Dual regulation role of GH3.5 in salicylic acid and auxin signaling during Arabidopsis-Pseudomonas syringae interaction

In-depth analysis of isochorismate synthase-derived metabolism in plant immunity: identification of meta-substituted benzoates and salicyloyl-malate

Isochorismate-derived metabolism enables biosynthesis of the plant defence hormone salicylic acid (SA) and its derivatives. In Arabidopsis thaliana, the stress-induced accumulation of SA depends on ISOCHORISMATE SYNTHASE1 (ICS1), and also requires the presumed isochorismate transporter ENHANCED DISEASE SUSCEPTIBILITY5 (EDS5) and the GH3 enzyme avrPphB SUSCEPTIBLE3 (PBS3). By comparative metabolite and structural analyses, we identified several hitherto unreported ICS1- and EDS5-dependent, biotic stress-inducible Arabidopsis metabolites. These involve meta-substituted SA derivatives (5-formyl-SA, 5-carboxy-SA, 5-carboxymethyl-SA), their benzoic acid (BA) analogues (3-formyl-BA, 3-carboxy-BA, 3-carboxymethyl-BA) and, besides the previously detected salicyloyl-aspartate (SA-Asp), the ester conjugate salicyloyl-malate (SA-Mal). SA functions as a biosynthetic precursor for SA-Mal and SA-Asp, but not for the meta-substituted SA- and BA-derivatives, which accumulate to moderate levels at later stages of bacterial infection. Interestingly, Arabidopsis leaves possess oxidising activity to effectively convert meta-formyl- into meta-carboxy-SA/BAs. In contrast to SA, exogenously applied meta-substituted SA/BA-derivatives and SA-Mal exert moderate impact on plant immunity and defence-related gene expression. While the isochorismate-derived metabolites are negatively regulated by the SA receptor NON-EXPRESSOR OF PR GENES1, SA conjugates (SA-Mal, SA-Asp, SA-glucose conjugates) and meta-substituted SA/BA-derivatives are oppositely affected by PBS3. Notably, our data indicate a PBS3-independent path to isochorismate-derived SA at later stages of bacterial infection, which does not considerably impact immune-related characteristics. Moreover, our results argue against a previously proposed role of EDS5 in the biosynthesis of the immune signal N-hydroxypipecolic acid and associated transport processes. We propose a significantly extended biochemical scheme of plant isochorismate metabolism that involves an alternative generation mode for benzoate- and salicylate-derivatives.

Indole-3-propionic acid regulates lateral root development by targeting auxin signaling in Arabidopsis

Indole-3-propionic acid (IPA) is known to be a microbe-derived compound with a similar structure to the phytohormone auxin (indole-3-acetic acid, IAA). Previous studies reported that IPA exhibited auxin-like bioactivities in plants. However, the underlying molecular mechanism is not totally understood. Here, we revealed that IPA modulated lateral root (LR) development via auxin signaling in the model plant Arabidopsis thaliana. Genetic analysis indicated that deficiency of the TIR1/AFB-Aux/IAA-ARF auxin signaling pathway abolished the effects of IPA on regulating LR development. Further biochemical, transcriptomic profiling and cell biological analyses revealed that IPA directly bound to the TIR1/AFB-Aux/IAA coreceptor complex and thus activated downstream gene expression. Therefore, our work revealed that IPA is a potential signaling molecule that modulates plant growth and development by targeting the TIR1/AFB-Aux/IAA-mediated auxin signaling pathway, providing potential insights into root growth regulation in plants.

CaIAA2-CaARF9 module mediates the trade-off between pepper growth and immunity

To challenge the invasion of various pathogens, plants re-direct their resources from plant growth to an innate immune defence system. However, the underlying mechanism that coordinates the induction of the host immune response and the suppression of plant growth remains unclear. Here we demonstrate that an auxin response factor, CaARF9, has dual roles in enhancing the immune resistance to Ralstonia solanacearum infection and in retarding plant growth by repressing the expression of its target genes as exemplified by Casmc4, CaLBD37, CaAPK1b and CaRROP1. The expression of these target genes not only stimulates plant growth but also negatively impacts pepper resistance to R. solanacearum. Under normal conditions, the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 is active when promoter-bound CaARF9 is complexed with CaIAA2. Under R. solanacearum infection, however, degradation of CaIAA2 is triggered by SA and JA-mediated signalling defence by the ubiquitin-proteasome system, which enables CaARF9 in the absence of CaIAA2 to repress the expression of Casmc4, CaLBD37, CaAPK1b and CaRROP1 and, in turn, impeding plant growth while facilitating plant defence to R. solanacearum infection. Our findings uncover an exquisite mechanism underlying the trade-off between plant growth and immunity mediated by the transcriptional repressor CaARF9 and its deactivation when complexed with CaIAA2.

Fidelity in plant hormone modifications catalyzed by Arabidopsis GH3 acyl acid amido synthetases

GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases conjugate amino acids to acyl acid hormones to either activate or inactivate the hormone molecule. The largest subgroup of GH3 proteins modify the growth-promoting hormone auxin (indole-3-acetic acid; IAA) with the second largest class activating the defense hormone jasmonic acid (JA). The two-step reaction mechanism of GH3 proteins provides a potential proofreading mechanism to ensure fidelity of hormone modification. Examining pyrophosphate release in the first-half reaction of Arabidopsis GH3 proteins that modify IAA (AtGH3.2/YDK2, AtGH3.5/WES1, AtGH3.17/VAS2), JA (AtGH3.11/JAR1), and other acyl acids (AtGH3.7, AtGH3.12/PBS3) indicates that acyl acid-AMP intermediates are hydrolyzed into acyl acid and AMP in the absence of the amino acid, a typical feature of pre-transfer editing mechanisms. Single-turnover kinetic analysis of AtGH3.2/YDK2 and AtGH3.5/WES1 shows that non-cognate acyl acid-adenylate intermediates are more rapidly hydrolyzed than the cognate IAA-adenylate. In contrast, AtGH3.11/JAR1 only adenylates JA, not IAA. While some of the auxin-conjugating GH3 proteins in Arabidopsis (i.e., AtGH3.5/WES1) accept multiple acyl acid substrates, others, like AtGH3.2/YDK2, are specific for IAA; however, both these proteins share similar active site residues. Biochemical analysis of chimeric variants of AtGH3.2/YDK2 and AtGH3.5/WES1 indicates that the C-terminal domain contributes to selection of cognate acyl acid substrates. These findings suggest that the hydrolysis of non-cognate acyl acid-adenylate intermediates, or proofreading, proceeds via a slowed structural switch that provides a checkpoint for fidelity before the full reaction proceeds.

Transcription factor WRKY75 maintains auxin homeostasis to promote tomato defense against Pseudomonas syringae

The hemibiotrophic bacterial pathogen Pseudomonas syringae infects a range of plant species and causes enormous economic losses. Auxin and WRKY transcription factors play crucial roles in plant responses to P. syringae, but their functional relationship in plant immunity remains unclear. Here, we characterized tomato (Solanum lycopersicum) SlWRKY75, which promotes defenses against P. syringae pv. tomato (Pst) DC3000 by regulating plant auxin homeostasis. Overexpressing SlWRKY75 resulted in low free indole-3-acetic acid (IAA) levels, leading to attenuated auxin signaling, decreased expansin transcript levels, upregulated expression of PATHOGENESIS-RELATED GENES (PRs) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENE 1 (NPR1), and enhanced tomato defenses against Pst DC3000. RNA interference-mediated repression of SlWRKY75 increased tomato susceptibility to Pst DC3000. Yeast one-hybrid, electrophoretic mobility shift assays, and luciferase activity assays suggested that SlWRKY75 directly activates the expression of GRETCHEN HAGEN 3.3 (SlGH3.3), which encodes an IAA-amido synthetase. SlGH3.3 enhanced tomato defense against Pst DC3000 by converting free IAA to the aspartic acid (Asp)-conjugated form IAA-Asp. In addition, SlWRKY75 interacted with a tomato valine-glutamine (VQ) motif-containing protein 16 (SlVQ16) in vivo and in vitro. SlVQ16 enhanced SlWRKY75-mediated transcriptional activation of SlGH3.3 and promoted tomato defense responses to Pst DC3000. Our findings illuminate a mechanism in which the SlVQ16-SlWRKY75 complex participates in tomato pathogen defense by positively regulating SlGH3.3-mediated auxin homeostasis.

Carrier-based delivery system of phytohormones in plants: stepping outside of the ordinary

Climate change is increasing the stresses on crops, resulting in reduced productivity and further augmenting global food security issues. The dynamic climatic conditions are a severe threat to the sustainability of the ecosystems. The role of technology in enhancing agricultural produce with the minimum environmental impact is hence crucial. Active molecule/Plant growth regulators (PGRs) are molecules helping plants' growth, development, and tolerance to abiotic and biotic stresses. However, their degradation, leaching in surrounding soil and ground water, as well as the assessment of the correct dose of application etc., are some of the technical disadvantages faced. They can be resolved by encapsulation/loading of PGRs on polymer matrices. Micro/nanoencapsulation is a revolutionary tool to deliver bioactive compounds in an economically affordable and environmentally friendly way. Carrier-based smart delivery systems could be a better alternative to PGRs application in the agriculture field than conventional methods (e.g., spraying). The physiochemical properties and release kinetics of PGRs from the encapsulating system are being explored. Therefore, the present review emphasizes the current status of PGRs encapsulation approach and their potential benefits to plants. This review also addressed the mechanistic action of carrier-based delivery systems for release, which may aid in developing smart delivery systems with specific tailored properties in future research.

Harnessing Phytohormones: Advancing Plant Growth and Defence Strategies for Sustainable Agriculture

Phytohormones, pivotal regulators of plant growth and development, are increasingly recognized for their multifaceted roles in enhancing crop resilience against environmental stresses. In this review, we provide a comprehensive synthesis of current research on utilizing phytohormones to enhance crop productivity and fortify their defence mechanisms. Initially, we introduce the significance of phytohormones in orchestrating plant growth, followed by their potential utilization in bolstering crop defences against diverse environmental stressors. Our focus then shifts to an in-depth exploration of phytohormones and their pivotal roles in mediating plant defence responses against biotic stressors, particularly insect pests. Furthermore, we highlight the potential impact of phytohormones on agricultural production while underscoring the existing research gaps and limitations hindering their widespread implementation in agricultural practices. Despite the accumulating body of research in this field, the integration of phytohormones into agriculture remains limited. To address this discrepancy, we propose a comprehensive framework for investigating the intricate interplay between phytohormones and sustainable agriculture. This framework advocates for the adoption of novel technologies and methodologies to facilitate the effective deployment of phytohormones in agricultural settings and also emphasizes the need to address existing research limitations through rigorous field studies. By outlining a roadmap for advancing the utilization of phytohormones in agriculture, this review aims to catalyse transformative changes in agricultural practices, fostering sustainability and resilience in agricultural settings.

Characterization of Almond Scion/Rootstock Communication in Cultivar and Rootstock Tissues through an RNA-Seq Approach

The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive planting systems, demanding cultivars that can adapt to distinct requirements of vigor and shape. Nevertheless, considering the capacity of the rootstock genotype to influence scion development, it is likely that the scion genotype reciprocally affects rootstock performance. In the context of this study, we conducted a transcriptomic analysis of the scion/rootstock interaction in young almond trees, with a specific focus on elucidating the scion impact on the rootstock molecular response. Two commercial almond cultivars were grafted onto two hybrid rootstocks, thereby generating four distinct combinations. Through RNA-Seq analysis, we discerned that indeed, the scion genotype exerts an influence on the rootstock expression profile. This influence manifests through the modulation of genes associated with hormonal regulation, cell division, root development, and light signaling. This intricate interplay between scion and rootstock communication plays a pivotal role in the development of both scion and rootstock, underscoring the critical importance of a correct choice when establishing new almond orchards.

The Roles of GRETCHEN HAGEN3 (GH3)-Dependent Auxin Conjugation in the Regulation of Plant Development and Stress Adaptation

The precise control of free auxin (indole-3-acetic acid, IAA) gradient, which is orchestrated by biosynthesis, conjugation, degradation, hydrolyzation, and transport, is critical for all aspects of plant growth and development. Of these, the GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetase family, pivotal in conjugating IAA with amino acids, has garnered significant interest. Recent advances in understanding GH3-dependent IAA conjugation have positioned GH3 functional elucidation as a hot topic of research. This review aims to consolidate and discuss recent findings on (i) the enzymatic mechanisms driving GH3 activity, (ii) the influence of chemical inhibitor on GH3 function, and (iii) the transcriptional regulation of GH3 and its impact on plant development and stress response. Additionally, we explore the distinct biological functions attributed to IAA-amino acid conjugates.

Plant resistance to tomato yellow leaf curl virus is enhanced by Bacillus amyloliquefaciens Ba13 through modulation of RNA interference

Introduction

Tomato yellow leaf curl virus (TYLCV), which is a typical member of the genus Begomovirus, causes severe crop yield losses worldwide. RNA interference (RNAi) is an important antiviral defense mechanism in plants, but whether plant beneficial microbes used as biocontrol agents would modulate RNAi in defense against TYLCV remains unclear.

Methods

Here, we employed whole-transcriptome, bisulfite, and small RNA sequencing to decipher the possible role of Bacillus amyloliquefaciens Ba13 as a bacterial biocontrol agent against TYLCV in RNAi modulation.

Results

Potted tomato plants were exposed to whiteflies for natural viral infection 14 days after bacterial inoculation. Compared with non-inoculated controls, the abundance of TYLCV gene in the leaves of inoculated plants decreased by 70.1% at 28 days post-infection, which mirrored the pattern observed for plant disease index. The expression of the ARGONAUTE family genes (e.g., AGO3, AGO4, AGO5, and AGO7) involved in antiviral defense markedly increased by 2.44-6.73-fold following bacterial inoculation. The methylation level at CpG site 228 (in the open reading frame region of the RNA interference suppressing gene AV2) and site 461 (in the open reading frame regions of AV1 and AV2) was 183.1 and 63.0% higher in inoculated plants than in non-inoculated controls, respectively. The abundances of 10 small interfering RNAs matched to the TYLCV genome were all reduced in inoculated plants, accompanied by enhancement of photosystem and auxin response pathways.

Discussion

The results indicate that the application of Ba. amyloliquefaciens Ba13 enhances plant resistance to TYLCV through RNAi modulation by upregulating RNAi-related gene expression and enhancing viral genome methylation.

Resequencing of global Lotus corniculatus accessions reveals population distribution and genetic loci, associated with cyanogenic glycosides accumulation and growth traits

BACKGROUND

Lotus corniculatus is a widely distributed perennial legume whose great adaptability to different environments and resistance to barrenness make it an excellent forage and ecological restoration plant. However, its molecular genetics and genomic relationships among populations are yet to be uncovered.

RESULT

Here we report on a genomic variation map from worldwide 272 L. corniculatus accessions by genome resequencing. Our analysis suggests that L. corniculatus accessions have high genetic diversity and could be further divided into three subgroups, with the genetic diversity centers were located in Transcaucasia. Several candidate genes and SNP site associated with CNglcs content and growth traits were identified by genome-wide associated study (GWAS). A non-synonymous in LjMTR was responsible for the decreased expression of CNglcs synthesis genes and LjZCD was verified to positively regulate CNglcs synthesis gene CYP79D3. The LjZCB and an SNP in LjZCA promoter were confirmed to be involved in plant growth.

CONCLUSION

This study provided a large number of genomic resources and described genetic relationship and population structure among different accessions. Moreover, we attempt to provide insights into the molecular studies and breeding of CNglcs and growth traits in L. corniculatus.

SlGH3.15, a member of the GH3 gene family, regulates lateral root development and gravitropism response by modulating auxin homeostasis in tomato

Multiple Gretchen Hagen 3 (GH3) genes have been implicated in a range of processes in plant growth and development through their roles in maintaining hormonal homeostasis. However, there has only been limited study on the functions of GH3 genes in tomato (Solanum lycopersicum). In this work, we investigated the important function of SlGH3.15, a member of the GH3 gene family in tomato. Overexpression of SlGH3.15 led to severe dwarfism in both the above- and below-ground sections of the plant, accompanied by a substantial decrease in free IAA content and reduction in the expression of SlGH3.9, a paralog of SlGH3.15. Exogenous supply of IAA negatively affected the elongation of the primary root and partially restored the gravitropism defects in SlGH3.15-overexpression lines. While no phenotypic change was observed in the SlGH3.15 RNAi lines, double knockout lines of SlGH3.15 and SlGH3.9 were less sensitive to treatments with the auxin polar transport inhibitor. Overall, these findings revealed important roles of SlGH3.15 in IAA homeostasis and as a negative regulator of free IAA accumulation and lateral root formation in tomato.

Non-specific effects of the CINNAMATE-4-HYDROXYLASE inhibitor piperonylic acid

Chemical inhibitors are often implemented for the functional characterization of genes to overcome the limitations associated with genetic approaches. Although it is well established that the specificity of the compound is key to success of a pharmacological approach, off-target effects are often overlooked or simply neglected in a complex biological setting. Here we illustrate the cause and implications of such secondary effects by focusing on piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H) that is frequently used to investigate the involvement of lignin during plant growth and development. When supplied to plants, we found that PA is recognized as a substrate by GRETCHEN HAGEN 3.6 (GH3.6), an amido synthetase involved in the formation of the indole-3-acetic acid (IAA) conjugate IAA-Asp. By competing for the same enzyme, PA interferes with IAA conjugation, resulting in an increase in IAA concentrations in the plant. In line with the broad substrate specificity of the GH3 family of enzymes, treatment with PA increased not only IAA levels but also those of other GH3-conjugated phytohormones, namely jasmonic acid and salicylic acid. Finally, we found that interference with the endogenous function of GH3s potentially contributes to phenotypes previously observed upon PA treatment. We conclude that deregulation of phytohormone homeostasis by surrogate occupation of the conjugation machinery in the plant is likely a general phenomenon when using chemical inhibitors. Our results hereby provide a novel and important basis for future reference in studies using chemical inhibitors.

Evolutionary Analysis of the Melon (Cucumis melo L.) GH3 Gene Family and Identification of GH3 Genes Related to Fruit Growth and Development

The indole-3-acetic acid (IAA) auxin is an important endogenous hormone that plays a key role in the regulation of plant growth and development. In recent years, with the progression of auxin-related research, the function of the Gretchen Hagen 3 (GH3) gene has become a prominent research topic. However, studies focusing on the characteristics and functions of melon GH3 family genes are still lacking. This study presents a systematic identification of melon GH3 gene family members based on genomic data. The evolution of melon GH3 family genes was systematically analyzed by means of bioinformatics, and the expression patterns of the GH3 family genes in different melon tissues during different fruit developmental stages and with various levels of 1-naphthaleneacetic acid (NAA) induction were analyzed with transcriptomics and RT-qPCR. The melon genome contains 10 GH3 genes distributed across seven chromosomes, and most of these genes are expressed in the plasma membrane. According to evolutionary analysis and the number of GH3 family genes, these genes can be divided into three subgroups, and they have been conserved throughout the evolution of melon. The melon GH3 gene has a wide range of expression patterns across distinct tissue types, with expression generally being higher in flowers and fruit. Through promoter analysis, we found that most cis-acting elements contained light- and IAA-responsive elements. Based on the RNA-seq and RT-qPCR analyses, it can be speculated that CmGH3-5, CmGH3-6 and CmGH3-7 may be involved in the process of melon fruit development. In conclusion, our findings suggest that the GH3 gene family plays an important role in the development of melon fruit. This study provides an important theoretical basis for further research on the function of the GH3 gene family and the molecular mechanism underlying the development of melon fruit.

Exogenous abscisic acid prolongs the dormancy of recalcitrant seed of Panax notoginseng

The seeds of Panax notoginseng (Burk.) F. H. Chen are typically characterized by their recalcitrance and after-ripening process and exhibit a high water content at harvest as well as a high susceptibility to dehydration. Storage difficulty and the low germination of recalcitrant seeds of P. notoginseng are known to cause an obstacle to agricultural production. In this study, the ratio of embryo to endosperm (Em/En) in abscisic acid (ABA) treatments (1 mg·l^-1 and 10 mg·l^-1, LA and HA) was 53.64% and 52.34%, respectively, which were lower than those in control check (CK) (61.98%) at 30 days of the after-ripening process (DAR). A total of 83.67% of seeds germinated in the CK, 49% of seeds germinated in the LA treatment, and 37.33% of seeds germinated in the HA treatment at 60 DAR. The ABA, gibberellin (GA), and auxin (IAA) levels were increased in the HA treatment at 0 DAR, while the jasmonic acid (JA) levels were decreased. ABA, IAA, and JA were increased, but GA was decreased with HA treatment at 30 DAR. A total of 4,742, 16,531, and 890 differentially expressed genes (DEGs) were identified between the HA-treated and CK groups, respectively, along with obvious enrichment in the ABA-regulated plant hormone pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The expression of pyracbactin resistance-like (PYL) and SNF1-related protein kinase subfamily 2 (SnRK2s) increased in the ABA-treated groups, whereas the expression of type 2C protein phosphatase (PP2C) decreased, both of which are related to the ABA signaling pathway. As a result of the changes in expression of these genes, increased ABA signaling and suppressed GA signaling could inhibit the growth of the embryo and the expansion of developmental space. Furthermore, our results demonstrated that MAPK signaling cascades might be involved in the amplification of hormone signaling. Meanwhile, our study uncovered that the exogenous hormone ABA could inhibit embryonic development, promote dormancy, and delay germination in recalcitrant seeds. These findings reveal the critical role of ABA in regulating the dormancy of recalcitrant seeds, and thereby provide a new insight into recalcitrant seeds in agricultural production and storage.

A Tea Plant (Camellia sinensis) FLOWERING LOCUS C-like Gene, CsFLC1, Is Correlated to Bud Dormancy and Triggers Early Flowering in Arabidopsis

Flowering and bud dormancy are crucial stages in the life cycle of perennial angiosperms in temperate climates. MADS-box family genes are involved in many plant growth and development processes. Here, we identified three MADS-box genes in tea plant belonging to the FLOWERING LOCUS C (CsFLC) family. We monitored CsFLC1 transcription throughout the year and found that CsFLC1 was expressed at a higher level during the winter bud dormancy and flowering phases. To clarify the function of CsFLC1, we developed transgenic Arabidopsis thaliana plants heterologously expressing 35S::CsFLC1. These lines bolted and bloomed earlier than the WT (Col-0), and the seed germination rate was inversely proportional to the increased CsFLC1 expression level. The RNA-seq of 35S::CsFLC1 transgenic Arabidopsis showed that many genes responding to ageing, flower development and leaf senescence were affected, and phytohormone-related pathways were especially enriched. According to the results of hormone content detection and RNA transcript level analysis, CsFLC1 controls flowering time possibly by regulating SOC1, AGL42, SEP3 and AP3 and hormone signaling, accumulation and metabolism. This is the first time a study has identified FLC-like genes and characterized CsFLC1 in tea plant. Our results suggest that CsFLC1 might play dual roles in flowering and winter bud dormancy and provide new insight into the molecular mechanisms of FLC in tea plants as well as other plant species.

High-Throughput Sequencing Reveals Novel microRNAs Involved in the Continuous Flowering Trait of Longan (Dimocarpus longan Lour.)

A major determinant of fruit production in longan (Dimocarpus longan Lour.) is the difficulty of blossoming. In this study, high-throughput microRNA sequencing (miRNA-Seq) was carried out to compare differentially expressed miRNAs (DEmiRNAs) and their target genes between a continuous flowering cultivar 'Sijimi' (SJ), and a unique cultivar 'Lidongben' (LD), which blossoms only once in the season. Over the course of our study, 1662 known miRNAs and 235 novel miRNAs were identified and 13,334 genes were predicted to be the target of 1868 miRNAs. One conserved miRNA and 29 new novel miRNAs were identified as differently expressed; among them, 16 were upregulated and 14 were downregulated. Through the KEGG pathway and cluster analysis of DEmiRNA target genes, three critical regulatory pathways, plant-pathogen interaction, plant hormone signal transduction, and photosynthesis-antenna protein, were discovered to be strongly associated with the continuous flowering trait of the SJ. The integrated correlation analysis of DEmiRNAs and their target mRNAs revealed fourteen important flowering-related genes, including COP1-like, Casein kinase II, and TCP20. These fourteen flowering-related genes were targeted by five miRNAs, which were novel-miR137, novel-miR76, novel-miR101, novel-miR37, and csi-miR3954, suggesting these miRNAs might play vital regulatory roles in flower regulation in longan. Furthermore, novel-miR137 was cloned based on small RNA sequencing data analysis. The pSAK277-miR137 transgenic Arabidopsis plants showed delayed flowering phenotypes. This study provides new insight into molecular regulation mechanisms of longan flowering.

SlS5H silencing reveals specific pathogen-triggered salicylic acid metabolism in tomato

BACKGROUND

Salicylic acid (SA) is a major plant hormone that mediates the defence pathway against pathogens. SA accumulates in highly variable amounts depending on the plant-pathogen system, and several enzyme activities participate in the restoration of its levels. Gentisic acid (GA) is the product of the 5-hydroxylation of SA, which is catalysed by S5H, an enzyme activity regarded as a major player in SA homeostasis. GA accumulates at high levels in tomato plants infected by Citrus Exocortis Viroid (CEVd), and to a lesser extend upon Pseudomonas syringae DC3000 pv. tomato (Pst) infection.

RESULTS

We have studied the induction of tomato SlS5H gene by different pathogens, and its expression correlates with the accumulation of GA. Transient over-expression of SlS5H in Nicotiana benthamiana confirmed that SA is processed by SlS5H in vivo. SlS5H-silenced tomato plants were generated, displaying a smaller size and early senescence, together with hypersusceptibility to the necrotrophic fungus Botrytis cinerea. In contrast, these transgenic lines exhibited an increased defence response and resistance to both CEVd and Pst infections. Alternative SA processing appears to occur for each specific pathogenic interaction to cope with SA levels. In SlS5H-silenced plants infected with CEVd, glycosylated SA was the most discriminant metabolite found. Instead, in Pst-infected transgenic plants, SA appeared to be rerouted to other phenolics such as feruloyldopamine, feruloylquinic acid, feruloylgalactarate and 2-hydroxyglutarate.

CONCLUSION

Using SlS5H-silenced plants as a tool to unbalance SA levels, we have studied the re-routing of SA upon CEVd and Pst infections and found that, despite the common origin and role for SA in plant pathogenesis, there appear to be different pathogen-specific, alternate homeostasis pathways.

Titanium nanoparticles activate a transcriptional response in Arabidopsis that enhances tolerance to low phosphate, osmotic stress and pathogen infection

Titanium is a ubiquitous element with a wide variety of beneficial effects in plants, including enhanced nutrient uptake and resistance to pathogens and abiotic stresses. While there is numerous evidence supporting the beneficial effects that Ti fertilization give to plants, there is little information on which genetic signaling pathways the Ti application activate in plant tissues. In this study, we utilize RNA-seq and ionomics technologies to unravel the molecular signals that Arabidopsis plants unleash when treated with Ti. RNA-seq analysis showed that Ti activates abscisic acid and salicylic acid signaling pathways and the expression of NUCLEOTIDE BINDING SITE-LEUCINE RICH REPEAT receptors likely by acting as a chemical priming molecule. This activation results in enhanced resistance to drought, high salinity, and infection with Botrytis cinerea in Arabidopsis. Ti also grants an enhanced nutritional state, even at suboptimal phosphate concentrations by upregulating the expression of multiple nutrient and membrane transporters and by modifying or increasing the production root exudates. Our results suggest that Ti might act similarly to the beneficial element Silicon in other plant species.

Genome-Wide Identification of Auxin-Responsive GH3 Gene Family in Saccharum and the Expression of ScGH3-1 in Stress Response

Gretchen Hagen3 (GH3), one of the three major auxin-responsive gene families, is involved in hormone homeostasis in vivo by amino acid splicing with the free forms of salicylic acid (SA), jasmonic acid (JA) or indole-3-acetic acid (IAA). Until now, the functions of sugarcane GH3 (SsGH3) family genes in response to biotic stresses have been largely unknown. In this study, we performed a systematic identification of the SsGH3 gene family at the genome level and identified 41 members on 19 chromosomes in the wild sugarcane species, Saccharum spontaneum. Many of these genes were segmentally duplicated and polyploidization was the main contributor to the increased number of SsGH3 members. SsGH3 proteins can be divided into three major categories (SsGH3-I, SsGH3-II, and SsGH3-III) and most SsGH3 genes have relatively conserved exon-intron arrangements and motif compositions. Diverse cis-elements in the promoters of SsGH3 genes were predicted to be essential players in regulating SsGH3 expression patterns. Multiple transcriptome datasets demonstrated that many SsGH3 genes were responsive to biotic and abiotic stresses and possibly had important functions in the stress response. RNA sequencing and RT-qPCR analysis revealed that SsGH3 genes were differentially expressed in sugarcane tissues and under Sporisorium scitamineum stress. In addition, the SsGH3 homolog ScGH3-1 gene (GenBank accession number: OP429459) was cloned from the sugarcane cultivar (Saccharum hybrid) ROC22 and verified to encode a nuclear- and membrane-localization protein. ScGH3-1 was constitutively expressed in all tissues of sugarcane and the highest amount was observed in the stem pith. Interestingly, it was down-regulated after smut pathogen infection but up-regulated after MeJA and SA treatments. Furthermore, transiently overexpressed Nicotiana benthamiana, transduced with the ScGH3-1 gene, showed negative regulation in response to the infection of Ralstonia solanacearum and Fusarium solani var. coeruleum. Finally, a potential model for ScGH3-1-mediated regulation of resistance to pathogen infection in transgenic N. benthamiana plants was proposed. This study lays the foundation for a comprehensive understanding of the sequence characteristics, structural properties, evolutionary relationships, and expression of the GH3 gene family and thus provides a potential genetic resource for sugarcane disease-resistance breeding.

Deciphering the Molecular Signatures Associated With Resistance to Botrytis cinerea in Strawberry Flower by Comparative and Dynamic Transcriptome Analysis

Gray mold caused by Botrytis cinerea, which is considered to be the second most destructive necrotrophic fungus, leads to major economic losses in strawberry (Fragaria × ananassa) production. B. cinerea preferentially infects strawberry flowers and fruits, leading to flower blight and fruit rot. Compared with those of the fruit, the mechanisms of flower defense against B. cinerea remain largely unexplored. Therefore, in this study, we aimed to unveil the resistance mechanisms of strawberry flower through dynamic and comparative transcriptome analysis with resistant and susceptible strawberry cultivars. Our experimental data suggest that resistance to B. cinerea in the strawberry flower is probably regulated at the transcriptome level during the early stages of infection and strawberry flower has highly complex and dynamic regulatory networks controlling a multi-layered defense response to B. cinerea. First of all, the higher expression of disease-resistance genes but lower expression of cell wall degrading enzymes and peroxidases leads to higher resistance to B. cinerea in the resistant cultivar. Interestingly, CPKs, RBOHDs, CNGCs, and CMLs comprised a calcium signaling pathway especially play a crucial role in enhancing resistance by increasing their expression. Besides, six types of phytohormones forming a complex regulatory network mediated flower resistance, especially JA and auxin. Finally, the genes involved in the phenylpropanoid and amino acids biosynthesis pathways were gene sets specially expressed or different expression genes, both of them contribute to the flower resistance to B. cinerea. These data provide the foundation for a better understanding of strawberry gray mold, along with detailed genetic information and resistant materials to enable genetic improvement of strawberry plant resistance to gray mold.

Connecting primary and specialized metabolism: Amino acid conjugation of phytohormones by GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases

GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases catalyze the ATP-dependent conjugation of phytohormones with amino acids. Traditionally, GH3 proteins are associated with synthesis of the bioactive jasmonate hormone (+)-7- iso -jasmonoyl-l-isoleucine (JA-Ile) and conjugation of indole-3-acetic acid (IAA) with amino acids that tag the hormone for degradation and/or storage. Modifications of JA and IAA by GH3 acyl acid amido synthetases help maintain phytohormones homeostasis. Recent studies broaden the roles of GH3 proteins to include the regulation of JA biosynthesis; the modification of other auxins (i.e., phenylacetic acid and indole-3-butyric acid); the conjugation of auxinic herbicides, such as 4-dichlorophenoxyacetic acid, 4-(2,4-dichlorophenoxy)butyric acid, and dicamba; and the missing step in the isochorismate pathway for the biosynthesis of salicylic acid. The GH3 protein family joins the growing number of versatile enzyme families that blur the line between primary and specialized metabolism for an increasing range of biology functions.

Accumulation of Salicylic Acid and Related Metabolites in Selaginella moellendorffii

Salicylic acid (SA) is a phytohormone that plays manifold roles in plant growth, defense, and other aspects of plant physiology. The concentration of free SA in plants is fine-tuned by a variety of structural modifications. SA is produced by all land plants, yet it is not known whether its metabolism is conserved in all lineages. Selaginella moellendorffii is a lycophyte and thus a representative of an ancient clade of vascular plants. Here, we evaluated the accumulation of SA and related metabolites in aerial parts of S. moellendorffii. We found that SA is primarily stored as the 2-O-β-glucoside. Hydroxylated derivatives of SA are also produced by S. moellendorffii and stored as β-glycosides. A candidate signal for SA aspartate was also detected. Phenylpropanoic acids also occur in S. moellendorffii tissue. Only o-coumaric acid is stored as the β-glycoside, while caffeic, p-coumaric, and ferulic acids accumulate as alkali-labile conjugates. An in silico search for enzymes involved in conjugation and catabolism of SA in the S. moellendorffii genome indicated that experimental characterization is necessary to clarify the physiological functions of the putative orthologs. This study sheds light on SA metabolism in an ancestral plant species and suggests directions towards elucidating the underlying mechanisms.

The GH3 amidosynthetases family and their role in metabolic crosstalk modulation of plant signaling compounds

The Gretchen Hagen 3 (GH3) genes encoding proteins belonging to the ANL superfamily are widespread in the plant kingdom. The ANL superfamily consists of three groups of adenylating enzymes: aryl- and acyl-CoA synthetases, firefly luciferase, and amino acid-activating adenylation domains of the nonribosomal peptide synthetases (NRPS). GH3s are cytosolic, acidic amidosynthetases of the firefly luciferase group that conjugate auxins, jasmonates, and benzoate derivatives to a wide group of amino acids. In contrast to auxins, which amide conjugates mainly serve as a storage pool of inactive phytohormone or are involved in the hormone degradation process, conjugation of jasmonic acid (JA) results in biologically active phytohormone jasmonyl-isoleucine (JA-Ile). Moreover, GH3s modulate salicylic acid (SA) concentration by conjugation of its precursor, isochorismate. GH3s, as regulators of the phytohormone level, are crucial for normal plant development as well as plant defense response to different abiotic and biotic stress factors. Surprisingly, recent studies indicate that FIN219/JAR1/GH3.11, one of the GH3 proteins, may act not only as an enzyme but is also able to interact with tau-class glutathione S-transferase (GSTU) and constitutive photomorphogenic 1 (COP1) proteins and regulate light and stress signaling pathways. The aim of this work is to summarize our current knowledge of the GH3 family.

The Role of Plant Hormones in the Interaction of Colletotrichum Species with Their Host Plants

Colletotrichum is a plant pathogenic fungus which is able to infect virtually every economically important plant species. Up to now no common infection mechanism has been identified comparing different plant and Colletotrichum species. Plant hormones play a crucial role in plant-pathogen interactions regardless whether they are symbiotic or pathogenic. In this review we analyze the role of ethylene, abscisic acid, jasmonic acid, auxin and salicylic acid during Colletotrichum infections. Different Colletotrichum strains are capable of auxin production and this might contribute to virulence. In this review the role of different plant hormones in plant—Colletotrichum interactions will be discussed and thereby auxin biosynthetic pathways in Colletotrichum spp. will be proposed.

Biosynthesis and Roles of Salicylic Acid in Balancing Stress Response and Growth in Plants

Salicylic acid (SA) is an important plant hormone with a critical role in plant defense against pathogen infection. Despite extensive research over the past 30 year or so, SA biosynthesis and its complex roles in plant defense are still not fully understood. Even though earlier biochemical studies suggested that plants synthesize SA from cinnamate produced by phenylalanine ammonia lyase (PAL), genetic analysis has indicated that in Arabidopsis, the bulk of SA is synthesized from isochorismate (IC) produced by IC synthase (ICS). Recent studies have further established the enzymes responsible for the conversion of IC to SA in Arabidopsis. However, it remains unclear whether other plants also rely on the ICS pathway for SA biosynthesis. SA induces defense genes against biotrophic pathogens, but represses genes involved in growth for balancing defense and growth to a great extent through crosstalk with the growth-promoting plant hormone auxin. Important progress has been made recently in understanding how SA attenuates plant growth by regulating the biosynthesis, transport, and signaling of auxin. In this review, we summarize recent progress in the biosynthesis and the broad roles of SA in regulating plant growth during defense responses. Further understanding of SA production and its regulation of both defense and growth will be critical for developing better knowledge to improve the disease resistance and fitness of crops.

Auxin Interactions with Other Hormones in Plant Development

Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is.

Beyond the Usual Suspects: Physiological Roles of the Arabidopsis Amidase Signature (AS) Superfamily Members in Plant Growth Processes and Stress Responses

The diversification of land plants largely relies on their ability to cope with constant environmental fluctuations, which negatively impact their reproductive fitness and trigger adaptive responses to biotic and abiotic stresses. In this limiting landscape, cumulative research attention has centred on deepening the roles of major phytohormones, mostly auxins, together with brassinosteroids, jasmonates, and abscisic acid, despite the signaling networks orchestrating the crosstalk among them are so far only poorly understood. Accordingly, this review focuses on the Arabidopsis Amidase Signature (AS) superfamily members, with the aim of highlighting the hitherto relatively underappreciated functions of AMIDASE1 (AMI1) and FATTY ACID AMIDE HYDROLASE (FAAH), as comparable coordinators of the growth-defense trade-off, by balancing auxin and ABA homeostasis through the conversion of their likely bioactive substrates, indole-3-acetamide and N-acylethanolamine.

Leaf direction: Lamina joint development and environmental responses

Plant architecture plays a major role in canopy photosynthesis and biomass production, and plants adjust their growth (and thus architecture) in response to changing environments. Leaf angle is one of the most important traits in rice (Oryza sativa L.) plant architecture, because leaf angle strongly affects leaf direction and rice production, with more-erect leaves being advantageous for high-density plantings. The degree of leaf bending depends on the morphology of the lamina joint, which connects the leaf and the sheath. In this review, we discuss cell morphology in different lamina joint tissues and describe the underlying genetic network that governs this morphology and thus regulates leaf direction. Furthermore, we focus on the mechanism by how environmental factors influence rice leaf angle. Our review provides a theoretical framework for the future genetic improvement of rice leaf orientation and plant architecture.

Metabolic regulation of systemic acquired resistance

Plants achieve an optimal balance between growth and defense by a fine-tuned biosynthesis and metabolic inactivation of immune-stimulating small molecules. Recent research illustrates that three common hubs are involved in the cooperative regulation of systemic acquired resistance (SAR) by the defense hormones N-hydroxypipecolic acid (NHP) and salicylic acid (SA). First, a common set of regulatory proteins is involved in their biosynthesis. Second, NHP and SA are glucosylated by the same glycosyltransferase, UGT76B1, and thereby inactivated in concert. And third, NHP confers immunity via the SA receptor NPR1 to reprogram plants at the level of transcription and primes plants for an enhanced defense capacity. An overview of SA and NHP metabolism is provided, and their contribution to long-distance signaling in SAR is discussed.

A methyl esterase 1 (PvMES1) promotes the salicylic acid pathway and enhances Fusarium wilt resistance in common beans

Methyl esterase (MES), PvMES1, contributes to the defense response toward Fusarium wilt in common beans by regulating the salicylic acid (SA) mediated signaling pathway from phenylpropanoid synthesis and sugar metabolism as well as others. Common bean (Phaseolus vulgaris L.) is an important food legume. Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli is one of the most serious soil-borne diseases of common bean found throughout the world and affects the yield and quality of the crop. Few sources of Fusarium wilt resistance exist in legumes and most are of quantitative inheritance. In this study, we have identified a methyl esterase (MES), PvMES1, that contributes to plant defense response by regulating the salicylic acid (SA) mediated signaling pathway in response to Fusarium wilt in common beans. The result showed the role of PvMES1 in regulating SA levels in common bean and thus the SA signaling pathway and defense response mechanism in the plant. Overexpression of the PvMES1 gene enhanced Fusarium wilt resistance; while silencing of the gene caused susceptibility to the diseases. RNA-seq analysis with these transiently modified plants showed that genes related to SA level changes included the following gene ontologies: (a) phenylpropanoid synthesis; (b) sugar metabolism; and (c) interaction between host and pathogen as well as others. These key signal elements activated the defense response pathway in common bean to Fusarium wilt. Collectively, our findings indicate that PvMES1 plays a pivotal role in regulating SA biosynthesis and signaling, and increasing Fusarium wilt resistance in common bean, thus providing novel insight into the practical applications of both SA and MES genes and pathways they contribute to for developing elite crop varieties with enhanced broad-spectrum resistance to this critical disease.

Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance

Plant diseases are among the major causes of crop yield losses around the world. To confer disease resistance, conventional breeding relies on the deployment of single resistance (R) genes. However, this strategy has been easily overcome by constantly evolving pathogens. Disabling susceptibility (S) genes is a promising alternative to R genes in breeding programs, as it usually offers durable and broad-spectrum disease resistance. In Arabidopsis, the S gene DMR6 (AtDMR6) encodes an enzyme identified as a susceptibility factor to bacterial and oomycete pathogens. Here, we present a model-to-crop translational work in which we characterize two AtDMR6 orthologs in tomato, SlDMR6-1 and SlDMR6-2. We show that SlDMR6-1, but not SlDMR6-2, is up-regulated by pathogen infection. In agreement, Sldmr6-1 mutants display enhanced resistance against different classes of pathogens, such as bacteria, oomycete, and fungi. Notably, disease resistance correlates with increased salicylic acid (SA) levels and transcriptional activation of immune responses. Furthermore, we demonstrate that SlDMR6-1 and SlDMR6-2 display SA-5 hydroxylase activity, thus contributing to the elucidation of the enzymatic function of DMR6. We then propose that SlDMR6 duplication in tomato resulted in subsequent subfunctionalization, in which SlDMR6-2 specialized in balancing SA levels in flowers/fruits, while SlDMR6-1 conserved the ability to fine-tune SA levels during pathogen infection of the plant vegetative tissues. Overall, this work not only corroborates a mechanism underlying SA homeostasis in plants, but also presents a promising strategy for engineering broad-spectrum and durable disease resistance in crops.

Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance

Plant diseases are among the major causes of crop yield losses around the world. To confer disease resistance, conventional breeding relies on the deployment of single resistance (R) genes. However, this strategy has been easily overcome by constantly evolving pathogens. Disabling susceptibility (S) genes is a promising alternative to R genes in breeding programs, as it usually offers durable and broad-spectrum disease resistance. In Arabidopsis, the S gene DMR6 (AtDMR6) encodes an enzyme identified as a susceptibility factor to bacterial and oomycete pathogens. Here, we present a model-to-crop translational work in which we characterize two AtDMR6 orthologs in tomato, SlDMR6-1 and SlDMR6-2. We show that SlDMR6-1, but not SlDMR6-2, is up-regulated by pathogen infection. In agreement, Sldmr6-1 mutants display enhanced resistance against different classes of pathogens, such as bacteria, oomycete, and fungi. Notably, disease resistance correlates with increased salicylic acid (SA) levels and transcriptional activation of immune responses. Furthermore, we demonstrate that SlDMR6-1 and SlDMR6-2 display SA-5 hydroxylase activity, thus contributing to the elucidation of the enzymatic function of DMR6. We then propose that SlDMR6 duplication in tomato resulted in subsequent subfunctionalization, in which SlDMR6-2 specialized in balancing SA levels in flowers/fruits, while SlDMR6-1 conserved the ability to fine-tune SA levels during pathogen infection of the plant vegetative tissues. Overall, this work not only corroborates a mechanism underlying SA homeostasis in plants, but also presents a promising strategy for engineering broad-spectrum and durable disease resistance in crops.

Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot

BACKGROUND

Ergot, caused by the fungal pathogen Claviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction between C. purpurea and hexaploid wheat we undertook an extensive examination of the reprogramming of the wheat transcriptome in response to C. purpurea infection through floral tissues (i.e. the stigma, transmitting and base ovule tissues of the ovary) and over time.

RESULTS

C. purpurea hyphae were observed to have grown into and down the stigma at 24 h (H) after inoculation. By 48H hyphae had grown through the transmitting tissue into the base, while by 72H hyphae had surrounded the ovule. By 5 days (D) the ovule had been replaced by fungal tissue. Differential gene expression was first observed at 1H in the stigma tissue. Many of the wheat genes differentially transcribed in response to C. purpurea infection were associated with plant hormones and included the ethylene (ET), auxin, cytokinin, gibberellic acid (GA), salicylic acid and jasmonic acid (JA) biosynthetic and signaling pathways. Hormone-associated genes were first detected in the stigma and base tissues at 24H, but not in the transmitting tissue. Genes associated with GA and JA pathways were seen in the stigma at 24H, while JA and ET-associated genes were identified in the base at 24H. In addition, several defence-related genes were differential expressed in response to C. purpurea infection, including antifungal proteins, endocytosis/exocytosis-related proteins, NBS-LRR class proteins, genes involved in programmed cell death, receptor protein kinases and transcription factors. Of particular interest was the identification of differential expression of wheat genes in the base tissue well before the appearance of fungal hyphae, suggesting that a mobile signal, either pathogen or plant-derived, is delivered to the base prior to colonisation.

CONCLUSIONS

Multiple host hormone biosynthesis and signalling pathways were significantly perturbed from an early stage in the wheat - C. purpurea interaction. Differential gene expression at the base of the ovary, ahead of arrival of the pathogen, indicated the potential presence of a long-distance signal modifying host gene expression.

High ammonium inhibits root growth in Arabidopsis thaliana by promoting auxin conjugation rather than inhibiting auxin biosynthesis

Ammonium (NH₄⁺) inhibits primary root (PR) growth in most plant species when present even at moderate concentrations. Previous studies have shown that transport of indole-3-acetic acid (IAA) is critical to maintaining root elongation under high-NH₄⁺ stress. However, the precise regulation of IAA homeostasis under high-NH₄⁺ stress (HAS) remains unclear. In this study, qRT-PCR, RNA-seq, free IAA and IAA conjugate and PR elongation measurements were conducted in genetic mutants to investigate the role of IAA biosynthesis and conjugation under HAS. Our data clearly show that HAS decreases free IAA in roots by increasing IAA inactivation but does not decrease IAA biosynthesis, and that the IAA-conjugating genes GH3.1, GH3.2, GH3.3, GH3.4, and GH3.6 function as the key genes in regulating high-NH₄⁺ sensitivity in the roots. Furthermore, the analysis of promoter::GUS staining in situ and genetic mutants reveals that HAS promotes IAA conjugation in the elongation zone (EZ), which may be responsible for the PR inhibition observed under HAS. This study provides potential new insight into the role of auxin in the improvement of tolerance to NH₄⁺.

Degradation of salicylic acid to catechol in Solanaceae by SA 1-hydroxylase

The hormone salicylic acid (SA) plays crucial roles in plant defense, stress responses, and in the regulation of plant growth and development. Whereas the biosynthetic pathways and biological functions of SA have been extensively studied, SA catabolism is less well understood. In this study, we report the identification and functional characterization of an FAD/NADH-dependent SA 1-hydroxylase from tomato (Solanum lycopersicum; SlSA1H), which catalyzes the oxidative decarboxylation of SA to catechol. Transcript levels of SlSA1H were highest in stems and its expression was correlated with the formation of the methylated catechol derivatives guaiacol and veratrole. Consistent with a role in SA catabolism, SlSA1H RNAi plants accumulated lower amounts of guaiacol and failed to produce any veratrole. Two O-methyltransferases involved in the conversion of catechol to guaiacol and guaiacol to veratrole were also functionally characterized. Subcellular localization analyses revealed the cytosolic localization of this degradation pathway. Phylogenetic analysis and functional characterization of SA1H homologs from other species indicated that this type of FAD/NADH-dependent SA 1-hydroxylases evolved recently within the Solanaceae family.

Roles of Phytohormones and Their Signaling Pathways in Leaf Development and Stress Responses

Phytohormones participate in various processes over the course of a plant's lifecycle. In addition to the five classical phytohormones (auxins, cytokinins, gibberellins, abscisic acid, and ethylene), phytohormones such as brassinosteroids, jasmonic acid, salicylic acid, strigolactones, and peptides also play important roles in plant growth and stress responses. Given the highly interconnected nature of phytohormones during plant development and stress responses, it is challenging to study the biological function of a single phytohormone in isolation. In the current Review, we describe the combined functions and signaling cascades (especially the shared points and pathways) of various phytohormones in leaf development, in particular, during leaf primordium initiation and the establishment of leaf polarity and leaf morphology as well as leaf development under various stress conditions. We propose a model incorporating the roles of multiple phytohormones in leaf development and stress responses to illustrate the underlying combinatorial signaling pathways. This model provides a reference for breeding stress-resistant crops.

Auxin Metabolism in Plants

The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism-which comprises biosynthesis, conjugation, and degradation-modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.

Physiological Characteristic Changes and Full-Length Transcriptome of Rose (Rosa chinensis) Roots and Leaves in Response to Drought Stress

Rose (Rosa chinensis) is the most important ornamental crops worldwide. However, the physiological and molecular mechanism of rose under drought stress remains elusive. In this study, we analyzed the changes of photosynthetic and phytohormone levels in the leaves and roots of rose seedlings grown under control (no drought), mild drought (MD) and severe drought stress. The total chlorophyll content and water use efficiency were significantly enhanced under MD in rose leaves. In addition, the concentration of ABA was higher in the leaves compared to the roots, whereas the roots accumulated more IAA, methylindole-3-acetic acid and indole-3-propionic acid. We also constructed the first full-length transcriptome for rose, and identified 96,201,862 full-length reads of average length 1,149 bp that included 65,789 novel transcripts. A total of 3,657 and 4,341 differentially expressed genes (DEGs) were identified in rose leaves and roots respectively. KEGG pathway analysis showed enrichment of plant hormone, signal transduction and photosynthesis are among the DEGs. 42,544 alternatively spliced isoforms were also identified, and alternative 3' splice site was the major alternative splicing (AS) event among the DEGs. Variations in the AS patterns of three genes between leaves and roots indicated the possibility of tissue-specific posttranscriptional regulation in response to drought stress. Furthermore, 2,410 novel long non-coding RNAs were detected that may participate in regulating the drought-induced DEGs. Our findings identified previously unknown splice sites and new genes in the rose transcriptome, and elucidated the drought stress-responsive genes as well as their intricate regulatory networks.

Heat shock protein 90 co-chaperone modules fine-tune the antagonistic interaction between salicylic acid and auxin biosynthesis in cassava

Heat shock protein 90 (HSP90) is an important molecular chaperone in plants. However, HSP90-mediated plant immune response remains elusive in cassava. In this study, cassava bacterial blight (CBB) induces the expression of MeHsf8, which directly targets MeHSP90.9 to activate its expression and immune response. Further identification of SHI-related sequence 1 (MeSRS1) and MeWRKY20 as MeHSP90.9 co-chaperones revealed the underlying mechanism of MeHSP90.9-mediated immune response. MeHSP90.9 interacts with MeSRS1 and MeWRKY20 to promote their transcriptional activation of salicylic acid (SA) biosynthetic gene avrPphB Susceptible 3 (MePBS3) and tryptophan metabolic gene N-acetylserotonin O-methyltransferase 2 (MeASMT2), respectively, so as to activate SA biosynthesis but inhibit tryptophan-derived auxin biosynthesis. Notably, genetic experiments confirmed that overexpressing MePBS3 and MeASMT2 could rescue the effects of silencing MeHsf8-MeHSP90.9 on disease resistance. This study highlights the dual regulation of SA and auxin biosynthesis by MeHSP90.9, providing the mechanistic understanding of MeHSP90.9 client partners in plant immunity.

Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis

The evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid, salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyse the physiological role of AMIDASE 1 (AMI1) in Arabidopsis plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalysing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plant's stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including jasmonic acid and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin and ABA homeostasis.

Utilization of Endophytes Fungi from Jatropha Leaves (Jatropha curcas L.) Against Fusarium oxysporum Causing Tuber Rot Disease Onion (Allium cepa var. Ascalonicum (L.) Backer)

Tuber rot is one of the important diseases in onion caused by Fusarium oxysporum. Endophytes are biological agents that are currently widely used in controlling plant diseases. Excessive use of pesticides and continuously has shown negative impacts such as resurgence, resistance to pests and pathogens, and the death of natural enemies. Currently, pests and pathogens control effort are directed at the utilization of natural enemies or better known as biological control. Endophyte is a microorganism that grows in plant tissues without causing symptoms. Endophytes allegedly capable of producing a variety of phytochemical compounds generated by their host. The leaves of Jatropha (Jatropha curcas L.) is one part of the plant that contains secondary metabolites.Phytochemical tests on the Jatropha show that Jatropha contains alkaloids, flavonoids, and saponins that are an antimicrobial potential of plant-pathogen control agents. This study aimed to determine the effect of some Endophytes isolates and their impact on the growth of F. oxysporum in vitro in onion.Exploration (endophyte isolation from Jatropha healthy leaves) and observation (antagonist test of Endophytes of the Jatropha leaves) method used in this study was a Completely Randomized Design (CRD) with a single factor (10 treatment) repeated three times. There were 14 endophytes isolated from Jatropha leaves with a growth ratio of 4.5 cm/2 days. The best treatment to inhibit the growth of F. oxysporum in vitro is Jc5, Jc8, Jc10.

Dual-Localized WHIRLY1 Affects Salicylic Acid Biosynthesis via Coordination of ISOCHORISMATE SYNTHASE1, PHENYLALANINE AMMONIA LYASE1, and S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE1

Salicylic acid (SA) influences developmental senescence and is spatiotemporally controlled by various mechanisms, including biosynthesis, transport, and conjugate formation. Altered localization of Arabidopsis WHIRLY1 (WHY1), a repressor of leaf natural senescence, in the nucleus or chloroplast causes a perturbation in SA homeostasis, resulting in adverse plant senescence phenotypes. WHY1 loss-of-function mutation resulted in SA peaking 5 d earlier compared to wild-type plants, which accumulated SA at 42 d after germination. SA accumulation coincided with an early leaf-senescence phenotype, which could be prevented by ectopic expression of the nuclear WHY1 isoform (nWHY1). However, expressing the plastid WHY1 isoform (pWHY1) greatly enhanced cellular SA levels. Transcriptome analysis in the WHY1 loss-of-function mutant background following expression of either pWHY1 or nWHY1 indicated that hormone metabolism-related genes were most significantly altered. The pWHY1 isoform predominantly affected stress-related gene expression, whereas nWHY1 primarily controlled developmental gene expression. Chromatin immunoprecipitation-quantitative PCR assays indicated that nWHY1 directly binds to the promoter region of isochorismate synthase1 (ICS1), thus activating its expression at later developmental stages, but that it indirectly activates S-adenosyl- l -Met-dependent methyltransferase1 (BSMT1) expression via ethylene response factor 109 (ERF109). Moreover, nWHY1 repressed expression of Phe ammonia lyase-encoding gene (PAL1) via R2R3-MYB member 15 (MYB15) during the early stages of development. Interestingly, rising SA levels exerted a feedback effect by inducing nWHY1 modification and pWHY1 accumulation. Thus, the alteration of WHY1 organelle isoforms and the feedback of SA are involved in a circularly integrated regulatory network during developmental or stress-induced senescence in Arabidopsis.

The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth

Elephant grass (2n = 4x = 28; Cenchrus purpureus Schumach.), also known as Napier grass, is an important forage grass and potential energy crop in tropical and subtropical regions of Asia, Africa and America. However, no study has yet reported a genome assembly for elephant grass at the chromosome scale. Here, we report a high‐quality chromosome‐scale genome of elephant grass with a total size of 1.97 Gb and a 1.5% heterozygosity rate, obtained using short‐read sequencing, single‐molecule long‐read sequencing and Hi‐C chromosome conformation capture. Evolutionary analysis showed that subgenome A' of elephant grass and pearl millet may have originated from a common ancestor more than 3.22 million years ago (MYA). Further, allotetraploid formation occurred at approximately 6.61 MYA. Syntenic analyses within elephant grass and with other grass species indicated that elephant grass has experienced chromosomal rearrangements. We found that some key enzyme‐encoding gene families related to the biosynthesis of anthocyanidins and flavonoids were expanded and highly expressed in leaves, which probably drives the production of these major anthocyanidin compounds and explains why this elephant grass cultivar has a high anthocyanidin content. In addition, we found a high copy number and transcript levels of genes involved in C₄ photosynthesis and hormone signal transduction pathways that may contribute to the fast growth of elephant grass. The availability of elephant grass genome data advances our knowledge of the genetic evolution of elephant grass and will contribute to further biological research and breeding as well as for other polyploid plants in the genus Cenchrus.

Salicylic acid regulates adventitious root formation via competitive inhibition of the auxin conjugation enzyme CsGH3.5 in cucumber hypocotyls

Exogenous SA treatment at appropriate concentrations promotes adventitious root formation in cucumber hypocotyls, via competitive inhibiting the IAA-Asp synthetase activity of CsGH3.5, and increasing the local free IAA level. Adventitious root formation is critical for the cutting propagation of horticultural plants. Indole-3-acetic acid (IAA) has been shown to play a central role in regulating this process, while for salicylic acid (SA), its exact effects and regulatory mechanism have not been elucidated. In this study, we showed that exogenous SA treatment at the concentrations of both 50 and 100 µM promoted adventitious root formation at the base of the hypocotyl of cucumber seedlings. At these concentrations, SA could induce the expression of CYCLIN and Cyclin-dependent Kinase (CDK) genes during adventitious rooting. IAA was shown to be involved in SA-induced adventitious root formation in cucumber hypocotyls. Exposure to exogenous SA led to a slight increase in the free IAA content, and pre-treatment with the auxin transport inhibitor 1-naphthylphthalamic acid (NPA) almost completely abolished the inducible effects of SA on adventitious root number. SA-induced IAA accumulation was also associated with the enhanced expression of Gretchen Hagen3.5 (CsGH3.5). The in vitro enzymatic assay indicated that CsGH3.5 has both IAA- and SA-amido synthetase activity and prefers aspartate (Asp) as the amino acid conjugate. The Asp concentration dictated the functional activity of CsGH3.5 on IAA. Both affinity and catalytic efficiency (K_cat/K_m) increased when the Asp concentration increased from 0.3 to 1 mM. In contrast, CsGH3.5 showed equal catalytic efficiency for SA at low and high Asp concentrations. Furthermore, SA functioned as a competitive inhibitor of the IAA-Asp synthetase activity of CsGH3.5. During adventitious formation, SA application indeed repressed the IAA-Asp levels in the rooting zone. These data show that SA plays an inducible role in adventitious root formation in cucumber through competitive inhibition of the auxin conjugation enzyme CsGH3.5. SA reduces the IAA conjugate levels, thereby increasing the local free IAA level and ultimately enhancing adventitious root formation.

Overexpression of Arabidopsis microRNA167 induces salicylic acid-dependent defense against Pseudomonas syringae through the regulation of its targets ARF6 and ARF8

microRNAs are powerful regulators of growth, development, and stress responses in plants. The Arabidopsis thaliana microRNA miR167 was previously found to regulate diverse processes including flower development, root development, and response to osmotic stress by controlling the patterns of expression of its target genes AUXIN RESPONSE FACTOR 6 (ARF6), ARF8, and IAA-Ala RESISTANT 3. Here, we report that miR167 also modulates defense against pathogens through ARF6 and ARF8. miR167 is differentially expressed in response to the bacterial pathogen Pseudomonas syringae, and overexpression of miR167 confers very high levels of resistance. This resistance appears to be due to suppression of auxin responses and is partially dependent upon salicylic acid signaling, and also depends upon altered stomatal behavior in these plants. Closure of stomata upon the detection of P. syringae is an important aspect of the basal defense response, as it prevents bacterial cells from entering the leaf interior and causing infection. Plants overexpressing miR167 constitutively maintain small stomatal apertures, resulting in very high resistance when the pathogen is inoculated onto the leaf surface. Additionally, the systemic acquired resistance (SAR) response is severely compromised in plants overexpressing miR167, in agreement with previous work showing that the activation of SAR requires intact auxin signaling responses. This work highlights a new role for miR167, and also emphasizes the importance of hormonal balance in short- and long-term defense and of stomata as an initial barrier to pathogen entry.

Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12-mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins.

The Proline-Rich Family Protein EXTENSIN33 Is Required for Etiolated Arabidopsis thaliana Hypocotyl Growth

Growth of etiolated Arabidopsis hypocotyls is biphasic. During the first phase, cells elongate slowly and synchronously. At 48 h after imbibition, cells at the hypocotyl base accelerate their growth. Subsequently, this rapid elongation propagates through the hypocotyl from base to top. It is largely unclear what regulates the switch from slow to fast elongation. Reverse genetics-based screening for hypocotyl phenotypes identified three independent mutant lines of At1g70990, a short extensin (EXT) family protein that we named EXT33, with shorter etiolated hypocotyls during the slow elongation phase. However, at 72 h after imbibition, these dark-grown mutant hypocotyls start to elongate faster than the wild type (WT). As a result, fully mature 8-day-old dark-grown hypocotyls were significantly longer than WTs. Mutant roots showed no growth phenotype. In line with these results, analysis of native promoter-driven transcriptional fusion lines revealed that, in dark-grown hypocotyls, expression occurred in the epidermis and cortex and that it was strongest in the growing part. Confocal and spinning disk microscopy on C-terminal protein-GFP fusion lines localized the EXT33-protein to the ER and cell wall. Fourier-transform infrared microspectroscopy identified subtle changes in cell wall composition between WT and the mutant, reflecting altered cell wall biomechanics measured by constant load extensometry. Our results indicate that the EXT33 short EXT family protein is required during the first phase of dark-grown hypocotyl elongation and that it regulates the moment and extent of the growth acceleration by modulating cell wall extensibility.

Stories of Salicylic Acid: A Plant Defense Hormone

Salicylic acid (SA) is a key plant hormone required for establishing resistance to many pathogens. SA biosynthesis involves two main metabolic pathways with multiple steps: the isochorismate and the phenylalanine ammonia-lyase pathways. Transcriptional regulations of SA biosynthesis are important for fine-tuning SA level in plants. We highlight here recent discoveries on SA biosynthesis and transcriptional regulations of SA biosynthesis. In addition, SA perception by NPR proteins is important to fulfil its function as a defense hormone. We highlight recent work to give a full picture of how NPR proteins support the role of SA in plant immunity. We also discuss challenges and potential opportunities for future research and application related to the functions of SA in plants.