Repression of Jasmonate-Dependent Defenses by Shade Involves Differential Regulation of Protein Stability of MYC Transcription Factors and Their JAZ Repressors in Arabidopsis

Green light induces Solanum lycopersicum JA synthesis and inhibits Botrytis cinerea infection cushion formation to resist grey mould disease

Light signals are prevalent and influence the survival strategies of both plants and the pathogenic fungi that infect them. In this study, we found that green light inhibits the infectivity of Botrytis cinerea on Solanum lycopersicum. Through transcriptome analysis and validation of S. lycopersicum leaves infected with B. cinerea, we discovered that green light enhances the synthesis of jasmonic acid and its related metabolites by upregulating the expression of OPR3 and JAR1 in S. lycopersicum. Additionally, green light boosts the activity of antioxidant enzymes like peroxidase, catalase, and ascorbic acid peroxidase in S. lycopersicum to combat tomato grey mould. Conversely, green light inhibits the expression of plant-induced colonization onset genes, mitogen-activated protein kinase genes, and the formation of infection cushions in B. cinerea. Our findings provide insights into the role of environmental green light signals in the interaction system between plants and phytopathogenic fungi.

Lighting the path: how light signaling regulates stomatal movement and plant immunity

Stomata, the small pores on the surfaces of plant leaves and stems, are crucial for gas exchange and also play a role in defense against pathogens. Stomatal movement is influenced not only by surrounding light conditions but also by the presence of foliar pathogens. Certain light wavelengths such as blue or high irradiance red light cause stomatal opening, making it easier for bacteria to enter through opened stomata and causing disease progression in plants. Illumination with blue or intense red light autophosphorylates phototropin, a blue light photoreceptor protein kinase, that in turn activates a signaling cascade to open the stomata. Undoubtedly stomatal defense is a fascinating aspect of plant immunology, especially in plant-foliar pathogen interactions. During these interactions, stomata fundamentally serve as entry points for intrusive pathogens and initiate the plant defense signaling cascade. This review highlights how light-activated photoreceptors such as cryptochromes (CRYs), phytochromes (phys), and UV-receptors (UVRs) influence stomatal movement and defense signaling after foliar pathogen intrusion. It also explores the link between stomatal defense, light signaling, and plant immunity, which is vital for safeguarding crops against pathogens.

The concerted function of a novel class of transcription factors, ZBFs, in light, jasmonate, and abscisic acid signaling pathways

Several classes of transcription factors have been investigated in light signaling pathways that bind to the light-responsive elements (LREs) present in the promoters of light regulatory genes for transcriptional regulation. Some of these transcription factors have been shown to bind to numerous promoters through genome-wide ChIP-on-chip (ChIP-chip) studies. Furthermore, through the integration of ChIP-seq and RNA-seq techniques, it has been demonstrated that a transcription factor modifies the expression of numerous genes with which it interacts. However, the mode of action of these transcription factors and their dependency on other regulators in the pathway has just started to be unraveled. In this review, we focus on a particular class of transcription factors, ZBFs (Z-box-binding factors), and their associated partners within the same or other classes of transcription factors and regulatory proteins during photomorphogenesis. Moreover, we have further made an attempt to summarize the crosstalk of these transcription factors with jasmonic acid-, abscisic acid-, and salicylic acid-mediated defense signaling pathways. This review offers an in-depth insight into the manner in which ZBFs and their interactors reshape cellular functions and plant behavior. The underlying principles not only contribute to a comprehensive understanding but also establish a framework for analyzing the interplay between early developmental events and hormone signaling, a regulation orchestrated by the ZBF family.

Lights, location, action: shade avoidance signalling over spatial scales

Plants growing in dense vegetation need to flexibly position their photosynthetic organs to ensure optimal light capture in a competitive environment. They do so through a suite of developmental responses referred to as the shade avoidance syndrome. Below ground, root development is also adjusted in response to above-ground neighbour proximity. Canopies are dynamic and complex environments with heterogeneous light cues in the far-red, red, blue, and UV spectrum, which can be perceived by photoreceptors in spatially separated plant tissues. Molecular regulation of plant architecture adjustment via PHYTOCHROME-INTERACTING FACTOR transcription factors and growth-related hormones such as auxin, gibberellic acid, brassinosteroids, and abscisic acid were historically studied without much attention to spatial or tissue-specific context. Recent developments and technologies have, however, sparked strong interest in spatially explicit understanding of shade avoidance regulation. Other environmental factors such as temperature and nutrient availability interact with the molecular shade avoidance regulation network, often depending on the spatial location of the signals, and the responding organs. Here, we review recent advances in how plants respond to heterogeneous light cues and integrate these with other environmental signals.

Unequal Genetic Redundancies Among MYC bHLH Transcription Factors Underlie Seedling Photomorphogenesis in Arabidopsis

Light is one of the most critical ecological cues controlling plant growth and development. Plants have evolved complex mechanisms to cope with fluctuating light signals. In Arabidopsis, bHLH transcription factors MYC2, MYC3, and MYC4 have been shown to play a vital role in protecting plants against herbivory and necrotrophic pathogens. While the role of MYC2 in light-mediated seedling development has been studied in some detail, the role of MYC3 and MYC4 still needs to be discovered. Here, we show that MYC4 negatively regulates seedling photomorphogenesis, while the MYC3 function seems redundant. However, the genetic analysis reveals that MYC3/MYC4 together act as positive regulators of seedling photomorphogenic growth as the myc3myc4 double mutants showed exaggerated hypocotyl growth compared to the myc3 and myc4 single mutants and Col-0. Intriguingly, the loss of MYC2 function in the myc3myc4 double mutant background (myc2myc3myc4) resulted in further enhancement in the hypocotyl growth than myc3myc4 double mutants in WL, BL and FRL, suggesting that MYC2/3/4 together play an essential and positive role in meditating optimal seedling photomorphogenesis. Besides, MYC3/MYC4 genetically and physically interact with HY5 to partially inhibit its function in controlling hypocotyl and photo-pigment accumulation. Moreover, our results suggest that COP1 physically interacts and degrades MYC3 and MYC4 through the 26S proteasomal pathway and controls their response to dark and light for fine-tuning HY5 function and seedling photomorphogenesis.

The role of the jasmonate signalling transcription factors MYC2/3/4 in circadian clock-mediated regulation of immunity in Arabidopsis

Plants are exposed to pathogens at specific, yet predictable times of the day-night cycle. In Arabidopsis, the circadian clock influences temporal differences in susceptibility to the necrotrophic pathogen Botrytis cinerea. The jasmonic acid (JA) pathway regulates immune responses against B. cinerea. The paralogous basic helix-loop-helix transcription factors MYC2, MYC3 and MYC4 are primary regulators of the JA pathway, but their role in regulating temporal variation in immunity is untested. This study aimed to investigate the roles of the MYC transcription factors in the temporal defence response to B. cinerea. We inoculated leaves from wild-type, myc single-, double- and triple-knockout mutants, and lines overexpressing MYC2, MYC3 or MYC4, with B. cinerea at two times of day in constant light, and compared lesion sizes. The presence of MYC2, MYC3 or MYC4 alone was sufficient to maintain temporal variation in susceptibility, but this was abolished in the myc234 triple-knockout mutant. Constitutive expression of MYC2, MYC3 or MYC4 abolished time-of-day differences in susceptibility. The data suggest that MYC2, MYC3 and MYC4 function redundantly in regulating temporal defence responses against B. cinerea and are a point of convergence between the JA pathway and the circadian clock in Arabidopsis.This article is part of the Theo Murphy meeting issue 'Circadian rhythms in infection and immunity'.

Phytochrome B promotes blast disease resistance and enhances yield in rice

Phytochromes are red/far-red light receptors that regulate various aspects of plant growth, development, and stress responses. The precise mechanism by which phytochrome B (PhyB)-mediated light signaling influences plant defense and development remains unclear. In this study, we showed that PhyB enhances rice (Oryza sativa) blast disease resistance, tillering, and grain size compared to wild-type plants. Notably, PhyB interacted with and degraded grassy tiller 1 (GT1), a negative regulator of tiller development. Knockdown of GT1 in a phyB background partially rescued the diminished tillering of phyB. However, GT1 negatively regulates rice resistance to blast, suggesting that PhyB degradation of GT1 promotes tillering but not blast resistance. Previously, PhyB was found to interact with and degrade phytochrome-interacting factor 15 (PIL15), a key regulator of seed development that reduces rice resistance to blast and seed size. pil15 mutation in phyB mutants rescued phyB seed size and blast resistance, suggesting that PhyB might interact with and degrade PIL15 to negatively regulate blast resistance and seed size. PIL15 directly activated sugar will be eventually exported transporter 2a (SWEET2a). sweet2a mutants were less susceptible to blast disease compared to wild type. Collectively, these data demonstrate that PhyB promotes rice yield and blast resistance by inhibiting the transcription factors GT1 and PIL15 and downstream signaling.

Transcription factor ABF3 modulates salinity stress-enhanced jasmonate signaling in Arabidopsis

Salinity is a severe abiotic stress that affects plant growth and yield. Salinity stress activates jasmonate (JA) signaling in Arabidopsis thaliana, but the underlying molecular mechanism remains to be elucidated. In this study, we confirmed the activation of JA signaling under saline conditions and demonstrated the importance of the CORONATINE INSENSITIVE1 (COI1)-mediated JA signaling for this process. Phenotypic analyses reflected the negative regulation of JASMONATE ZIM-DOMAIN (JAZ) repressors during salinity stress-enhanced JA signaling. Mechanistic analyses revealed that JAZ proteins physically interact with ABSCISIC ACID-RESPONSIVE ELEMENT BINDING FACTOR1 (ABF1), AREB1/ABF2, ABF3, and AREB2/ABF4, which belong to the basic leucine zipper (bZIP) transcription factor family and respond to salinity stress. Analyses on the ABF3 overexpression plants and ABF mutants indicated the positive role of ABF3 in regulating JA signaling under saline condition. Furthermore, ABF3 overexpression partially recovered the JA-related phenotypes of JAZ1-Δ3A plants. Moreover, ABF3 was observed to indirectly activate ALLENE OXIDE SYNTHASE (AOS) transcription, but this activation was inhibited by JAZ1. In addition, ABF3 competitively bind to JAZ1, thereby decreasing the interaction between JAZ1 and MYC2, which is the master transcription factor controlling JA signaling. Collectively, our findings have clarified the regulatory effects of ABF3 on JA signaling and provide new insights into how JA signaling is enhanced following an exposure to salinity stress.

Far-red light increases maize volatile emissions in response to volatile cues from neighbouring plants

Plants perceive the presence and defence status of their neighbours through light and volatile cues, but how plants integrate both stimuli is poorly understood. We investigated if and how low Red to Far red light (R:FR) ratios, indicative of shading or canopy closure, affect maize (Zea mays) responses to herbivore-induced plant volatiles (HIPVs), including the green leaf volatile (Z)-3-hexenyl acetate. We modulated light signalling and perception by using FR supplementation and a phyB1phyB2 mutant, and we determined volatile release as a response readout. To gain mechanistic insights, we examined expression of volatile biosynthesis genes, hormone accumulation, and photosynthesis. Exposure to a full blend of HIPVs or (Z)-3-hexenyl acetate induced maize volatile release. Short-term FR supplementation increased this response. In contrast, prolonged FR supplementation or constitutive phytochrome B inactivation in phyB1phyB2 plants showed the opposite response. Short-term FR supplementation enhanced photosynthesis and stomatal conductance and (Z)-3-hexenyl acetate-induced JA-Ile levels. We conclude that a FR-enriched light environment can prompt maize plants to respond more strongly to HIPVs emitted by neighbours, which might be explained by changes in photosynthetic processes and phytochrome B signalling. Our findings reveal interactive responses to light and volatile cues with potentially important consequences for plant-plant and plant-herbivore interactions.

Advances in functional studies of plant MYC transcription factors

Myelocytomatosis (MYC) transcription factors (TFs) belong to the basic helix-loop-helix (bHLH) family in plants and play a central role in governing a wide range of physiological processes. These processes encompass plant growth, development, adaptation to biotic and abiotic stresses, as well as secondary metabolism. In recent decades, significant strides have been made in comprehending the multifaceted regulatory functions of MYCs. This advancement has been achieved through the cloning of MYCs and the characterization of plants with MYC deficiencies or overexpression, employing comprehensive genome-wide 'omics' and protein-protein interaction technologies. MYCs act as pivotal components in integrating signals from various phytohormones' transcriptional regulators to orchestrate genome-wide transcriptional reprogramming. In this review, we have compiled current research on the role of MYCs as molecular switches that modulate signal transduction pathways mediated by phytohormones and phytochromes. This comprehensive overview allows us to address lingering questions regarding the interplay of signals in response to environmental cues and developmental shift. It also sheds light on the potential implications for enhancing plant resistance to diverse biotic and abiotic stresses through genetic improvements achieved by plant breeding and synthetic biology efforts.

MdWER interacts with MdERF109 and MdJAZ2 to mediate methyl jasmonate- and light-induced anthocyanin biosynthesis in apple fruit

Anthocyanin generation in apples (Malus domestica) and the pigmentation that results from it may be caused by irradiation and through administration of methyl jasmonate (MeJA). However, their regulatory interrelationships associated with fruit coloration are not well defined. To determine whether MdERF109, a transcription factor (TF) involved in light-mediated coloration and anthocyanin biosynthesis, has synergistic effects with other proteins, we performed a yeast two-hybrid assessment and identified another TF, MdWER. MdWER was induced by MeJA treatment, and although overexpression of MdWER alone did not promote anthocyanin accumulation co-overexpression with MdERF109 resulted in significantly increase in anthocyanin biosynthesis. MdWER may form a protein complex with MdERF109 to promote anthocyanin accumulation by enhancing combinations between the proteins and their corresponding genes. In addition, MdWER, as a MeJA responsive protein, interacts with the anthocyanin repressor MdJAZ2. Transient co-expression in apple fruit and protein interaction assays allowed us to conclude that MdERF109 and MdJAZ2 interact with MdWER and take part in the production of anthocyanins upon MeJA treatment and irradiation. Our findings validate a role for the MdERF109-MdWER-MdJAZ2 module in anthocyanin biosynthesis and uncover a novel mechanism for how light and MeJA signals are coordinated anthocyanin biosynthesis in apple fruit.

A Regulatory Mechanism on Pathways: Modulating Roles of MYC2 and BBX21 in the Flavonoid Network

Genes of metabolic pathways are individually or collectively regulated, often via unclear mechanisms. The anthocyanin pathway, well known for its regulation by the MYB/bHLH/WDR (MBW) complex but less well understood in its connections to MYC2, BBX21, SPL9, PIF3, and HY5, is investigated here for its direct links to the regulators. We show that MYC2 can activate the structural genes of the anthocyanin pathway but also suppress them (except F3'H) in both Arabidopsis and Oryza when a local MBW complex is present. BBX21 or SPL9 can activate all or part of the structural genes, respectively, but the effects can be largely overwritten by the local MBW complex. HY5 primarily influences expressions of the early genes (CHS, CHI, and F3H). TF-TF relationships can be complex here: PIF3, BBX21, or SPL9 can mildly activate MYC2; MYC2 physically interacts with the bHLH (GL3) of the MBW complex and/or competes with strong actions of BBX21 to lessen a stimulus to the anthocyanin pathway. The dual role of MYC2 in regulating the anthocyanin pathway and a similar role of BBX21 in regulating BAN reveal a network-level mechanism, in which pathways are modulated locally and competing interactions between modulators may tone down strong environmental signals before they reach the network.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Decoding plant adaptation: deubiquitinating enzymes UBP12 and UBP13 in hormone signaling, light response, and developmental processes

Ubiquitination, a vital post-translational modification in plants, plays a significant role in regulating protein activity, localization, and stability. This process occurs through a complex enzyme cascade that involves E1, E2, and E3 enzymes, leading to the covalent attachment of ubiquitin molecules to substrate proteins. Conversely, deubiquitinating enzymes (DUBs) work in opposition to this process by removing ubiquitin moieties. Despite extensive research on ubiquitination in plants, our understanding of the function of DUBs is still emerging. UBP12 and UBP13, two plant DUBs, have received much attention recently and are shown to play pivotal roles in hormone signaling, light perception, photoperiod responses, leaf development, senescence, and epigenetic transcriptional regulation. This review summarizes current knowledge of these two enzymes, highlighting the central role of deubiquitination in regulating the abundance and activity of critical regulators such as receptor kinases and transcription factors during phytohormone and developmental signaling.

Rose long noncoding RNA lncWD83 promotes flowering by modulating ubiquitination of the floral repressor RcMYC2L

Long noncoding RNAs (lncRNAs) play important roles in various signaling pathways in vascular plants. However, the crosstalk between lncRNAs and E3 ubiquitin ligases has been barely reported. In this study, we demonstrate that the lncRNA lncWD83 from rose (Rosa chinensis) 'Old blush' activates flowering by modulating the ubiquitination of the floral repressor MYC2 LIKE (RcMYC2L). Flowering was substantially delayed in rose by virus-induced gene silencing of lncWD83. In an in vitro pull-down assay, lncWD83 associated with PLANT U-BOX PROTEIN 11 (PUB11), a U-box-containing E3 ubiquitin ligase. Seedlings with knocked down RcPUB11 transcripts phenocopied the later-flowering phenotype of lncWD83-silenced seedlings. RcMYC2L physically interacted with RcPUB11 and was ubiquitinated in an RcPUB11-dependent manner in vitro. Accordingly, silencing RcMYC2L fully reversed the later-flowering phenotype resulting from RcPUB11 knockdown. Furthermore, RcMYC2L bound to G-box-related motifs in the FLOWERING LOCUS T (RcFT) promoter and repressed its transcription. However, RcPUB11 alleviated this repression of RcFT expression via proteasomal degradation of RcMYC2L, and lncWD83 enhanced this degradation by associating with RcPUB11. Therefore, lncWD83 promotes flowering by modulating the ubiquitination of the floral repressor RcMYC2L in rose plants. These findings reveal a distinct regulatory mechanism for an lncRNA in facilitating ubiquitin-mediated proteolysis to regulate rose flowering.

Review: Losing JAZ4 for growth and defense

JAZ proteins are involved in the regulation of the jasmonate signaling pathway, which is responsible for various physiological processes, such as defense response, adaptation to abiotic stress, growth, and development in Arabidopsis. The conserved domains of JAZ proteins can serve as binding sites for a broad array of regulatory proteins and the diversity of these protein-protein pairings result in a variety of functional outcomes. Plant growth and defense are two physiological processes that can conflict with each other, resulting in undesirable plant trade-offs. Recent observations have revealed a distinguishing feature of JAZ4; it acts as negative regulator of both plant immunity and growth and development. We suggest that these complex biological processes can be decoupled at the JAZ4 regulatory node, due to prominent expression of JAZ4 in specific tissues and organs. This spatial separation of actions could explain the increased disease resistance and size of the plant root and shoot in the absence of JAZ4. At the tissue level, JAZ4 could play a role in crosstalk between hormones such as ethylene and auxin to control organ differentiation. Deciphering biding of JAZ4 to specific regulators in different tissues and the downstream responses is key to unraveling molecular mechanisms toward developing new crop improvement strategies.

Autophagy promotes jasmonate-mediated defense against nematodes

Autophagy, as an intracellular degradation system, plays a critical role in plant immunity. However, the involvement of autophagy in the plant immune system and its function in plant nematode resistance are largely unknown. Here, we show that root-knot nematode (RKN; Meloidogyne incognita) infection induces autophagy in tomato (Solanum lycopersicum) and different atg mutants exhibit high sensitivity to RKNs. The jasmonate (JA) signaling negative regulators JASMONATE-ASSOCIATED MYC2-LIKE 1 (JAM1), JAM2 and JAM3 interact with ATG8s via an ATG8-interacting motif (AIM), and JAM1 is degraded by autophagy during RKN infection. JAM1 impairs the formation of a transcriptional activation complex between ETHYLENE RESPONSE FACTOR 1 (ERF1) and MEDIATOR 25 (MED25) and interferes with transcriptional regulation of JA-mediated defense-related genes by ERF1. Furthermore, ERF1 acts in a positive feedback loop and regulates autophagy activity by transcriptionally activating ATG expression in response to RKN infection. Therefore, autophagy promotes JA-mediated defense against RKNs via forming a positive feedback circuit in the degradation of JAMs and transcriptional activation by ERF1.

Transcriptomic and physiological shade avoidance responses in potato (Solanum tuberosum) plants

Plants detect competitors in shaded environments by perceiving a reduction in photosynthetically active radiation (PAR) and the reduction between the red and far-red light (R:FR) ratio and blue photons. These light signals are detected by phytochromes and cryptochromes, which trigger shade avoidance responses such as shoot and petiole elongation and lead to increased susceptibility to pathogen attack. We studied morphological, anatomical, and photosynthesis differences in potato plants (Solanum tuberosum var. Spunta) exposed to sunlight or simulated shade in a greenhouse. We found that simulated shade strongly induced stem and internode elongation with a higher production of free auxin in stems and a lower production of tubers. The mesophyll thickness of the upper leaves of plants grown in simulated shade was lower, but the epidermis was wider compared with the leaves of plants cultivated in sunlight. In addition, the photosynthesis rate was lower in the upper leaves exposed to nonsaturated irradiances and higher in the basal leaves at saturated irradiances compared with control plants. RNA-seq analysis showed that 146 and 155 genes were up- and downregulated by shade, respectively. By quantitative reverse transcription polymerase chain reaction, we confirmed that FLOWERING LOCUS T (FT), WRKY-like, and PAR1b were induced, while FLAVONOL 4-SULFOTRANSFERASE was repressed under shade. In shaded plants, leaves and tubers were more susceptible to the necrotrophic fungus Botrytis cinerea attack. Overall, our work demonstrates configurational changes between growth and defense decisions in potato plants cultivated in simulated shade.

Light and jasmonic acid coordinately regulate the phosphate responses under shade and phosphate starvation conditions in Arabidopsis

In the natural ecosystem, plants usually grow at high vegetation density for yield maximization. The high-density planting triggers a variety of strategies to avoid canopy shade and competes with their neighbors for light and nutrition, which are collected termed shade avoidance responses. The molecular mechanism underlying shade avoidance and nutrition has expanded largely in the past decade; however, how these two responses intersect remains poorly understood. Here, we show that simulated shade undermined Pi starvation response and the phytohormone JA is involved in this process. We found that the JA signaling repressor JAZ proteins directly interact with PHR1 to repress its transcriptional activity on downstream targets, including phosphate starvation induced genes. Furthermore, FHY3 and FAR1, the negative regulators of shade avoidance, directly bind to promoters of NIGT1.1 and NIGT1.2 to activate their expression, and this process is also antagonized by JAZ proteins. All these results finally result in attenuation of Pi starvation response under shade and Pi-depleted conditions. Our findings unveil a previously unrecognized molecular framework whereby plants integrate light and hormone signaling to modulate phosphate responses under plant competition.

FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation

Plants can sense the shade from neighboring plants by detecting a reduction of the red:far-red light (R:FR) ratio. Phytochrome B (phyB) is the primary photoreceptor that perceives shade light and regulates jasmonic acid (JA) signaling. However, the molecular mechanisms underlying phyB and JA signaling integration in shade responses remain largely unknown. Here, we show the interaction of phyB and FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT1 (JAR1) in a functional demand manner in Arabidopsis (Arabidopsis thaliana) seedling development. Genetic evidence and interaction studies indicated that phyB and FIN219 synergistically and negatively regulate shade-induced hypocotyl elongation. Moreover, phyB interacted with various isoforms of FIN219 under high and low R:FR light. Methyl jasmonate (MeJA) treatment, FIN219 mutation, and PHYBOE digalactosyldiacylglycerol synthase1-1 (dgd1-1) plants, which show increased levels of JA, altered the patterns of phyB-associated nuclear speckles under the same conditions. Surprisingly, PHYBOE dgd1-1 showed a shorter hypocotyl phenotype than its parental mutants under shade conditions. Microarray assays using PHYBOE and PHYBOE fin219-2 indicated that PHYB overexpression substantially affects defense response-related genes under shade light and coregulates expression of auxin-responsive genes with FIN219. Thus, our findings reveal that phyB substantially crosstalks with JA signaling through FIN219 to modulate seedling development under shade light.

BBX24 Interacts with JAZ3 to Promote Growth by Reducing DELLA Activity in Shade Avoidance

Shade avoidance syndrome (SAS) is a strategy of major adaptive significance and typically includes elongation of the stem and petiole, leaf hyponasty, reduced branching and phototropic orientation of the plant shoot toward canopy gaps. Both cryptochrome 1 and phytochrome B (phyB) are the major photoreceptors that sense the reduction in the blue light fluence rate and the low red:far-red ratio, respectively, and both light signals are associated with plant density and the resource reallocation when SAS responses are triggered. The B-box (BBX)-containing zinc finger transcription factor BBX24 has been implicated in the SAS as a regulator of DELLA activity, but this interaction does not explain all the observed BBX24-dependent regulation in shade light. Here, through a combination of transcriptional meta-analysis and large-scale identification of BBX24-interacting transcription factors, we found that JAZ3, a jasmonic acid signaling component, is a direct target of BBX24. Furthermore, we demonstrated that joint loss of BBX24 and JAZ3 function causes insensitivity to DELLA accumulation, and the defective shade-induced elongation in this mutant is rescued by loss of DELLA or phyB function. Therefore, we propose that JAZ3 is part of the regulatory network that controls the plant growth in response to shade, through a mechanism in which BBX24 and JAZ3 jointly regulate DELLA activity. Our results provide new insights into the participation of BBX24 and JA signaling in the hypocotyl shade avoidance response in Arabidopsis.

Red-light receptor phytochrome B inhibits BZR1-NAC028-CAD8B signaling to negatively regulate rice resistance to sheath blight

Phytochrome (Phy)-regulated light signalling plays important roles in plant growth, development, and stress responses. However, its function in rice defence against sheath blight disease (ShB) remains unclear. Here, we found that PhyB mutation or shade treatment promoted rice resistance to ShB, while resistance was reduced by PhyB overexpression. Further analysis showed that PhyB interacts with phytochrome-interacting factor-like 15 (PIL15), brassinazole resistant 1 (BZR1), and vascular plant one-zinc-finger 2 (VOZ2). Plants overexpressing PIL15 were more susceptible to ShB in contrast to bzr1-D-overexpressing plants compared with the wild-type, suggesting that PhyB may inhibit BZR1 to negatively regulate rice resistance to ShB. Although BZR1 is known to regulate brassinosteroid (BR) signalling, the observation that BR signalling negatively regulated resistance to ShB indicated an independent role for BZR1 in controlling rice resistance. It was also found that the BZR1 ligand NAC028 positively regulated resistance to ShB. RNA sequencing showed that cinnamyl alcohol dehydrogenase 8B (CAD8B), involved in lignin biosynthesis was upregulated in both bzr1-D- and NAC028-overexpressing plants compared with the wild-type. Yeast-one hybrid, ChIP, and transactivation assays demonstrated that BZR1 and NAC028 activate CAD8B directly. Taken together, the analyses demonstrated that PhyB-mediated light signalling inhibits the BZR1-NAC028-CAD8B pathway to regulate rice resistance to ShB.

Jasmonic Acid as a Mediator in Plant Response to Necrotrophic Fungi

Jasmonic acid (JA) and its derivatives, all named jasmonates, are the simplest phytohormones which regulate multifarious plant physiological processes including development, growth and defense responses to various abiotic and biotic stress factors. Moreover, jasmonate plays an important mediator's role during plant interactions with necrotrophic oomycetes and fungi. Over the last 20 years of research on physiology and genetics of plant JA-dependent responses to pathogens and herbivorous insects, beginning from the discovery of the JA co-receptor CORONATINE INSENSITIVE1 (COI1), research has speeded up in gathering new knowledge on the complexity of plant innate immunity signaling. It has been observed that biosynthesis and accumulation of jasmonates are induced specifically in plants resistant to necrotrophic fungi (and also hemibiotrophs) such as mostly investigated model ones, i.e., Botrytis cinerea, Alternaria brassicicola or Sclerotinia sclerotiorum. However, it has to be emphasized that the activation of JA-dependent responses takes place also during susceptible interactions of plants with necrotrophic fungi. Nevertheless, many steps of JA function and signaling in plant resistance and susceptibility to necrotrophs still remain obscure. The purpose of this review is to highlight and summarize the main findings on selected steps of JA biosynthesis, perception and regulation in the context of plant defense responses to necrotrophic fungal pathogens.

MYB30 integrates light signals with antioxidant biosynthesis to regulate plant responses during postsubmergence recovery

Submergence is an abiotic stress that limits agricultural production world-wide. Plants sense oxygen levels during submergence and postsubmergence reoxygenation and modulate their responses. Increasing evidence suggests that completely submerged plants are often exposed to low-light stress, owing to the depth and turbidity of the surrounding water; however, how light availability affects submergence tolerance remains largely unknown. Here, we showed that Arabidopsis thaliana MYB DOMAIN PROTEIN30 (MYB30) is an important transcription factor that integrates light signaling and postsubmergence stress responses. MYB DOMAIN PROTEIN30 protein abundance decreased upon submergence and accumulated during reoxygenation. Under submergence conditions, CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), a central regulator of light signaling, caused the ubiquitination and degradation of MYB30. In response to desubmergence, however, light-induced MYB30 interacted with MYC2, a master transcription factor involved in jasmonate signaling, and activated the expression of the VITAMIN C DEFECTIVE1 (VTC1) and GLUTATHIONE SYNTHETASE1 (GSH1) gene families to enhance antioxidant biosynthesis. Consistent with this, the myb30 knockout mutant showed increased sensitivity to submergence, which was partially rescued by overexpression of VTC1 or GSH1. Thus, our findings uncover the mechanism by which the COP1-MYB30 module integrates light signals with cellular oxidative homeostasis to coordinate plant responses to postsubmergence stress.

Tuning the Wavelength: Manipulation of Light Signaling to Control Plant Defense

The growth-defense trade-off in plants is a phenomenon whereby plants must balance the allocation of their resources between developmental growth and defense against attack by pests and pathogens. Consequently, there are a series of points where growth signaling can negatively regulate defenses and where defense signaling can inhibit growth. Light perception by various photoreceptors has a major role in the control of growth and thus many points where it can influence defense. Plant pathogens secrete effector proteins to manipulate defense signaling in their hosts. Evidence is emerging that some of these effectors target light signaling pathways. Several effectors from different kingdoms of life have converged on key chloroplast processes to take advantage of regulatory crosstalk. Moreover, plant pathogens also perceive and react to light in complex ways to regulate their own growth, development, and virulence. Recent work has shown that varying light wavelengths may provide a novel way of controlling or preventing disease outbreaks in plants.

Jasmonate-regulated root growth inhibition and root hair elongation

The phytohormone jasmonate is an essential endogenous signal in the regulation of multiple plant processes for environmental adaptation, such as primary root growth inhibition and root hair elongation. Perception of environmental stresses promotes the accumulation of jasmonate, which is sensed by the CORONATINE INSENSITIVE1 (COI1)-JASMONATE ZIM-DOMAIN (JAZ) co-receptor, triggering the degradation of JAZ repressors and induction of transcriptional reprogramming. The basic helix-loop-helix (bHLH) subgroup IIIe transcription factors MYC2, MYC3, and MYC4 are the most extensively characterized JAZ-binding factors and together stimulate jasmonate-signaled primary root growth inhibition. Conversely, the bHLH subgroup IIId transcription factors (i.e. bHLH3 and bHLH17) physically associate with JAZ proteins and suppress jasmonate-induced root growth inhibition. For root hair development, JAZ proteins interact with and inhibit ROOT HAIR DEFECTIVE 6 (RHD6) and RHD6 LIKE1 (RSL1) transcription factors to modulate jasmonate-enhanced root hair elongation. Moreover, jasmonate also interacts with other signaling pathways (such as ethylene and auxin) to regulate primary root growth and/or root hair elongation. Here, we review recent progress into jasmonate-mediated primary root growth and root hair development.

Genome-Wide Identification of bHLH Transcription Factor Family in Malus sieversii and Functional Exploration of MsbHLH155.1 Gene under Valsa Canker Infection

Xinjiang wild apple (Malus sieversii) is an ancient relic; a plant with abundant genetic diversity and disease resistance. Several transcription factors were studied in response to different biotic and abiotic stresses on the wild apple. Basic/helix-loop-helix (bHLH) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, no study has yet been conducted on the bHLH gene in M. sieversii. Based on the genome of M. sieversii, 184 putative MsbHLH genes were identified, and their physicochemical properties were studied. MsbHLH covered 23 subfamilies and lacked two subfamily genes of Arabidopsis thaliana based on the widely used classification method. Moreover, MsbHLH exon-intron structures matched subfamily classification, as evidenced by the analysis of their protein motifs. The analysis of cis-acting elements revealed that many MsbHLH genes share stress- and hormone-related cis-regulatory elements. These MsbHLH transcription factors were found to be involved in plant defense responses based on the protein-protein interactions among the differentially expressed MsbHLHs. Furthermore, 94 MsbHLH genes were differentially expressed in response to pathogenic bacteria. The qRT-PCR results also showed differential expression of MsbHLH genes. To further verify the gene function of bHLH, our study used the transient transformation method to obtain the overexpressed MsbHLH155.1 transgenic plants and inoculated them. Under Valsa canker infection, the lesion phenotype and physiological and biochemical indexes indicated that the antioxidant capacity of plants could increase and reduce the damage caused by membrane peroxidation. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of bHLH genes in M. sieversii and lays a foundation for a better understanding disease resistance in plants, as well as providing candidate genes for the development of M. sieversii resistance breeding.

Towards greenhouse cultivation of Artemisia annua: The application of LEDs in regulating plant growth and secondary metabolism

Artemisinin is a sesquiterpene lactone produced in glandular trichomes of Artemisia annua, and is extensively used in the treatment of malaria. Growth and secondary metabolism of A. annua are strongly regulated by environmental conditions, causing unstable supply and quality of raw materials from field grown plants. This study aimed to bring A. annua into greenhouse cultivation and to increase artemisinin production by manipulating greenhouse light environment using LEDs. A. annua plants were grown in a greenhouse compartment for five weeks in vegetative stage with either supplemental photosynthetically active radiation (PAR) (blue, green, red or white) or supplemental radiation outside PAR wavelength (far-red, UV-B or both). The colour of supplemental PAR hardly affected plant morphology and biomass, except that supplemental green decreased plant biomass by 15% (both fresh and dry mass) compared to supplemental white. Supplemental far-red increased final plant height by 23% whereas it decreased leaf area, plant fresh and dry weight by 30%, 17% and 7%, respectively, compared to the treatment without supplemental radiation. Supplemental UV-B decreased plant leaf area and dry weight (both by 7%). Interestingly, supplemental green and UV-B increased leaf glandular trichome density by 11% and 9%, respectively. However, concentrations of artemisinin, arteannuin B, dihydroartemisinic acid and artemisinic acid only exhibited marginal differences between the light treatments. There were no interactive effects of far-red and UV-B on plant biomass, morphology, trichome density and secondary metabolite concentrations. Our results illustrate the potential of applying light treatments in greenhouse production of A. annua to increase trichome density in vegetative stage. However, the trade-off between light effects on plant growth and trichome initiation needs to be considered. Moreover, the underlying mechanisms of light spectrum regulation on artemisinin biosynthesis need further clarification to enhance artemisinin yield in greenhouse production of A. annua.

COP1 controls salt stress tolerance by modulating sucrose content

The E3 ubiquitin ligase Constitutive Photomorphogenic 1 (COP1) plays evolutionarily conserved and divergent roles. In plants, COP1 regulates a large number of developmental processes including photomorphogenesis, seedling emergence, and gravitropism. Nevertheless, its function in abiotic stress tolerance remains largely unknown. Here, we demonstrate the role of COP1 in salt stress tolerance in Arabidopsis thaliana. In soil, cop1-4 and cop1-6 mutants were more tolerant to high salinity than wild-type (WT) plants during vegetative growth. However, in high salt-containing Murashige and Skoog (MS) medium, cop1-4 and cop1-6 seedlings exhibited significantly impaired growth compared with WT plants. Notably, cop1-4 and cop1-6 seedlings recovered their growth to the WT level upon exogenous sucrose treatment even under high salinity conditions. Compared with WT plants, the sucrose content of cop1-4 mutants was much higher at the vegetative growth stage but similar at the seedling stage. Upon exogenous sucrose supply, root elongation was significantly stimulated in cop1-4 seedlings but only slightly stimulated in WT plants. Thus, no significant difference was observed in root length between the two genotypes. Altogether, our data indicate that cop1 mutants are more tolerant to salt stress than WT plants, and the salt tolerance of cop1 mutants is correlated with their sucrose content.

CK2 promotes jasmonic acid signaling response by phosphorylating MYC2 in Arabidopsis

Jasmonic acid (JA) signaling plays a pivotal role in plant development and defense. MYC2 is a master transcription factor in JA signaling, and was found to be phosphorylated and negatively regulated by MAP kinase and receptor-like kinase. However, the kinases that positively regulate MYC2 through phosphorylation and promote MYC2-mediated activation of JA response have not been identified. Here, we identified CK2 as a kinase that phosphorylates MYC2 and thus regulates the JA signaling. CK2 holoenzyme can interact with MYC2 using its regulatory subunits and phosphorylate MYC2 at multiple sites with its catalytic subunits. Inhibition of CK2 activity in a dominant-negative plant line, CK2mut, repressed JA response. On the other hand, increasing CK2 activity by overexpression of CKB4, a regulatory subunit gene of CK2, enhanced JA response in a MYC2-dependent manner. Substitution of the Ser and Thr residues at phosphorylation sites of MYC2 by CK2 with Ala impaired MYC2 function in activating JA response. Further investigations evidenced that CK2 facilitated the JA-induced increase of MYC2 binding to the promoters of JA-responsive genes in vivo. Our study demonstrated that CK2 plays a positive role in JA signaling, and reveals a previously undiscovered mechanism that regulates MYC2 function.

COP1 mutation causes low leaf temperature under various abiotic stresses in Arabidopsis thaliana

Stomata are microscopic pores on epidermal cells of leaves and stems that regulate water loss and gas exchange between the plant and its environment. Constitutive photomorphogenic 1 (COP1) is an E3 ubiquitin ligase that is involved in plant growth and development and multiple abiotic stress responses by regulating the stability of various target proteins. However, little is known about how COP1 controls stomatal aperture and leaf temperature under various environmental conditions. Here, we show that COP1 participates in leaf temperature and stomatal closure regulation under normal and stress conditions in Arabidopsis. Leaf temperature of cop1 mutants was relatively lower than that of wild type (WT) under drought, salt, and heat stress and after abscisic acid (ABA), CaCl2, and H2O2 treatments. However, leaf temperature was generally higher in both WT and cop1 mutants after abiotic stress and chemical treatment than that of untreated WT and cop1 mutants. Stomatal aperture was wider in cop1 mutants than that in WT under all conditions tested, although the extent of stomatal closure varied between WT and cop1 mutants. Under dark conditions, leaf temperature was also lower in cop1 mutants than that in WT. Expression of the genes encoding ABA receptors, ABA biosynthesis proteins, positive regulators of stomatal closure and heat tolerance, and ABA-responsive proteins was lower in cop1 mutants that that in WT. In addition, expression of respiration-related genes was lower in cop1 mutants that that in WT. Taken together, the data provide evidence that mutations in COP1 lead to wider stomatal aperture and higher leaf temperature under normal and stress conditions, indicating that leaf temperature is highly correlated with stomatal aperture.

Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview

Secondary metabolites are incontestably key specialized molecules with proven health-promoting effects on human beings. Naturally synthesized secondary metabolites are considered an important source of pharmaceuticals, food additives, cosmetics, flavors, etc., Therefore, enhancing the biosynthesis of these relevant metabolites by maintaining natural authenticity is getting more attention. The application of exogenous jasmonates (JAs) is well recognized for its ability to trigger plant growth and development. JAs have a large spectrum of action that covers seed germination, hypocotyl growth regulation, root elongation, petal expansion, and apical hook growth. This hormone is considered as one of the key regulators of the plant's growth and development when the plant is under biotic or abiotic stress. The JAs regulate signal transduction through cross-talking with other genes in plants and thereby deploy an appropriate metabolism in the normal or stressed conditions. It has also been found to be an effective chemical elicitor for the synthesis of naturally occurring secondary metabolites. This review discusses the significance of JAs in the growth and development of plants and the successful outcomes of jasmonate-driven elicitation of secondary metabolites including flavonoids, anthraquinones, anthocyanin, xanthonoid, and more from various plant species. However, as the enhancement of these metabolites is essentially measured via in vitro cell culture or foliar spray, the large-scale production is significantly limited. Recent advancements in the plant cell culture technology lay the possibilities for the large-scale manufacturing of plant-derived secondary metabolites. With the insights about the genetic background of the metabolite biosynthetic pathway, synthetic biology also appears to be a potential avenue for accelerating their production. This review, therefore, also discussed the potential manoeuvres that can be deployed to synthesis plant secondary metabolites at the large-scale using plant cell, tissue, and organ cultures.

Shade suppresses wound-induced leaf repositioning through a mechanism involving PHYTOCHROME KINASE SUBSTRATE (PKS) genes

Shaded plants challenged with herbivores or pathogens prioritize growth over defense. However, most experiments have focused on the effect of shading light cues on defense responses. To investigate the potential interaction between shade-avoidance and wounding-induced Jasmonate (JA)-mediated signaling on leaf growth and movement, we used repetitive mechanical wounding of leaf blades to mimic herbivore attacks. Phenotyping experiments with combined treatments on Arabidopsis thaliana rosettes revealed that shade strongly inhibits the wound effect on leaf elevation. By contrast, petiole length is reduced by wounding both in the sun and in the shade. Thus, the relationship between the shade and wounding/JA pathways varies depending on the physiological response, implying that leaf growth and movement can be uncoupled. Using RNA-sequencing, we identified genes with expression patterns matching the hyponastic response (opposite regulation by both stimuli, interaction between treatments with shade dominating the wound signal). Among them were genes from the PKS (Phytochrome Kinase Substrate) family, which was previously studied for its role in phototropism and leaf positioning. Interestingly, we observed reduced shade suppression of the wounding effect in pks2pks4 double mutants while a PKS4 overexpressing line showed constitutively elevated leaves and was less sensitive to wounding. Our results indicate a trait-specific interrelationship between shade and wounding cues on Arabidopsis leaf growth and positioning. Moreover, we identify PKS genes as integrators of external cues in the control of leaf hyponasty further emphasizing the role of these genes in aerial organ positioning.

Plants face different types of stressful situations without the ability to relocate to favorable environments. For example, increasing plant density reduces access to sunlight as plants start to shade each other. Foliar shading represents a stress that many plants cope with by changing their morphology. This includes elongation of stem-like structures and repositioning of leaves to favor access to unfiltered sunlight. Plants also defend themselves against various pathogens including herbivores. Defense mechanisms include the production of deterrent chemical and morphological adaptations such as stunted growth and downwards leaf repositioning. Here we studied the morphological response of plants when simultaneously facing shade and herbivore stress. When facing both stresses petiole growth was intermediate between the shade-enhanced and wound-repressed response. In contrast, the shade cue overrides the wounding cue leading to a similar upwards leaf repositioning in the combined treatments or in the response to shade alone. Using gene expression analyses and genetics we identified two members of the Phytochrome Kinase Substrate family as playing a signal integration role when plants simultaneously faced both stresses. This contributes to our understanding of the mechanisms underlying plant morphological adaptations when facing multiple stresses.

Genome-wide analysis of JAZ family genes expression patterns during fig (Ficus carica L.) fruit development and in response to hormone treatment

BACKGROUND

Jasmonate-ZIM domain (JAZ) repressors negatively regulate signal transduction of jasmonates, which regulate plant development and immunity. However, no comprehensive analysis of the JAZ gene family members has been done in the common fig (Ficus carica L.) during fruit development and hormonal treatment.

RESULTS

In this study, 10 non-redundant fig JAZ family genes (FcJAZs) distributed on 7 chromosomes were identified in the fig genome. Phylogenetic and structural analysis showed that FcJAZ genes can be grouped into 5 classes. All the classes contained relatively complete TIFY and Jas domains. Yeast two hybrid (Y2H) results showed that all FcJAZs proteins may interact with the identified transcription factor, FcMYC2. Tissue-specific expression analysis showed that FcJAZs were highly expressed in the female flowers and roots. Expression patterns of FcJAZs during the fruit development were analyzed by RNA-Seq and qRT-PCR. The findings showed that, most FcJAZs were significantly downregulated from stage 3 to 5 in the female flower, whereas downregulation of these genes was observed in the fruit peel from stage 4 to 5. Weighted-gene co-expression network analysis (WGCNA) showed the expression pattern of FcJAZs was correlated with hormone signal transduction and plant-pathogen interaction. Putative cis-elements analysis of FcJAZs and expression patterns of FcJAZs which respond to hormone treatments revealed that FcJAZs may regulate fig fruit development by modulating the effect of ethylene or gibberellin.

CONCLUSIONS

This study provides a comprehensive analysis of the FcJAZ family members and provides information on FcJAZs contributions and their role in regulating the common fig fruit development.

Light-Engineering Technology for Enhancing Plant Disease Resistance

Insect vector-borne diseases are a major constraint to a wide variety of crops. Plants integrate environmental light and internal signalings to defend dual stresses both from the vector insects and vector-transmitted pathogens. In this review, we highlight a studies that demonstrate how light regulates plants deploying mechanisms against vector-borne diseases. Four major host defensive pathways involved in the host defense network against multiple biotic stresses are reviewed: innate immunity, phytohormone signaling, RNA interference, and protein degradation. The potential with light-engineering technology with light emitting diodes (LEDs) and genome engineering technology for fine-tuning crop defense and yield are also discussed.

The Multifaceted Roles of MYC2 in Plants: Toward Transcriptional Reprogramming and Stress Tolerance by Jasmonate Signaling

Environmental stress is one of the major restrictions on plant development and foodstuff production. The adaptive response in plants largely occurs through an intricate signaling system, which is crucial for regulating the stress-responsive genes. Myelocytomatosis (MYC) transcription factors are the fundamental regulators of the jasmonate (JA) signaling branch that participates in plant development and multiple stresses. By binding to the cis-acting elements of a large number of stress-responsive genes, JA-responsive transcription factors activate the stress-resistant defense genes. The mechanism of stress responses concerns myriad regulatory processes at the physiological and molecular levels. Discovering stress-related regulatory factors is of great value in disclosing the response mechanisms of plants to biotic or abiotic stress, which could guide the genetic improvement of plant resistance. This review summarizes recent researches in various aspects of MYC2-mediated JA signaling and emphasizes MYC2 involvement in plant growth and stress response.

Phytochrome B regulates jasmonic acid-mediated defense response against Botrytis cinerea in Arabidopsis

The phytochrome B mediated light signaling integrates with various phytohormone signalings to control plant immune response. However, it is still unclear whether phyB-mediated light signaling has an effect on the biosynthesis of jasmonate during plant defense response against Botrytis cinerea. In this study, we demonstrated that phyB-mediated light signaling has a role in this process. Initially, we confirmed that phyb plants were obviously less resistant to B. cinerea while phyB overexpressing plants showed significantly enhanced resistance. We also found that the expression of numerous JA biosynthesis genes was promoted upon treatment with red or white light when compared to that of darkness, and that this promotion is dependent on phyB. Consistent with the gene expression results, phyb plants accumulated reduced pool of JA-Ile, indicating that phyB-mediated light signaling indeed increased JA biosynthesis. Further genetic analysis showed that light-mediated JAZ9 degradation and phyB-enhanced resistance were dependent on the receptor COI1, and that pif1/3/4/5 (pifq) can largely rescue the severe symptom of phyb. Taken together, our study demonstrates that phyB may participate in plant defense against B. cinerea through the modulation of the biosynthesis of JA.

The co-chaperone HOP3 participates in jasmonic acid signaling by regulating CORONATINE-INSENSITIVE 1 activity

HOPs (HSP70-HSP90 organizing proteins) are a highly conserved family of HSP70 and HSP90 co-chaperones whose role in assisting the folding of various hormonal receptors has been extensively studied in mammals. In plants, HOPs are mainly associated with stress response, but their potential involvement in hormonal networks remains completely unexplored. In this article we describe that a member of the HOP family, HOP3, is involved in the jasmonic acid (JA) pathway and is linked to plant defense responses not only to pathogens, but also to a generalist herbivore. The JA pathway regulates responses to Botrytis cinerea infection and to Tetranychus urticae feeding; our data demonstrate that the Arabidopsis (Arabidopsis thaliana) hop3-1 mutant shows an increased susceptibility to both. The hop3-1 mutant exhibits reduced sensitivity to JA derivatives in root growth assays and downregulation of different JA-responsive genes in response to methyl jasmonate, further revealing the relevance of HOP3 in the JA pathway. Interestingly, yeast two-hybrid assays and in planta co-immunoprecipitation assays found that HOP3 interacts with COI1, suggesting that COI1 is a target of HOP3. Consistent with this observation, COI1 activity is reduced in the hop3-1 mutant. All these data strongly suggest that, specifically among HOPs, HOP3 plays a relevant role in the JA pathway by regulating COI1 activity in response to JA and, consequently, participating in defense signaling to biotic stresses.

SUMOylation of different targets fine-tunes phytochrome signaling

Plants monitor their surrounding ambient light environment by specialized photoreceptor proteins. Among them, phytochromes monitor red and far-red light. These molecules perceive photons, undergo a conformational change, and regulate diverse light signaling pathways, resulting in the mediation of key developmental and growth responses throughout the whole life of plants. Posttranslational modifications of the photoreceptors and their signaling partners may modify their function. For example, the regulatory role of phosphorylation has been investigated for decades by using different methodological approaches. In the past few years, a set of studies revealed that ubiquitin-like short protein molecules, called small ubiquitin-like modifiers (SUMOs) are attached reversibly to different members of phytochrome signaling pathways, including phytochrome B, the dominant receptor of red light signaling. Furthermore, SUMO attachment modifies the action of the target proteins, leading to altered light signaling and photomorphogenesis. This review summarizes recent results regarding SUMOylation of various target proteins, the regulation of their SUMOylation level, and the physiological consequences of SUMO attachment. Potential future research directions are also discussed.

Comparative phenotypic and transcriptomic analyses unravel conserved and distinct mechanisms underlying shade avoidance syndrome in Brassicaceae vegetables

Background

Plants grown under shade are exposed to low red/far-red ratio, thereby triggering an array of altered phenotypes called shade avoidance syndrome (SAS). Shade negatively influences plant growth, leading to a reduction in agricultural productivity. Understanding of SAS is crucial for sustainable agricultural practices, especially for high-density indoor farming. Brassicaceae vegetables are widely consumed around the world and are commonly cultivated in indoor farms. However, our understanding of SAS in Brassicaceae vegetables and their genome-wide transcriptional regulatory networks are still largely unexplored.

Results

Shade induced common signs of SAS, including hypocotyl elongation and reduced carotenoids/anthocyanins biosynthesis, in two different Brassicaceae species: Brassica rapa (Choy Sum and Pak Choy) and Brassica oleracea (Kai Lan). Phenotype-assisted transcriptome analysis identified a set of genes induced by shade in these species, many of which were related to auxin biosynthesis and signaling [e.g. YUCCA8 (YUC8), YUC9, and INDOLE-3-ACETIC ACID INDUCIBLE (IAAs)] and other phytohormones signaling pathways including brassinosteroids and ethylene. The genes functioning in plant defense (e.g. MYB29 and JASMONATE-ZIM-DOMAIN PROTEIN 9) as well as in biosynthesis of anthocyanins and glucosinolates were repressed upon shade. Besides, each species also exhibited distinct SAS phenotypes. Shade strongly reduced primary roots and elongated petioles of B. oleracea, Kai Lan. However, these SAS phenotypes were not clearly recognized in B. rapa, Choy Sum and Pak Choy. Some auxin signaling genes (e.g. AUXIN RESPONSE FACTOR 19, IAA10, and IAA20) were specifically induced in B. oleracea, while homologs in B. rapa were not up-regulated under shade. Contrastingly, shade-exposed B. rapa vegetables triggered the ethylene signaling pathway earlier than B. oleracea, Kai Lan. Interestingly, shade induced the transcript levels of LONG HYPOCOTYL IN FAR-RED 1 (HFR1) homolog in only Pak Choy as B. rapa. As HFR1 is a key negative regulator of SAS in Arabidopsis, our finding suggests that Pak Choy HFR1 homolog may also function in conferring higher shade tolerance in this variety.

Conclusions

Our study shows that two Brassicaceae species not only share a conserved SAS mechanism but also exhibit distinct responses to shade, which will provide comprehensive information to develop new shade-tolerant cultivars that are suitable for high-density indoor farms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08076-1.

Decoupling of Plant Growth and Accumulation of Biologically Active Compounds in Leaves, Roots, and Root Exudates of Hypericum perforatum L. by the Combination of Jasmonate and Far-Red Lighting

The plant hormone jasmonic acid (JA) fine tunes the growth–defense dilemma by inhibiting plant growth and stimulating the accumulation of secondary compounds. We investigated the interactions between JA and phytochrome B signaling on growth and the accumulation of selected secondary metabolites in Hypericum perforatum L., a medically important plant, by spraying plants with methyl jasmonate (MeJA) and by adding far-red (FR) lighting. MeJA inhibited plant growth, decreased fructose concentration, and enhanced the accumulation of most secondary metabolites. FR enhanced plant growth and starch accumulation and did not decrease the accumulation of most secondary metabolites. MeJA and FR acted mostly independently with no observable interactions on plant growth or secondary metabolite levels. The accumulation of different compounds (e.g., hypericin, flavonols, flavan-3-ols, and phenolic acid) in shoots, roots, and root exudates showed different responses to the two treatments. These findings indicate that the relationship between growth and secondary compound accumulation is specific and depends on the classes of compounds and/or their organ location. The combined application of MeJA and FR enhanced the accumulation of most secondary compounds without compromising plant growth. Thus, the negative correlations between biomass and the content of secondary compounds predicted by the growth-defense dilemma were overcome.

Repressors of anthocyanin biosynthesis

Anthocyanins play a variety of adaptive roles in both vegetative tissues and reproductive organs of plants. The broad functionality of these compounds requires sophisticated regulation of the anthocyanin biosynthesis pathway to allow proper localization, timing, and optimal intensity of pigment deposition. While it is well-established that the committed steps of anthocyanin biosynthesis are activated by a highly conserved MYB-bHLH-WDR (MBW) protein complex in virtually all flowering plants, anthocyanin repression seems to be achieved by a wide variety of protein and small RNA families that function in different tissue types and in response to different developmental, environmental, and hormonal cues. In this review, we survey recent progress in the identification of anthocyanin repressors and the characterization of their molecular mechanisms. We find that these seemingly very different repression modules act through a remarkably similar logic, the so-called 'double-negative logic'. Much of the double-negative regulation of anthocyanin production involves signal-induced degradation or sequestration of the repressors from the MBW protein complex. We discuss the functional and evolutionary advantages of this logic design compared with simple or sequential positive regulation. These advantages provide a plausible explanation as to why plants have evolved so many anthocyanin repressors.

Role of jasmonic acid in plants: the molecular point of view

Recent updates in JA biosynthesis, signaling pathways and the crosstalk between JA and others phytohormones in relation with plant responses to different stresses. In plants, the roles of phytohormone jasmonic acid (JA), amino acid conjugate (e.g., JA-Ile) and their derivative emerged in last decades as crucial signaling compounds implicated in stress defense and development in plants. JA has raised a great interest, and the number of researches on JA has increased rapidly highlighting the importance of this phytohormone in plant life. First, JA was considered as a stress hormone implicated in plant response to biotic stress (pathogens and herbivores) which confers resistance to biotrophic and hemibiotrophic pathogens contrarily to salicylic acid (SA) which is implicated in plant response to necrotrophic pathogens. JA is also implicated in plant responses to abiotic stress (such as soil salinity, wounding and UV). Moreover, some researchers have recently revealed that JA controls several physiological processes like root growth, growth of reproductive organs and, finally, plant senescence. JA is also involved in the biosynthesis of various metabolites (e.g., phytoalexins and terpenoids). In plants, JA signaling pathways are well studied in few plants essentially Arabidopsis thaliana, Nicotiana benthamiana, and Oryza sativa L. confirming the crucial role of this hormone in plants. In this review, we highlight the last foundlings about JA biosynthesis, JA signaling pathways and its implication in plant maturation and response to environmental constraints.

A New Approach for Wounding Research: MYC2 Gene Expression and Protein Stability in Wounded Arabidopsis Protoplasts

Wounding is a constant threat to plant survival throughout their lifespan; therefore, understanding the biological responses to wounds at the cellular level is important. The protoplast system is versatile for molecular biology, however, no wounding studies on this system have been reported. We established a new approach for wounding research using mechanically damaged Arabidopsis mesophyll protoplasts. Wounded protoplasts showed typical wounding responses, such as increased MPK6 kinase activity and upregulated JAZ1 expression. We also assessed expression profiles and protein stability of the basic helix-loop-helix transcription factor MYC2 in wounded protoplasts. Promoter activity, gene expression, and protein stability of MYC2 were compromised, but recovered in the early stage of wounding. In the late stage, the promoter activity and expression of MYC2 were increased, but the protein stability was not changed. According to the results of the present study, this new cell-based approach will be of use in various molecular studies on plant wounding.

The DUB family in Populus: identification, characterization, evolution and expression patterns

Background

The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants.

Results

In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus.

Conclusions

The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07844-3.

New Insights on the Regulation of Glucosinolate Biosynthesis via COP1 and DELLA Proteins in Arabidopsis Thaliana

The biosynthesis of defensive secondary metabolites, such as glucosinolates (GSLs), is a costly process, which requires nutrients, ATP, and reduction equivalents, and, therefore, needs well-orchestrated machinery while coordinating defense and growth. We discovered that the key repressor of light signaling, the CONSTITUTIVE PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYTOCHROME A-105 (COP1/SPA) complex, is a crucial component of GSL biosynthesis regulation. Various mutants in this COP1/SPA complex exhibited a strongly reduced level of GSL and a low expression of jasmonate (JA)-dependent genes. Furthermore, cop1, which is known to accumulate DELLA proteins in the dark, shows reduced gibberellin (GA) and JA signaling, thereby phenocopying other DELLA-accumulating mutants. This phenotype can be complemented by a dominant gain-of-function allele of MYC3 and by crossing with a mutant having low DELLA protein levels. Hence, SPA1 interacts with DELLA proteins in a yeast two-hybrid screen, whereas high levels of DELLA inhibit MYC function and suppress JA signaling. DELLA accumulation leads to reduced synthesis of GSL and inhibited growth. Thus, the COP1/SPA-mediated degradation of DELLA not only affects growth but also regulates the biosynthesis of GSLs.

LEDs Make It Resilient: Effects on Plant Growth and Defense

Light spectral composition influences plant growth and metabolism, and has important consequences for interactions with plant-feeding arthropods and their natural enemies. In greenhouse horticulture, light spectral composition can be precisely manipulated by light-emitting diodes (LEDs), and LEDs are already used to optimize crop production and quality. However, because light quality also modulates plant secondary metabolism and defense, it is important to understand the underlying mechanisms in the context of the growth-defense trade-off. We review the effects of the spectral composition of supplemental light currently used, or potentially used, in greenhouse horticulture on the mechanisms underlying plant growth and defense. This information is important for exploring opportunities to optimize crop performance and pest management, and thus for developing resilient crop-production systems.

Shade Avoidance: Expanding the Color and Hormone Palette

Major strides have been made over the past decade in elucidating the mechanisms that mediate shade-avoidance responses. The canonical PHYTOCHROME INTERACTING FACTOR (PIF)-auxin pathway that begins with inactivation of phytochrome B (phyB) by a low red:far-red (R:FR) ratio, and that leads to increased elongation, has been thoroughly characterized in arabidopsis (Arabidopsisthaliana) seedlings. Nevertheless, studies in other life stages and plant species have demonstrated the role of other wavelengths, photoreceptors, and hormones in the orchestration of shade-avoidance responses. We highlight recent developments that illustrate how canopy light cues regulate signaling through auxin, gibberellins (GAs), jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), and strigolactones (SLs) to modulate key aspects of plant growth, metabolism, and defense.

Control of Plant Growth and Defense by Photoreceptors: From Mechanisms to Opportunities in Agriculture

Plants detect and respond to the proximity of competitors using light signals perceived by photoreceptor proteins. A low ratio of red to far-red radiation (R:FR ratio) is a key signal of competition that is sensed by the photoreceptor phytochrome B (phyB). Low R:FR ratios increase the synthesis of growth-related hormones, including auxin and gibberellins, promoting stem elongation and other shade-avoidance responses. Other photoreceptors that help plants to optimize their developmental configuration and resource allocation patterns in the canopy include blue light photoreceptors, such as cryptochromes and phototropins, and UV receptors, such as UVR8. All photoreceptors act by directly or indirectly controlling the activity of two major regulatory nodes for growth and development: the COP1/SPA ubiquitin E3 ligase complex and the PIF transcription factors. phyB is also an important modulator of hormonal pathways that regulate plant defense against herbivores and pathogens, including the jasmonic acid signaling pathway. In this Perspective, we discuss recent advances on the studies of the mechanisms that link photoreceptors with growth and defense. Understanding these mechanisms is important to provide a functional platform for breeding programs aimed at improving plant productivity, stress tolerance, and crop health in species of agronomic interest, and to manipulate the light environments in protected agriculture.