Light Modulates Ethylene Synthesis, Signaling, and Downstream Transcriptional Networks to Control Plant Development

MORF2-mediated plastidial retrograde signaling is involved in stress response and skotomorphogenesis beyond RNA editing

Retrograde signaling modulates the expression of nuclear genome-encoded organelle proteins to adjust organelle function in response to environmental cues. MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2) was initially recognized as a plastidial RNA-editing factor but recently shown to interact with GUN1. Given the central role of GUN1 in chloroplast retrograde signaling and the unviable phenotype of morf2 mutants that is inconsistent with many viable mutants involved in RNA editing, we hypothesized that MORF2 has functions either dosage dependent or beyond RNA editing. Using an inducible Clustered Interspaced Short Palindromic Repeat interference (iCRISPRi) approach, we were able to reduce the MORF2 transcripts in a controlled manner. In addition to MORF2-dosage dependent RNA-editing errors, we discovered that reducing MORF2 by iCRISPRi stimulated the expression of stress responsive genes, triggered plastidial retrograde signaling, repressed ethylene signaling and skotomorphogenesis, and increased accumulation of hydrogen peroxide. These findings along with previous discoveries suggest that MORF2 is an effective regulator involved in plastidial metabolic pathways whose reduction can readily activate multiple retrograde signaling molecules possibly involving reactive oxygen species to adjust plant growth. In addition, our newly developed iCRISPRi approach provided a novel genetic tool for quantitative reverse genetics studies on hub genes in plants.

Ethylene signaling increases reactive oxygen species accumulation to drive root hair initiation in Arabidopsis

Root hair initiation is a highly regulated aspect of root development. The plant hormone ethylene and its precursor, 1-amino-cyclopropane-1-carboxylic acid, induce formation and elongation of root hairs. Using confocal microscopy paired with redox biosensors and dyes, we demonstrated that treatments that elevate ethylene levels lead to increased hydrogen peroxide accumulation in hair cells prior to root hair formation. In the ethylene-insensitive receptor mutant, etr1-3, and the signaling double mutant, ein3eil1, the increase in root hair number or reactive oxygen species (ROS) accumulation after ACC and ethylene treatment was lost. Conversely, etr1-7, a constitutive ethylene signaling receptor mutant, has increased root hair formation and ROS accumulation, similar to ethylene-treated Col-0 seedlings. The caprice and werewolf transcription factor mutants have decreased and elevated ROS levels, respectively, which are correlated with levels of root hair initiation. The rhd2-6 mutant, with a defect in the gene encoding the ROS-synthesizing RESPIRATORY BURST OXIDASE HOMOLOG C (RBOHC), and the prx44-2 mutant, which is defective in a class III peroxidase, showed impaired ethylene-dependent ROS synthesis and root hair formation via EIN3EIL1-dependent transcriptional regulation. Together, these results indicate that ethylene increases ROS accumulation through RBOHC and PRX44 to drive root hair formation.

Supplemental Blue Light Frequencies Improve Ripening and Nutritional Qualities of Tomato Fruits

Tomatoes (Solanum lycopersicum L. Micro-Tom) were grown in a plastic greenhouse. When plants anthesis, the 100 μmol m^-2 s^-1 blue light-emitting diode (LED) light (430 ± 10 nm) was supplemented from 6:00 to 18:00. There were 5 treatments, which contained different blue light frequencies with the same intensity: S6 (30 min blue light and 30 min pause), S8 (30 min blue light and 15 min pause), S10 (30 min blue and 8 min pause), S12 (continuous blue light for 12 h), and control (CK) (natural light, without any supplemental light). Agronomic traits and nutritional qualities of tomato fruits were measured at 30, 34, 38, 42, and 46 days after anthesis (DAA), respectively. Different frequencies of supplemental blue light could accelerate flowering of tomato plants and promote fruit ripening about 3-4 days early via promoting ethylene evolution of fruits, which significantly facilitated the processes of color change and maturity in tomato fruits. The contents of lycopene, total phenolic compounds, total flavonoids, vitamin C, and soluble sugar, as well as the overall antioxidant activity of tomato fruits were significantly enhanced by all the supplemental blue light treatments. In all, different frequencies of supplemental blue light prominently reinforced the antioxidant levels and nutritional qualities of tomato fruits, especially lycopene content, and S10 was more optimal for tomato fruits production in a plastic greenhouse.

To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses

Plants often live in adverse environmental conditions and are exposed to various stresses, such as heat, cold, heavy metals, salt, radiation, poor lighting, nutrient deficiency, drought, or flooding. To adapt to unfavorable environments, plants have evolved specialized molecular mechanisms that serve to balance the trade-off between abiotic stress responses and growth. These mechanisms enable plants to continue to develop and reproduce even under adverse conditions. Ethylene, as a key growth regulator, is leveraged by plants to mitigate the negative effects of some of these stresses on plant development and growth. By cooperating with other hormones, such as jasmonic acid (JA), abscisic acid (ABA), brassinosteroids (BR), auxin, gibberellic acid (GA), salicylic acid (SA), and cytokinin (CK), ethylene triggers defense and survival mechanisms thereby coordinating plant growth and development in response to abiotic stresses. This review describes the crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses.

EIN3 and RSL4 interfere with an MYB-bHLH-WD40 complex to mediate ethylene-induced ectopic root hair formation in Arabidopsis

The alternating cell specifications of root epidermis to form hair cells or nonhair cells in Arabidopsis are determined by the expression level of GL2, which is activated by an MYB-bHLH-WD40 (WER-GL3-TTG1) transcriptional complex. The phytohormone ethylene (ET) has a unique effect of inducing N-position epidermal cells to form root hairs. However, the molecular mechanisms underlying ET-induced ectopic root hair development remain enigmatic. Here, we show that ET promotes ectopic root hair formation through down-regulation of GL2 expression. ET-activated transcription factors EIN3 and its homolog EIL1 mediate this regulation. Molecular and biochemical analyses further revealed that EIN3 physically interacts with TTG1 and interferes with the interaction between TTG1 and GL3, resulting in reduced activation of GL2 by the WER-GL3-TTG1 complex. Furthermore, we found through genetic analysis that the master regulator of root hair elongation, RSL4, which is directly activated by EIN3, also participates in ET-induced ectopic root hair development. RSL4 negatively regulates the expression of GL2, likely through a mechanism similar to that of EIN3. Therefore, our work reveals that EIN3 may inhibit gene expression by affecting the formation of transcription-activating protein complexes and suggests an unexpected mutual inhibition between the hair elongation factor, RSL4, and the hair specification factor, GL2. Overall, this study provides a molecular framework for the integration of ET signaling and intrinsic root hair development pathway in modulating root epidermal cell specification.

The regulation of ACC synthase protein turnover: a rapid route for modulating plant development and stress responses

The phytohormone ethylene regulates plant growth, development, and stress responses. The strict fine-tuning of the regulation of ethylene biosynthesis contributes to the diverse roles of ethylene in plants. Pyridoxal 5'-phosphate-dependent 1-aminocyclopropane-1-carboxylic acid synthase, a rate-limiting enzyme in ethylene biosynthesis, is central and often rate-limiting to regulate ethylene concentration in plants. The post-translational regulation of ACS is a major pathway controlling ethylene biosynthesis in response to various stimuli. We conclude that the regulation of ACS turnover may serve as a central hub for the rapid integration of developmental, environmental, and hormonal signals, all of which influence plant growth and stress responses.

Activation of Local and Systemic Defence Responses by Flg22 Is Dependent on Daytime and Ethylene in Intact Tomato Plants

The first line of plant defence responses against pathogens can be induced by the bacterial flg22 and can be dependent on various external and internal factors. Here, we firstly studied the effects of daytime and ethylene (ET) using Never ripe (Nr) mutants in the local and systemic defence responses of intact tomato plants after flg22 treatments. Flg22 was applied in the afternoon and at night and rapid reactions were detected. The production of hydrogen peroxide and nitric oxide was induced by flg22 locally, while superoxide was induced systemically, in wild type plants in the light period, but all remained lower at night and in Nr leaves. Flg22 elevated, locally, the ET, jasmonic acid (JA) and salicylic acid (SA) levels in the light period; these levels did not change significantly at night. Expression of Pathogenesis-related 1 (PR1), Ethylene response factor 1 (ERF1) and Defensin (DEF) showed also daytime- and ET-dependent changes. Enhanced ERF1 and DEF expression and stomatal closure were also observable in systemic leaves of wild type plants in the light. These data demonstrate that early biotic signalling in flg22-treated leaves and distal ones is an ET-dependent process and it is also determined by the time of day and inhibited in the early night phase.

Identify of Fast-Growing Related Genes Especially in Height Growth by Combining QTL Analysis and Transcriptome in Salix matsudana (Koidz)

The study on the fast-growing traits of trees, mainly valued by tree height (TH) and diameter at breast height (DBH), is of great significance to promote the development of the forest industry. Quantitative trait locus (QTL) mapping based on high-density genetic maps is an efficient approach to identify genetic regions for fast-growing traits. In our study, a high-density genetic map for the F₁ population was constructed. The genetic map had a total size of 5,484.07 centimorgan (cM), containing 5,956 single nucleotide polymorphisms (SNPs) based on Specific Length Amplified Fragment sequencing. Six fast-growing related stable QTL were identified on six chromosomes, and five stable QTL were identified by a principal component analysis (PCA). By combining the RNA-seq analysis for the two parents and two progenies with the qRT-PCR analysis, four candidate genes, annotated as DnaJ, 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), Caffeic acid 3-O-methyltransferase 1 (COMT1), and Dirigent protein 6 (DIR6), that may regulate height growth were identified. Several lignin biosynthesis-related genes that may take part in height growth were detected. In addition, 21 hotspots in this population were found. The results of this study will provide an important foundation for further studies on the molecular and genetic regulation of TH and DBH.

Light- and hormone-mediated development in non-flowering plants: An overview

Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.

Dark-Induced Hormonal Regulation of Plant Growth and Development

The sessile nature of plants has made them extremely sensitive and flexible toward the constant flux of the surrounding environment, particularly light and dark. The light is perceived as a signal by specific receptors which further transduce the information through the signaling intermediates and effector proteins to modulate gene expression. Signal transduction induces changes in hormone levels that alters developmental, physiological and morphological processes. Importance of light for plants growth is well recognized, but a holistic understanding of key molecular and physiological changes governing plants development under dark is awaited. Here, we describe how darkness acts as a signal causing alteration in hormone levels and subsequent modulation of the gene regulatory network throughout plant life. The emphasis of this review is on dark mediated changes in plant hormones, regulation of signaling complex COP/DET/FUS and the transcription factors PIFs which affects developmental events such as apical hook development, elongated hypocotyls, photoperiodic flowering, shortened roots, and plastid development. Furthermore, the role of darkness in shade avoidance and senescence is discussed.

Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture

Tissue culture is an essential tool for the regeneration of uniform plant material. However, tissue culture conditions can be a source of abiotic stress for plants, leading to changes in the DNA sequence and methylation patterns. Despite the growing evidence on biochemical processes affected by abiotic stresses, how these altered biochemical processes affect DNA sequence and methylation patterns remains largely unknown. In this study, the methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach was used to investigate de novo methylation, demethylation, and sequence variation in barley regenerants derived by anther culture. Additionally, we used Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy to identify the spectral features of regenerants, which were then analyzed by mediation analysis. The infrared spectrum ranges (710-690 and 1010-940 cm-1) identified as significant in the mediation analysis were most likely related to β-glucans, cellulose, and S-adenosyl-L-methionine (SAM). Additionally, the identified compounds participated as predictors in moderated mediation analysis, explaining the role of demethylation of CHG sites (CHG_DMV) in in vitro tissue culture-induced sequence variation, depending on the duration of tissue culture. The data demonstrate that ATR-FTIR spectroscopy is a useful tool for studying the biochemical compounds that may affect DNA methylation patterns and sequence variation, if combined with quantitative characteristics determined using metAFLP molecular markers and mediation analysis. The role of β-glucans, cellulose, and SAM in DNA methylation, and in cell wall, mitochondria, and signaling, are discussed to highlight the putative cellular mechanisms involved in sequence variation.

Ethylene signaling in plants

Ethylene is a gaseous phytohormone and the first of this hormone class to be discovered. It is the simplest olefin gas and is biosynthesized by plants to regulate plant development, growth, and stress responses via a well-studied signaling pathway. One of the earliest reported responses to ethylene is the triple response. This response is common in eudicot seedlings grown in the dark and is characterized by reduced growth of the root and hypocotyl, an exaggerated apical hook, and a thickening of the hypocotyl. This proved a useful assay for genetic screens and enabled the identification of many components of the ethylene-signaling pathway. These components include a family of ethylene receptors in the membrane of the endoplasmic reticulum (ER); a protein kinase, called constitutive triple response 1 (CTR1); an ER-localized transmembrane protein of unknown biochemical activity, called ethylene-insensitive 2 (EIN2); and transcription factors such as EIN3, EIN3-like (EIL), and ethylene response factors (ERFs). These studies led to a linear model, according to which in the absence of ethylene, its cognate receptors signal to CTR1, which inhibits EIN2 and prevents downstream signaling. Ethylene acts as an inverse agonist by inhibiting its receptors, resulting in lower CTR1 activity, which releases EIN2 inhibition. EIN2 alters transcription and translation, leading to most ethylene responses. Although this canonical pathway is the predominant signaling cascade, alternative pathways also affect ethylene responses. This review summarizes our current understanding of ethylene signaling, including these alternative pathways, and discusses how ethylene signaling has been manipulated for agricultural and horticultural applications.