides insights for further investigation of functional analysis in petunia JAZ family proteins.

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

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

Molecular Basis of Natural Variation in Photoperiodic Flowering Responses

Plants exhibit different flowering behaviors in response to variable photoperiods across a wide geographical range. Here, we identify MYC3, a bHLH transcription factor, and its cis-element form the long-sought regulatory module responsible for cis-regulatory changes at the florigen gene FLOWERING LOCUS T (FT) that mediate natural variation in photoperiodic flowering responses in Arabidopsis. MYC3 is stabilized by DELLAs in the gibberellin pathway to suppress FT through binding the ACGGAT motif and antagonizing CONSTANS (CO) activation. Changing photoperiods modulate the relative abundance of MYC3 and CO, thus determining either of them as the predominant regulator for FT expression under different day lengths. Cis-regulatory changes in the MYC3 binding site at FT are associated with natural variation in day-length requirement for flowering in Arabidopsis accessions. Our findings reveal that environmental and developmental signals converge at MYC3 suppression of FT, an elementary event underlying natural variation in photoperiodic flowering responses.

MED25 connects enhancer-promoter looping and MYC2-dependent activation of jasmonate signalling

The lipid-derived hormone jasmonate (JA) regulates plant immunity and adaptive growth by triggering a genome-wide transcriptional programme. In Arabidopsis thaliana, JA-triggered transcriptional programming is largely orchestrated by the master transcription factor MYC2. The function of MYC2 is dependent on its physical interaction with the MED25 subunit of the Mediator transcriptional co-activator complex. Here we report the identification of JA enhancers (JAEs) through profiling the occupancy pattern of MYC2 and MED25. JA regulates the dynamic chromatin looping between JAEs and their promoters in a MED25-dependent manner, while MYC2 auto-regulates itself through JAEs. Interestingly, the JAE of the MYC2 locus (named ME2) positively regulates MYC2 expression during short-term JA responses but negatively regulates it during constant JA responses. We demonstrate that new gene editing tools open up new avenues to elucidate the in vivo function of enhancers. Our work provides a paradigm for functional study of plant enhancers in the regulation of specific physiological processes.

MED25 connects enhancer-promoter looping and MYC2-dependent activation of jasmonate signalling

The lipid-derived hormone jasmonate (JA) regulates plant immunity and adaptive growth by triggering a genome-wide transcriptional programme. In Arabidopsis thaliana, JA-triggered transcriptional programming is largely orchestrated by the master transcription factor MYC2. The function of MYC2 is dependent on its physical interaction with the MED25 subunit of the Mediator transcriptional co-activator complex. Here we report the identification of JA enhancers (JAEs) through profiling the occupancy pattern of MYC2 and MED25. JA regulates the dynamic chromatin looping between JAEs and their promoters in a MED25-dependent manner, while MYC2 auto-regulates itself through JAEs. Interestingly, the JAE of the MYC2 locus (named ME2) positively regulates MYC2 expression during short-term JA responses but negatively regulates it during constant JA responses. We demonstrate that new gene editing tools open up new avenues to elucidate the in vivo function of enhancers. Our work provides a paradigm for functional study of plant enhancers in the regulation of specific physiological processes.

The study of hormonal metabolism of Trincadeira and Syrah cultivars indicates new roles of salicylic acid, jasmonates, ABA and IAA during grape ripening and upon infection with Botrytis cinerea

Hormones play an important role in fruit ripening and in response to biotic stress. Nevertheless, analyses of hormonal profiling during plant development and defense are scarce. In this work, changes in hormonal metabolism in grapevine (Vitis vinifera) were compared between a susceptible (Trincadeira) and a tolerant (Syrah) variety during grape ripening and upon infection with Botrytis cinerea. Infection of grapes with the necrotrophic pathogen Botrytis cinerea leads to significant economic losses worldwide. Peppercorn-sized fruits were infected in the field and mock-treated and infected berries were collected at green, veraison and harvest stages for hormone analysis and targeted qPCR analysis of genes involved in hormonal metabolism and signaling. Results indicate a substantial reprogramming of hormonal metabolism during grape ripening and in response to fungal attack. Syrah and Trincadeira presented differences in the metabolism of abscisic acid (ABA), indole-3-acetic acid (IAA) and jasmonates during grape ripening that may be connected to fruit quality. On the other hand, high basal levels of salicylic acid (SA), jasmonates and IAA at an early stage of ripening, together with activated SA, jasmonates and IAA signaling, likely enable a fast defense response leading to grape resistance/ tolerance towards B. cinerea. The balance among the different phytohormones seems to depend on the ripening stage and on the intra-specific genetic background and may be fundamental in providing resistance or susceptibility. In addition, this study indicated the involvement of SA and IAA in defense against necrotrophic pathogens and gains insights into possible strategies for conventional breeding and/or gene editing aiming at improving grape quality and grape resistance against Botrytis cinerea.

JASSY, a chloroplast outer membrane protein required for jasmonate biosynthesis

Jasmonates are vital plant hormones that not only act in the stress response to biotic and abiotic influences, such as wounding, pathogen attack, and cold acclimation, but also drive developmental processes in cooperation with other plant hormones. The biogenesis of jasmonates starts in the chloroplast, where several enzymatic steps produce the jasmonate precursor 12-oxophytodienoic acid (OPDA) from α-linolenic acid. OPDA in turn is exported into the cytosol for further conversion into active jasmonates, which subsequently induces the expression of multiple genes in the nucleus. Despite its obvious importance, the export of OPDA across the chloroplast membranes has remained elusive. In this study, we characterized a protein residing in the chloroplast outer membrane, JASSY, which has proven indispensable for the export of OPDA from the chloroplast. We provide evidence that JASSY has channel-like properties and propose that it thereby facilitates OPDA transport. Consequently, a lack of JASSY in Arabidopsis leads to a deficiency in accumulation of jasmonic acids, which results in impaired expression of jasmonate target genes on exposure to various stresses. This results in plants that are more susceptible to pathogen attack and also exhibit defects in cold acclimation.

Induction of PR-10 genes and metabolites in strawberry plants in response to Verticillium dahliae infection

BACKGROUND

The soil-borne vascular pathogen Verticillium dahliae causes severe wilt symptoms in a wide range of plants including strawberry (Fragaria × ananassa). To enhance our understanding of the effects of V. dahliae on the growth and development of F. × ananassa, the expression patterns of 21 PR-10 genes were investigated by qPCR analysis and metabolite changes were determined by LC-MS in in vitro F. × ananassa plants upon pathogen infection.

RESULTS

The expression patterns of the 21 isoforms showed a wide range of responses. Four PR-10 genes were highly induced in leaves upon pathogen infection while eight members were significantly up-regulated in roots. A simultaneously induced expression in leaves and roots was detected for five PR-10 genes. Interestingly, two isoforms were expressed upon infection in all three tissues (leaves, roots and stems) while no induction was detected for two other members. Accumulation of antifungal catechin and epicatechin was detected upon pathogen infection in roots and stems at late stages, while caffeic acid and citric acid were observed only in infected roots. Production of abscisic acid, salicylic acid, jasmonic acid (JA), gibberellic acid and indole acetic acid (IAA) was induced in infected leaves and stems at early stages. IAA and JA were the sole hormones to be ascertained in infected roots at late stages.

CONCLUSIONS

The induction of several PR-10 genes upon infection of strawberry plants with V. dahliae suggest a role of PR-10 genes in the defense response against this pathogen. Production of phytohormones in the early stages of infection and antifungal metabolites in late stages suppose that they are implicated in this response. The results may possibly improve the control measures of the pathogen.