Functional interconnections of HY1 with MYC2 and HY5 in Arabidopsis seedling development

MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis

Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9, which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.

A microbiota-root-shoot circuit favours Arabidopsis growth over defence under suboptimal light

Bidirectional root-shoot signalling is probably key in orchestrating stress responses and ensuring plant survival. Here, we show that Arabidopsis thaliana responses to microbial root commensals and light are interconnected along a microbiota-root-shoot axis. Microbiota and light manipulation experiments in a gnotobiotic plant system reveal that low photosynthetically active radiation perceived by leaves induces long-distance modulation of root bacterial communities but not fungal or oomycete communities. Reciprocally, microbial commensals alleviate plant growth deficiency under low photosynthetically active radiation. This growth rescue was associated with reduced microbiota-induced aboveground defence responses and altered resistance to foliar pathogens compared with the control light condition. Inspection of a set of A. thaliana mutants reveals that this microbiota- and light-dependent growth-defence trade-off is directly explained by belowground bacterial community composition and requires the host transcriptional regulator MYC2. Our work indicates that aboveground stress responses in plants can be modulated by signals from microbial root commensals.

Periodic root branching is influenced by light through an HY1-HY5-auxin pathway

The spacing of lateral roots (LRs) along the main root in plants is driven by an oscillatory signal, often referred to as the "root clock" that represents a pre-patterning mechanism that can be influenced by environmental signals. Light is an important environmental factor that has been previously reported to be capable of modulating the root clock, although the effect of light signaling on the LR pre-patterning has not yet been fully investigated. In this study, we reveal that light can activate the transcription of a photomorphogenic gene HY1 to maintain high frequency and amplitude of the oscillation signal, leading to the repetitive formation of pre-branch sites. By grafting and tissue-specific complementation experiments, we demonstrated that HY1 generated in the shoot or locally in xylem pole pericycle cells was sufficient to regulate LR branching. We further found that HY1 can induce the expression of HY5 and its homolog HYH, and act as a signalosome to modulate the intracellular localization and expression of auxin transporters, in turn promoting auxin accumulation in the oscillation zone to stimulate LR branching. These fundamental mechanistic insights improve our understanding of the molecular basis of light-controlled LR formation and provide a genetic interconnection between shoot- and root-derived signals in regulating periodic LR branching.

Enhancing Luminescence and Controlling the Mn Valence State of Gd3Ga5-x-δAlx-y+δO12:yMn Phosphors by the Design of the Garnet Structure

Gd₃Ga_5-x-δAl_x-y+δO₁₂:yMn solid solutions with improving luminescence properties were prepared via cation substitution and a controllable Mn valence state. The abnormal autoreduction from Mn⁴⁺ to Mn²⁺ ions was observed during the formation of Gd₃Ga_5-x-δAl_x-y+δO₁₂:yMn. The doped manganese ions occupy octahedral Ga³⁺(1) and Al³⁺(1) sites to form the Mn²⁺ luminescent center with red emission at 630 nm and Mn⁴⁺ luminescent centers with deep red light emission at 698 nm, respectively, matching well with the red light absorption of phytochrome (P_R) and the far-red light absorption of phytochrome (P_FR). With the design of the concentration of Al³⁺ and doped manganese ions, the photoluminescence (PL) of Mn⁴⁺/Mn²⁺ (corresponding to P_FR/P_R) can be tuned, which is very useful for controlling the plant growth. Moreover, the PL intensity of Gd₃Ga_5-x-δAl_x-y+δO₁₂:yMn can be increased by 6.8 times by substituting Al³⁺ for Ga³⁺. The thermal stability is also enhanced significantly. Finally, a series of warm white-light-emitting diodes (WLEDs) with good performance were fabricated using the as-prepared Gd₃Ga_5-x-δAl_x-0.012+δO₁₂:0.012Mn phosphor. The results show that the designed Gd₃Ga_5-x-δAl_x-y+δO₁₂:yMn phosphors have potential practical values in plant-growth light-emitting diodes (LEDs) and high-performance WLEDs. Moreover, our strategy not only provides a unique inspiration for tuning the valence states of Mn but also designs new advanced luminescent materials.

Beyond Light: Insights Into the Role of Constitutively Photomorphogenic1 in Plant Hormonal Signaling

Light is an important environmental factor with profound effects in plant growth and development. Constitutively photomorphogenic1 (COP1) is a vital component of the light signaling pathway as a negative regulator of photomorphogenesis. Although the role of COP1 in light signaling has been firmly established for some time, recent studies have proven that COP1 is also a crucial part of multiple plant hormonal regulatory pathways. In this article, we review the available evidence involving COP1 in hormone signaling, its molecular mechanisms, and its contribution to the complicated regulatory network linking light and plant hormone signaling.

OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development

Plants have evolved an intricate network of sensory photoreceptors and signaling components to regulate their development. Among the light signaling components identified to date, HY5, a basic leucine zipper (bZIP) transcription factor, has been investigated extensively. However, most of the work on HY5 has been carried out in Arabidopsis (Arabidopsis thaliana), a dicot. In this study, based on homology search and phylogenetic analysis, we identified three homologs of AtHY5 in monocots; however, AtHYH (HY5 homolog) homologs are absent in the monocots analyzed. Out of the three homologs identified in rice (Oryza sativa), we have functionally characterized OsbZIP48OsbZIP48 was able to complement the Athy5 mutant. OsbZIP48 protein levels are developmentally regulated in rice. Moreover, the OsbZIP48 protein does not degrade in dark-grown rice and Athy5 seedlings complemented with OsbZIP48, which is in striking contrast to AtHY5. In comparison with AtHY5, which does not cause any change in hypocotyl length when overexpressed in Arabidopsis, the overexpression of full-length OsbZIP48 in rice transgenics reduced the plant height considerably. Microarray analysis revealed that OsKO2, which encodes ent-kaurene oxidase 2 of the gibberellin biosynthesis pathway, is down-regulated in OsbZIP48^OE and up-regulated in OsbZIP48^KD transgenics as compared with the wild type. Electrophoretic mobility shift assay showed that OsbZIP48 binds directly to the OsKO2 promoter. The RNA interference lines and the T-DNA insertional mutant of OsbZIP48 showed seedling-lethal phenotypes despite the fact that roots were more proliferative during early stages of development in the T-DNA insertional mutant. These data provide credible evidence that OsbZIP48 performs more diverse functions in a monocot system like rice in comparison with its Arabidopsis ortholog, HY5.

Photoreceptor Mediated Plant Growth Responses: Implications for Photoreceptor Engineering toward Improved Performance in Crops

Rising temperatures during growing seasons coupled with altered precipitation rates presents a challenging task of improving crop productivity for overcoming such altered weather patterns and cater to a growing population. Light is a critical environmental factor that exerts a powerful influence on plant growth and development ranging from seed germination to flowering and fruiting. Higher plants utilize a suite of complex photoreceptor proteins to perceive surrounding red/far-red (phytochromes), blue/UV-A (cryptochromes, phototropins, ZTL/FKF1/LKP2), and UV-B light (UVR8). While genomic studies have also shown that light induces extensive reprogramming of gene expression patterns in plants, molecular genetic studies have shown that manipulation of one or more photoreceptors can result in modification of agronomically beneficial traits. Such information can assist researchers to engineer photoreceptors via genome editing technologies to alter expression or even sensitivity thresholds of native photoreceptors for targeting aspects of plant growth that can confer superior agronomic value to the engineered crops. Here we summarize the agronomically important plant growth processes influenced by photoreceptors in crop species, alongwith the functional interactions between different photoreceptors and phytohormones in regulating these responses. We also discuss the potential utility of synthetic biology approaches in photobiology for improving agronomically beneficial traits of crop plants by engineering designer photoreceptors.

Heme oxygenase 1 defects lead to reduced chlorophyll in Brassica napus

We previously described a Brassica napus chlorophyll-deficient mutant (ygl) with yellow-green seedling leaves and mapped the related gene, BnaC.YGL, to a 0.35 cM region. However, the molecular mechanisms involved in this chlorophyll defect are still unknown. In this study, the BnaC07.HO1 gene (equivalent to BnaC.YGL) was isolated by the candidate gene approach, and its function was confirmed by genetic complementation. Comparative sequencing analysis suggested that BnaC07.HO1 was lost in the mutant, while a long noncoding-RNA was inserted into the promoter of the homologous gene BnaA07.HO1. This insert was widely present in B. napus cultivars and down-regulated BnaA07.HO1 expression. BnaC07.HO1 was highly expressed in the seedling leaves and encoded heme oxygenase 1, which was localized in the chloroplast. Biochemical analysis showed that BnaC07.HO1 can catalyze heme conversion to form biliverdin IXα. RNA-seq analysis revealed that the loss of BnaC07.HO1 impaired tetrapyrrole metabolism, especially chlorophyll biosynthesis. According, the levels of chlorophyll intermediates were reduced in the ygl mutant. In addition, gene expression in multiple pathways was affected in ygl. These findings provide molecular evidences for the basis of the yellow-green leaf phenotype and further insights into the crucial role of HO1 in B. napus.

De novo Sequencing of the Leaf Transcriptome Reveals Complex Light-Responsive Regulatory Networks in Camellia sinensis cv. Baijiguan

Tea plants (Camellia sinensis L.) possess high genetic diversity that is important for breeding. One cultivar, Baijiguan, exhibits a yellow leaf phenotype, reduced chlorophyll (Chl) content, and aberrant chloroplast structures under high light intensity. In contrast, under low light intensity, the flush shoot from Baijiguan becomes green, the Chl content increases significantly, and the chloroplasts exhibit normal structures. To understand the underlying molecular mechanisms for these observations, we performed de novo transcriptome sequencing and digital gene expression (DGE) profiling using Illumina sequencing technology. De novo transcriptome assembly identified 88,788 unigenes, including 1652 transcription factors from 25 families. In total, 1993 and 2576 differentially expressed genes (DEGs) were identified in Baijiguan plants treated with 3 and 6 days of shade, respectively. Gene Ontology (GO) and pathway enrichment analyses indicated that the DEGs are predominantly involved in the ROS scavenging system, chloroplast development, photosynthetic pigment synthesis, secondary metabolism, and circadian systems. The light-responsive gene POR (protochlorophyllide oxidoreductase) and transcription factor HY5 were identified. Quantitative real-time PCR (qRT-PCR) analysis of 20 selected DEGs confirmed the RNA-sequencing (RNA-Seq) results. Overall, these findings suggest that high light intensity inhibits the expression of photosystem II 10-kDa protein (PsbR) in Baijiguan, thus affecting PSII stability, chloroplast development and chlorophyll biosynthesis.

Citrullus colocynthis NAC transcription factors CcNAC1 and CcNAC2 are involved in light and auxin signaling

Two novel NAC transcription factors from C itrullus colocynthis implicated in light and auxin signaling pathway. NAC transcription factors (NAM, ATAF1, 2, CUC2) have multiple functions in plant growth and development. Two NACs, CcNAC1 and CcNAC2, were recently identified in the highly drought-tolerant cucurbit species, Citrullus colocynthis. This study examines the functional role of these genes under different qualities of light based on the in silico analysis of the CcNAC1 and CcNAC2 promoters that revealed the presence of several light-associated motifs. The impact of both light and auxin on CcNAC1 and CcNAC2 expression was examined in C. colocynthis leaves, and using reporter (pCcNAC1, 2::GUS) lines in Arabidopsis. Furthermore, the effects of constitutive overexpression (OE-CcNAC1, 2) in Arabidopsis were also examined under a range of conditions to confirm reporter line linkages. White, blue, red, and far-red light treatments resulted in similar patterns of quantitative changes in CcNAC1and CcNAC2 expression in both species, with the highest transcript increases following red light. Photomorphogenic changes in Arabidopsis hypocotyls were correlated with gene transcript levels. In the absence of light, hypocotyls of OE-CcNAC1/CcNAC2 lines were significantly longer as compared to WT. The addition of exogenous auxin (+IAA) to growth medium also resulted in changes to the hypocotyl lengths of overexpression lines and spatiotemporal reporter line changes in seedlings. Our data suggest that CcNAC1, 2 might be functionally important in the light signaling pathway, and appear connected to the hormone auxin. This is the first study to indicate that NAC genes might play a role in both light and auxin signaling pathways.

A mitogen-activated protein kinase cascade module, MKK3-MPK6 and MYC2, is involved in blue light-mediated seedling development in Arabidopsis

Mitogen-activated protein kinase (MAPK) pathways are involved in several signal transduction processes in eukaryotes. Light signal transduction pathways have been extensively studied in plants; however, the connection between MAPK and light signaling pathways is currently unknown. Here, we show that MKK3-MPK6 is activated by blue light in a MYC2-dependent manner. MPK6 physically interacts with and phosphorylates a basic helix-loop-helix transcription factor, MYC2, and is phosphorylated by a MAPK kinase, MKK3. Furthermore, MYC2 binds to the MPK6 promoter and regulates its expression in a feedback regulatory mechanism in blue light signaling. We present mutational and physiological studies that illustrate the function of the MKK3-MPK6-MYC2 module in Arabidopsis thaliana seedling development and provide a revised mechanistic view of photomorphogenesis.

The Arabidopsis thaliana hypocotyl, a model to identify and study control mechanisms of cellular expansion

Developmental biology studies in general benefit from model organisms that are well characterized. Arabidopsis thaliana fulfills this criterion and represents one of the best experimental systems to study developmental processes in higher plants. Light is a crucial factor that drives photosynthesis, but that also regulates plant morphogenesis. As the hypocotyl is completely embryonic of origin, its growth occurs solely by expansion of the cells and this process is strongly dependent on the light conditions. In this review, we provide evidence that the hypocotyl serves as ideal model object to study cell expansion mechanisms and its regulation. We focus on the regulation of hypocotyl development by light and highlight the key modulating proteins in this signaling cascade. Downstream of light-signaling, cellular expansion is greatly dependent on specific cell wall depositions, which is related to cortical microtubular (re)arrangements and on composition and/or extensibility of the cell wall. We discuss possible further experimental approaches to broaden our knowledge on hypocotyl development, which will give an outlook on the probable evolution of the field.

LeMYC2 acts as a negative regulator of blue light mediated photomorphogenic growth, and promotes the growth of adult tomato plants

BACKGROUND

Arabidopsis ZBF1/MYC2bHLH transcription factor is a repressor of photomorphogenesis, and acts as a point of cross talk in light, abscisic acid (ABA) and jasmonic acid (JA) signaling pathways. MYC2 also functions as a positive regulator of lateral root development and flowering time under long day conditions. However, the function of MYC2 in growth and development remains unknown in crop plants.

RESULTS

Here, we report the functional analyses of LeMYC2 in tomato (Lycopersicon esculentum). The amino acid sequence of LeMYC2 showed extensive homology with Arabidopsis MYC2, containing the conserved bHLH domain. To study the function of LeMYC2 in tomato, overexpression and RNA interference (RNAi) LeMYC2 tomato transgenic plants were generated. Examination of seedling morphology, physiological responses and light regulated gene expression has revealed that LeMYC2 works as a negative regulator of blue light mediated photomorphogenesis. Furthermore, LeMYC2 specifically binds to the G-box of LeRBCS-3A promoter. Overexpression of LeMYC2 has led to increased root length with more number of lateral roots. The tomato plants overexpressing LeMYC2 have reduced internode distance with more branches, and display the opposite morphology to RNAi transgenic lines. Furthermore, this study shows that LeMYC2 promotes ABA and JA responsiveness.

CONCLUSIONS

Collectively, this study highlights that working in light, ABA and JA signaling pathways LeMYC2 works as an important regulator for growth and development in tomato plants.

Z-box binding transcription factors (ZBFs): a new class of transcription factors in Arabidopsis seedling development

One set of genes encoding diverse groups of transcription factors that interact with the Z-box (ATACGTGT; a potential Z-DNA forming sequence) is called ZBFs (Z-box Binding Factors). ZBFs include ZBF1, ZBF2, and ZBF3, which encode ZBF1/MYC2 (bHLH), ZBF2/GBF1 (bZIP), and ZBF3/CAM7 (Calmodulin) proteins, respectively. With several recent reports, it is becoming increasingly evident that ZBFs play crucial roles in Arabidopsis seedling photomorphogenesis. ZBFs integrate signals from various wavelengths of light to coordinate the regulation of transcriptional networks that affect multiple facets of plant growth and development. The function of each ZBF is qualitatively and quantitatively distinct. The zbf mutants display pleiotropic effects including altered hypocotyl elongation, cotyledon expansion, lateral root development, and flowering time. In this inaugural review, we discuss the identification, molecular functions, and interacting partners of ZBFs in light-mediated Arabidopsis seedling development.

MYC2: the master in action

Jasmonates (JAs) are plant hormones with essential roles in plant defense and development. The basic-helix-loop-helix (bHLH) transcription factor (TF) MYC2 has recently emerged as a master regulator of most aspects of the jasmonate (JA) signaling pathway in Arabidopsis. MYC2 coordinates JA-mediated defense responses by antagonistically regulating two different branches of the JA signaling pathway that determine resistance to pests and pathogens, respectively. MYC2 is required for induced systemic resistance (ISR) triggered by beneficial soil microbes while MYC2 function is targeted by pathogens during effector-mediated suppression of innate immunity in roots. Another notable function of MYC2 is the regulation of crosstalk between the signaling pathways of JA and those of other phytohormones such as abscisic acid (ABA), salicylic acid (SA), gibberellins (GAs), and auxin (IAA). MYC2 also regulates interactions between JA signaling and light, phytochrome signaling, and the circadian clock. MYC2 is involved in JA-regulated plant development, lateral and adventitious root formation, flowering time, and shade avoidance syndrome. Related bHLH TFs MYC3 and MYC4 also regulate both overlapping and distinct MYC2-regulated functions in Arabidopsis while MYC2 orthologs act as 'master switches' that regulate JA-mediated biosynthesis of secondary metabolites. Here, we briefly review recent studies that revealed mechanistic new insights into the mode of action of this versatile TF.

Deep sequencing reveals transcriptome re-programming of Taxus × media cells to the elicitation with methyl jasmonate

Background

Plant cell culture represents an alternative source for producing high-value secondary metabolites including paclitaxel (Taxol®), which is mainly produced in Taxus and has been widely used in cancer chemotherapy. The phytohormone methyl jasmonate (MeJA) can significantly increase the production of paclitaxel, which is induced in plants as a secondary metabolite possibly in defense against herbivores and pathogens. In cell culture, MeJA also elicits the accumulation of paclitaxel; however, the mechanism is still largely unknown.

Methodology/Principal Findings

To obtain insight into the global regulation mechanism of MeJA in the steady state of paclitaxel production (7 days after MeJA addition), especially on paclitaxel biosynthesis, we sequenced the transcriptomes of MeJA-treated and untreated Taxus × media cells and obtained ∼ 32.5 M high quality reads, from which 40,348 unique sequences were obtained by de novo assembly. Expression level analysis indicated that a large number of genes were associated with transcriptional regulation, DNA and histone modification, and MeJA signaling network. All the 29 known genes involved in the biosynthesis of terpenoid backbone and paclitaxel were found with 18 genes showing increased transcript abundance following elicitation of MeJA. The significantly up-regulated changes of 9 genes in paclitaxel biosynthesis were validated by qRT-PCR assays. According to the expression changes and the previously proposed enzyme functions, multiple candidates for the unknown steps in paclitaxel biosynthesis were identified. We also found some genes putatively involved in the transport and degradation of paclitaxel. Potential target prediction of miRNAs indicated that miRNAs may play an important role in the gene expression regulation following the elicitation of MeJA.

Conclusions/Significance

Our results shed new light on the global regulation mechanism by which MeJA regulates the physiology of Taxus cells and is helpful to understand how MeJA elicits other plant species besides Taxus.

Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites

BACKGROUND

From initial seed germination through reproduction, plants continuously reprogram their transcriptional repertoire to facilitate growth and development. This dynamic is mediated by a diverse but inextricably-linked catalog of regulatory proteins called transcription factors (TFs). Statistically quantifying TF binding site (TFBS) abundance in promoters of differentially expressed genes can be used to identify binding site patterns in promoters that are closely related to stress-response. Output from today's transcriptomic assays necessitates statistically-oriented software to handle large promoter-sequence sets in a computationally tractable fashion.

RESULTS

We present Marina, an open-source software for identifying over-represented TFBSs from amongst large sets of promoter sequences, using an ensemble of 7 statistical metrics and binding-site profiles. Through software comparison, we show that Marina can identify considerably more over-represented plant TFBSs compared to a popular software alternative.

CONCLUSIONS

Marina was used to identify over-represented TFBSs in a two time-point RNA-Seq study exploring the transcriptomic interplay between soybean (Glycine max) and soybean rust (Phakopsora pachyrhizi). Marina identified numerous abundant TFBSs recognized by transcription factors that are associated with defense-response such as WRKY, HY5 and MYB2. Comparing results from Marina to that of a popular software alternative suggests that regardless of the number of promoter-sequences, Marina is able to identify significantly more over-represented TFBSs.

HY1 genetically interacts with GBF1 and regulates the activity of the Z-box containing promoters in light signaling pathways in Arabidopsis thaliana

Arabidopsis HY1/HO1, heme oxygenase enzyme, catalyses the oxygenation of heme to produce biliverdin, an essential step in the phytochrome-chromophore biosynthesis pathway. GBF1/ZBF2 is a G/Z-box binding bZIP protein that plays a dual but opposite regulatory roles in blue light-mediated seedling development and gene expression. Here, we show the genetic interactions of HY1 and GBF1 in seedling photomorphogenesis, and the role of HY1 in the regulation of promoters containing the Z-box light responsive element. Our results indicate that whereas the additional mutation in GBF1 does not affect the phenotype of hy1 mutant seedlings in red or far-red light, the additional mutation in HY1 suppresses the hyper photomorphogenic phenotype of gbf1 in BL. Further, transgenic studies using promoter-reporter constructs indicate that functional HY1 is essential for the optimal induction of Z-box containing synthetic and native promoters at various stages of Arabidopsis growth and development. Thus, this study establishes a functional relation of HY1 with GBF1, and HY1-mediated regulation of Z-box containing promoters in Arabidopsis seedling development.