Evolution of Plant Hormone Response Pathways

Attenuated total reflection Fourier-transform infrared spectroscopy for the prediction of hormone concentrations in plants

Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and ultimately the overall growth and yield of plants. Many currently available methods to quantify such growth regulators quickly and accurately require extensive sample purification using complex analytic techniques. Herein we used ultra-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to create and validate the prediction of hormone concentrations made using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectral profiles of both freeze-dried ground leaf tissue and extracted xylem sap of Japanese knotweed (Reynoutria japonica) plants grown under different environmental conditions. In addition to these predictions made with partial least squares regression, further analysis of spectral data was performed using chemometric techniques, including principal component analysis, linear discriminant analysis, and support vector machines (SVM). Plants grown in different environments had sufficiently different biochemical profiles, including plant hormonal compounds, to allow successful differentiation by ATR-FTIR spectroscopy coupled with SVM. ATR-FTIR spectral biomarkers highlighted a range of biomolecules responsible for the differing spectral signatures between growth environments, such as triacylglycerol, proteins and amino acids, tannins, pectin, polysaccharides such as starch and cellulose, DNA and RNA. Using partial least squares regression, we show the potential for accurate prediction of plant hormone concentrations from ATR-FTIR spectral profiles, calibrated with hormonal data quantified by UHPLC-HRMS. The application of ATR-FTIR spectroscopy and chemometrics offers accurate prediction of hormone concentrations in plant samples, with advantages over existing approaches.

Take your sunscreen: plant photoreceptor systems in Serritaenia testaceovaginata

This article comments on:

Busch A, Gerbracht JV, Davies K, Hoecker U, Hess S. 2024. Comparative transcriptomics elucidates the cellular responses of an aeroterrestrial zygnematophyte to UV radiation. Journal of Experimental Botany 75, 3624–3642.

Research Overview and Trends of the Effects of Gibberellins (GAs) on Rice Biological Processes: A Bibliometric Analysis

Rice (Oryza sativa L.) is a vital crop that feeds more than half of the world's population. Gibberellins (GAs), a crucial phytohormone, play a significant role in the growth and development of rice. Since 1985, there has been a notable increase in the number of studies investigating the effects of GA on various biological processes in rice. Nevertheless, conducting scientific and quantitative research on the extensive literature available poses significant challenges, particularly in understanding the development trajectory of the field, examining major contributors, and identifying emerging research trends. The objective of this study is to address these challenges by analyzing global research patterns and trends using bibliometric methods from 1985 to 2024. Through the application of advanced analytical tools, progress in this field is studied in depth and the global research landscape is characterized from multiple dimensions including countries, institutions, authors, and journals. The analysis of 2118 articles extracted and screened from the Web of Science Core dataset shows a steady growth in the number of publications. The research published in China and the USA has significantly advanced the development of the field. In particular, institutions such as the Chinese Academy of Sciences and Nagoya University have shown impressive productivity. Lee In-Jung stands out as the most influential author. The journal Plant Physiology publishes the highest number of articles. The study also provides a thorough examination of current research hotspots, indicating a predominant focus on understanding the role of GAs in the biological processes that regulate diverse rice phenotypes, including plant height, seed dormancy, germination, and stress resistance. By tracing the development characteristics and key points in this area, this study contributes to a quantitative and comprehensive understanding of the impact of GAs on rice.

The landscape of transcription factor promoter activity during vegetative development in Marchantia

Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.

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

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

Carotenoid biosynthesis genes LcLCYB, LcLCYE, and LcBCH from wolfberry confer increased carotenoid content and improved salt tolerance in tobacco

Carotenoids play essential roles in plant growth and development and provide plants with a tolerance to a series of abiotic stresses. In this study, the function and biological significance of lycopene β-cyclase, lycopene ε-cyclase, and β-carotene hydroxylase, which are responsible for the modification of the tetraterpene skeleton procedure, were isolated from Lycium chinense and analyzed. The overexpression of lycopene β-cyclase, lycopene ε-cyclase, and β-carotene hydroxylase promoted the accumulation of total carotenoids and photosynthesis enhancement, reactive oxygen species scavenging activity, and proline content of tobacco seedlings after exposure to the salt stress. Furthermore, the expression of the carotenoid biosynthesis genes and stress-related genes (ascorbate peroxidase, catalase, peroxidase, superoxide dismutase, and pyrroline-5-carboxylate reductase) were detected and showed increased gene expression level, which were strongly associated with the carotenoid content and reactive oxygen species scavenging activity. After exposure to salt stress, the endogenous abscisic acid content was significantly increased and much higher than those in control plants. This research contributes to the development of new breeding aimed at obtaining stronger salt tolerance plants with increased total carotenoids and vitamin A content.

Phytohormones in a universe of regulatory metabolites: lessons from jasmonate

Small-molecule phytohormones exert control over plant growth, development, and stress responses by coordinating the patterns of gene expression within and between cells. Increasing evidence indicates that currently recognized plant hormones are part of a larger group of regulatory metabolites that have acquired signaling properties during the evolution of land plants. This rich assortment of chemical signals reflects the tremendous diversity of plant secondary metabolism, which offers evolutionary solutions to the daunting challenges of sessility and other unique aspects of plant biology. A major gap in our current understanding of plant regulatory metabolites is the lack of insight into the direct targets of these compounds. Here, we illustrate the blurred distinction between classical phytohormones and other bioactive metabolites by highlighting the major scientific advances that transformed the view of jasmonate from an interesting floral scent to a potent transcriptional regulator. Lessons from jasmonate research generally apply to other phytohormones and thus may help provide a broad understanding of regulatory metabolite-protein interactions. In providing a framework that links small-molecule diversity to transcriptional plasticity, we hope to stimulate future research to explore the evolution, functions, and mechanisms of perception of a broad range of plant regulatory metabolites.

Light Supplementation in Pitaya Orchards Induces Pitaya Flowering in Winter by Promoting Phytohormone Biosynthesis

The interaction between light and phytohormones is crucial for plant growth and development. The practice of supplementing light at night during winter to promote pitaya flowering and thereby enhance yield has been shown to be crucial and widely used. However, it remains unclear how supplemental winter light regulates phytohormone levels to promote flowering in pitaya. In this study, through analyzing the transcriptome data of pitaya at four different stages (NL, L0, L1, L2), we observed that differentially expressed genes (DEGs) were mainly enriched in the phytohormone biosynthesis pathway. We further analyzed the data and found that cytokinin (CK) content first increased at the L0 stage and then decreased at the L1 and L2 stages after supplemental light treatment compared to the control (NL). Gibberellin (GA), auxin (IAA), salicylic acid (SA), and jasmonic acid (JA) content increased during the formation of flower buds (L1, L2 stages). In addition, the levels of GA, ethylene (ETH), IAA, and abscisic acid (ABA) increased in flower buds after one week of development (L2f). Our results suggest that winter nighttime supplemental light can interact with endogenous hormone signaling in pitaya, particularly CK, to regulate flower bud formation. These results contribute to a better understanding of the mechanism of phytohormone interactions during the induction of flowering in pitaya under supplemental light in winter.

SMXL5 attenuates strigolactone signaling in Arabidopsis thaliana by inhibiting SMXL7 degradation

Hormone-activated proteolysis is a recurring theme of plant hormone signaling mechanisms. In strigolactone signaling, the enzyme receptor DWARF14 (D14) and an F-box protein, MORE AXILLARY GROWTH2 (MAX2), mark SUPPRESSOR OF MAX2 1-LIKE (SMXL) family proteins SMXL6, SMXL7, and SMXL8 for rapid degradation. Removal of these transcriptional corepressors initiates downstream growth responses. The homologous proteins SMXL3, SMXL4, and SMXL5, however, are resistant to MAX2-mediated degradation. We discovered that the smxl4 smxl5 mutant has enhanced responses to strigolactone. SMXL5 attenuates strigolactone signaling by interfering with AtD14-SMXL7 interactions. SMXL5 interacts with AtD14 and SMXL7, providing two possible ways to inhibit SMXL7 degradation. SMXL5 function is partially dependent on an ethylene-responsive-element binding-factor-associated amphiphilic repression (EAR) motif, which typically mediates interactions with the TOPLESS family of transcriptional corepressors. However, we found that loss of the EAR motif reduces SMXL5-SMXL7 interactions and the attenuation of strigolactone signaling by SMXL5. We hypothesize that integration of SMXL5 into heteromeric SMXL complexes reduces the susceptibility of SMXL6/7/8 proteins to strigolactone-activated degradation and that the EAR motif promotes the formation or stability of these complexes. This mechanism may provide a way to spatially or temporally fine-tune strigolactone signaling through the regulation of SMXL5 expression or translation.

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

The plant macronutrient phosphorus is a scarce resource and plant-available phosphate is limiting in most soil types. Generally, a gene regulatory module called the phosphate starvation response (PSR) enables efficient phosphate acquisition by roots and translocation to other organs. Plants growing on moderate to nutrient-rich soils need to co-ordinate availability of different nutrients and repress the highly efficient PSR to adjust phosphate acquisition to the availability of other macro- and micronutrients, and in particular nitrogen. PSR repression is mediated by a small family of single SYG1/Pho81/XPR1 (SPX) domain proteins. The SPX domain binds higher order inositol pyrophosphates that signal cellular phosphorus status and modulate SPX protein interaction with PHOSPHATE STARVATION RESPONSE1 (PHR1), the central transcriptional regulator of PSR. Sequestration by SPX repressors restricts PHR1 access to PSR gene promoters. Here we focus on SPX4 that primarily acts in shoots and sequesters many transcription factors other than PHR1 in the cytosol to control processes beyond the classical PSR, such as nitrate, auxin, and jasmonic acid signalling. Unlike SPX1 and SPX2, SPX4 is subject to proteasomal degradation not only by singular E3 ligases, but also by SCF-CRL complexes. Emerging models for these different layers of control and their consequences for plant acclimation to the environment will be discussed.

Molecular evolution and interaction of 14-3-3 proteins with H+-ATPases in plant abiotic stresses

Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHAs) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with evolutionary insights across multiple plant species. Here, we comprehensively review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins and functional domains that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3and AHA genes in a eudicotyledon (Arabidopsis thaliana), a monocotyledon (Hordeum vulgare), and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and AHAs respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses.

AsHSP26.2, a creeping bentgrass chloroplast small heat shock protein positively regulates plant development

KEY MESSAGE

The creeping bentgrass small heat shock protein AsHSP26.2 positively regulates plant growth and is a novel candidate for use in crop genetic engineering for enhanced biomass production and grain yield. Small heat shock proteins (sHSPs), a family of proteins with high level of diversity, significantly influence plant stress tolerance and plant development. We have cloned a creeping bentgrass chloroplast-localized sHSP gene, AsHSP26.2 responsive to IAA, GA and 6-BA stimulation. Transgenic creeping bentgrass overexpressing AsHSP26.2 exhibited significantly enhanced plant growth with increased stolon number and length as well as enlarged leaf blade width and leaf sheath diameters, but inhibited leaf trichomes initiation and development in the abaxial epidermis. These phenotypes are completely opposite to those displayed in the transgenic plants overexpressing AsHSP26.8, another chloroplast sHSP26 isoform that contains additional seven amino acids (AEGQGDG) between the consensus regions III and IV (Sun et al., Plant Cell Environ 44:1769-1787, 2021). Furthermore, AsHSP26.2 overexpression altered phytohormone biosynthesis and signaling transduction, resulting in elevated auxin and gibberellins (GA) accumulation. The results obtained provide novel insights implicating the sHSPs in plant growth and development regulation, and strongly suggest AsHSP26.2 to be a novel candidate for use in crop genetic engineering for enhanced plant biomass production and grain yield.

Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution

The phytohormone auxin, and its directional transport through tissues, plays a fundamental role in the development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using a radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In the Arabidopsis root epidermis, bryophytic PINs have no defined polarity. Pharmacological interference revealed a strong cytoskeletal dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal the divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and the co-evolution of PIN sequence-based and cell-based polarity mechanisms.

Unraveling the regulatory network of miRNA expression in Potato Y virus-infected of Nicotiana benthamiana using integrated small RNA and transcriptome sequencing

Potato virus Y (PVY) disease is a global problem that causes significant damage to crop quality and yield. As traditional chemical control methods are ineffective against PVY, it is crucial to explore new control strategies. MicroRNAs (miRNAs) play a crucial role in plant and animal defense responses to biotic and abiotic stresses. These endogenous miRNAs act as a link between antiviral gene pathways and host immunity. Several miRNAs target plant immune genes and are involved in the virus infection process. In this study, we conducted small RNA sequencing and transcriptome sequencing on healthy and PVY-infected N. benthamiana tissues (roots, stems, and leaves). Through bioinformatics analysis, we predicted potential targets of differentially expressed miRNAs using the N. benthamiana reference genome and the PVY genome. We then compared the identified differentially expressed mRNAs with the predicted target genes to uncover the complex relationships between miRNAs and their targets. This study successfully constructed a miRNA-mRNA network through the joint analysis of Small RNA sequencing and transcriptome sequencing, which unveiled potential miRNA targets and identified potential binding sites of miRNAs on the PVY genome. This miRNA-mRNA regulatory network suggests the involvement of miRNAs in the virus infection process.

Age-dependent dendrobine biosynthesis in Dendrobium nobile: insights into endophytic fungal interactions

Introduction

Dendrobium nobile (D. nobile), a valued Chinese herb known for its diverse pharmacological effects, owes much of its potency to the bioactive compound dendrobine. However, dendrobine content varies significantly with plant age, and the mechanisms governing this variation remain unclear. This study delves into the potential role of endophytic fungi in shaping host-microbe interactions and influencing plant metabolism.

Methods

Using RNA-seq, we examined the transcriptomes of 1-year-old, 2-year-old, and 3-year-old D. nobile samples and through a comprehensive analysis of endophytic fungal communities and host gene expression in D. nobile stems of varying ages, we aim to identify associations between specific fungal taxa and host genes.

Results

The results revealing 192 differentially expressed host genes. These genes exhibited a gradual decrease in expression levels as the plants aged, mirroring dendrobine content changes. They were enriched in 32 biological pathways, including phagosome, fatty acid degradation, alpha-linolenic acid metabolism, and plant hormone signal transduction. Furthermore, a significant shift in the composition of the fungal community within D. nobile stems was observed along the age gradient. Olipidium, Hannaella, and Plectospherella dominated in 1-year-old plants, while Strelitziana and Trichomerium prevailed in 2-year-old plants. Conversely, 3-year-old plants exhibited additional enrichment of endophytic fungi, including the genus Rhizopus. Two gene expression modules (mediumpurple3 and darkorange) correlated significantly with dominant endophytic fungi abundance and dendrobine accumulation. Key genes involved in dendrobine synthesis were found associated with plant hormone synthesis.

Discussion

This study suggests that the interplay between different endophytic fungi and the hormone signaling system in D. nobile likely regulates dendrobine biosynthesis, with specific endophytes potentially triggering hormone signaling cascades that ultimately influence dendrobine synthesis.

Jasmonates and salicylic acid: Evolution of defense hormones in land plants

The emergence of plant hormone signaling pathways is deeply intertwined with land plant evolution. In angiosperms, two plant hormones, salicylic Acid (SA) and Jasmonates (JAs), play a key role in plant defense, where JAs-mediated defenses are typically activated in response to herbivores and necrotrophic pathogens, whereas SA is prioritized against hemi/biotrophic pathogens. Thus, studying the evolution of SA and JAs and their crosstalk is essential to understand the evolution of molecular plant-microbe interactions (EvoMPMI) in land plants. Recent advances in the evolution of SA and JAs biosynthesis, signaling, and crosstalk in land plants illustrated that the insight gained in angiosperms does not necessarily apply to non-seed plant lineages, where the receptors perceive different ligands and the hormones activate pathways independently on the canonical receptors. In this review, recent findings on the two main defense hormones (JAs and SA) in non-seed plants, including functional studies in the bryophyte model Marchantia polymorpha, will be discussed.

Highly sensitive analysis of photoregulation and dynamic distribution of phytohormones based on nanoconfined liquid phase nanoextraction

BACKGROUND

As a vital energy source, light is one of the most significant environmental signals for plants' growth and development. The crosstalk amongst phytohormones regulated by light exhibits quantitative dynamic changes, but methodologies to analyze their distribution during plant growth are still limited. Rapid, highly sensitive, low-invasive detection and simultaneous assessment of the levels of multiple classes of phytohormones have important phytology applications, however the existing sample pretreatment strategies remain intricate, laborious, and far from being developed for in vivo high-sensitivity testing. (81) RESULTS: We applied a nanoconfined liquid phase nanoextraction (NLPNE) technique based on acidified carbon nanofibers (ACNFs) in combination with LC-ESI-MS/MS for highly sensitive analysis of acidic phytohormones' photoregulation and dynamic distribution. In this system, the mass transfer ability of analytes entering the nanoconfined space is significantly improved given the nanoconfined effect. In particular, the accelerated and strong adsorption of alkaline compounds to the ACNFs surface provide minimum interference for acidic compounds (photosensitive phytohormones), which facilitates their simple, fast, and selective quantification with improved sensitivity. The ACNFs-NLPNE strategy achieved quantitative enrichment of multi-class phytohormones in less than 5 min, and detection limits down to 0.49 fg mL-1. Moreover, we monitored the phytohormone changes under red and blue monochromatic light with relative standard deviations <13.4 %. The results further indicated that short-time red light regulation promoted Lepidium sativum L. growth while blue light inhibited it. (141) SIGNIFICANCE: A nanoconfinement effect-based sample pretreatment platform was developed for monitoring photoregulation phytohormones dynamic distribution with higher sensitivity and stability. Our findings highlighted the importance of the NLPNE approach in providing an accurate plant crosstalk information at the molecular level, which opens a promising avenue for investigating internal hormonal responses to external stimuli. (52).

Continuous In Vivo Monitoring of Indole-3-Acetic Acid and Salicylic Acid in Tomato Leaf Veins Based on an Electrochemical Microsensor

Indole-3-acetic acid (IAA) and salicylic acid (SA), as critical plant hormones, are involved in multiple physiological regulatory processes of plants. Simultaneous and continuous in vivo detection of IAA and SA will help clarify the mechanisms of their regulation and crosstalk. First, this study reports the development and application of an electrochemical microsensor for simultaneous and continuous in vivo detection of IAA and SA. This electrochemical microsensor system consisted of a tip (length, 2 mm) of platinum wire (diameter, 0.1 mm) modified with carbon cement and multi-walled carbon nanotubes, an untreated tip (length, 2 mm) of platinum wire (diameter, 0.1 mm), as well as a tip (length, 2 mm) of Ag/AgCl wire (diameter, 0.1 mm). It was capable of detecting IAA in the level ranging from 0.1 to 30 µM and SA ranging from 0.1 to 50 µM based on the differential pulse voltammetry or amperometric i-t., respectively. The dynamics of IAA and SA levels in tomato leaf veins under high salinity stress were continuously detected in vivo, and very little damage occurred. Compared to conventional detection methods, the constructed microsensor is not only suitable for continuously detecting IAA and SA in microscopic plant tissue in vivo, it also reduces the damage done to plants during the detection. More importantly, the continuous and dynamic changes in IAA and SA data obtained in stiu through this system not only can help clarify the interaction mechanisms of IAA and SA in plants, it also helps to evaluate the health status of plants, which will promote the development of basic research in botany and precision agriculture.

Species differences in hormonally mediated gene expression underlie the evolutionary loss of sexually dimorphic coloration in Sceloporus lizards

Phenotypic sexual dimorphism often involves the hormonal regulation of sex-biased expression for underlying genes. However, it is generally unknown whether the evolution of hormonally mediated sexual dimorphism occurs through upstream changes in tissue sensitivity to hormone signals, downstream changes in responsiveness of target genes, or both. Here, we use comparative transcriptomics to explore these possibilities in 2 species of Sceloporus lizards exhibiting different patterns of sexual dichromatism. Sexually dimorphic S. undulatus develops blue and black ventral coloration in response to testosterone, while sexually monomorphic S. virgatus does not, despite exhibiting similar sex differences in circulating testosterone levels. We administered testosterone implants to juveniles of each species and used RNAseq to quantify gene expression in ventral skin. Transcriptome-wide responses to testosterone were stronger in S. undulatus than in S. virgatus, suggesting species differences in tissue sensitivity to this hormone signal. Species differences in the expression of genes for androgen metabolism and sex hormone-binding globulin were consistent with this idea, but expression of the androgen receptor gene was higher in S. virgatus, complicating this interpretation. Downstream of androgen signaling, we found clear species differences in hormonal responsiveness of genes related to melanin synthesis, which were upregulated by testosterone in S. undulatus, but not in S. virgatus. Collectively, our results indicate that hormonal regulation of melanin synthesis pathways contributes to the development of sexual dimorphism in S. undulatus, and that changes in the hormonal responsiveness of these genes in S. virgatus contribute to the evolutionary loss of ventral coloration.

Electroporation-based delivery of proteins in Penium margaritaceum and other zygnematophycean algae

Zygnematophycean algae represent the streptophyte group identified as the closest sister clade to land plants. Their phylogenetic position and growing genomic resources make these freshwater algae attractive models for evolutionary studies in the context of plant terrestrialization. However, available genetic transformation protocols are limited and exclusively DNA-based. To expand the zygnematophycean toolkit, we developed a DNA-free method for protein delivery into intact cells using electroporation. We use confocal microscopy coupled with fluorescence lifetime imaging to assess the delivery of mNeonGreen into algal cells. We optimized the method to obtain high efficiency of delivery and cell recovery after electroporation in two strains of Penium margaritaceum and show that the experimental setup can also be used to deliver proteins in other zygnematophycean species such as Closterium peracerosum-strigosum-littorale complex and Mesotaenium endlicherianum. We discuss the possible applications of this proof-of-concept method.

Dynamic gene regulatory networks improving spike fertility through regulation of floret primordia fate in wheat

The developmental process of spike is critical for spike fertility through affecting floret primordia fate in wheat; however, the genetic regulation of this dynamic and complex developmental process remains unclear. Here, we conducted a high temporal-resolution analysis of spike transcriptomes and monitored the number and morphology of floret primordia within spike. The development of all floret primordia in a spike was clearly separated into three distinct phases: differentiation, pre-dimorphism and dimorphism. Notably, we identified that floret primordia with meiosis ability at the pre-dimorphism phase usually develop into fertile floret primordia in the next dimorphism phase. Compared to control, increasing plant space treatment achieved the maximum increasement range (i.e., 50%) in number of fertile florets by accelerating spike development. The process of spike fertility improvement was directed by a continuous and dynamic regulatory network involved in transcription factor and genes interaction. This was based on the coordination of genes related to heat shock protein and jasmonic acid biosynthesis during differentiation phase, and genes related to lignin, anthocyanin and chlorophyll biosynthesis during dimorphism phase. The multi-dimensional association with high temporal-resolution approach reported here allows rapid identification of genetic resource for future breeding studies to realise the maximum spike fertility potential in more cereal crops.

Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence

Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.

Role of Strigolactones in the Host Specificity of Broomrapes and Witchweeds

Root parasitic plants of the Orobanchaceae, broomrapes and witchweeds, pose a severe problem to agriculture in Europe, Asia and especially Africa. These parasites are totally dependent on their host for survival, and therefore, their germination is tightly regulated by host presence. Indeed, their seeds remain dormant in the soil until a host root is detected through compounds called germination stimulants. Strigolactones (SLs) are the most important class of germination stimulants. They play an important role in planta as a phytohormone and, upon exudation from the root, function in the recruitment of symbiotic arbuscular mycorrhizal fungi. Plants exude mixtures of various different SLs, possibly to evade detection by these parasites and still recruit symbionts. Vice versa, parasitic plants must only respond to the SL composition that is exuded by their host, or else risk germination in the presence of non-hosts. Therefore, parasitic plants have evolved an entire clade of SL receptors, called HTL/KAI2s, to perceive the SL cues. It has been demonstrated that these receptors each have a distinct sensitivity and specificity to the different known SLs, which possibly allows them to recognize the SL-blend characteristic of their host. In this review, we will discuss the molecular basis of SL sensitivity and specificity in these parasitic plants through HTL/KAI2s and review the evidence that these receptors contribute to host specificity of parasitic plants.

Complexity of SMAX1 signaling during seedling establishment

Karrikins (KARs) are small butenolide compounds identified in the smoke of burning vegetation. Along with the stimulating effects on seed germination, KARs also regulate seedling vigor and adaptive behaviors, such as seedling morphogenesis, root hair development, and stress acclimation. The pivotal KAR signaling repressor, SUPPRESSOR OF MAX2 1 (SMAX1), plays central roles in these developmental and morphogenic processes through an extensive signaling network that governs seedling responses to endogenous and environmental cues. Here, we summarize the versatile roles of SMAX1 reported in recent years and discuss how SMAX1 integrates multiple growth hormone signals into optimizing seedling establishment. We also discuss the evolutionary relevance of the SMAX1-mediated signaling pathways during the colonization of aqueous plants to terrestrial environments.

Unraveling the Mechanisms of Virus-Induced Symptom Development in Plants

Plant viruses, as obligate intracellular parasites, induce significant changes in the cellular physiology of host cells to facilitate their multiplication. These alterations often lead to the development of symptoms that interfere with normal growth and development, causing USD 60 billion worth of losses per year, worldwide, in both agricultural and horticultural crops. However, existing literature often lacks a clear and concise presentation of the key information regarding the mechanisms underlying plant virus-induced symptoms. To address this, we conducted a comprehensive review to highlight the crucial interactions between plant viruses and host factors, discussing key genes that increase viral virulence and their roles in influencing cellular processes such as dysfunction of chloroplast proteins, hormone manipulation, reactive oxidative species accumulation, and cell cycle control, which are critical for symptom development. Moreover, we explore the alterations in host metabolism and gene expression that are associated with virus-induced symptoms. In addition, the influence of environmental factors on virus-induced symptom development is discussed. By integrating these various aspects, this review provides valuable insights into the complex mechanisms underlying virus-induced symptoms in plants, and emphasizes the urgency of addressing viral diseases to ensure sustainable agriculture and food production.

Current insights into posttranscriptional regulation of fleshy fruit ripening

Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.

The origin and early evolution of cytokinin signaling

Angiosperms, especially Arabidopsis and rice, have long been at the center of plant research. However, technological advances in sequencing have led to a dramatic increase in genome and transcriptome data availability across land plants and, more recently, among green algae. These data allowed for an in-depth study of the evolution of different protein families - including those involved in the metabolism and signaling of phytohormones. While most early studies on phytohormone evolution were phylogenetic, those studies have started to be complemented by genetic and biochemical studies in recent years. Examples of such functional analyses focused on ethylene, jasmonic acid, abscisic acid, and auxin. These data have been summarized recently. In this review, we will focus on the progress in our understanding of cytokinin biology. We will use these data to synthesize key points about the evolution of cytokinin metabolism and signaling, which might apply to the evolution of other phytohormones as well.

Plant-Derived Smoke and Karrikin 1 in Seed Priming and Seed Biotechnology

Plant-derived smoke and smoke water (SW) can stimulate seed germination in numerous plants from fire-prone and fire-free areas, including cultivated plants and agricultural weeds. Smoke contains thousands of compounds; only several stimulants and inhibitors have been isolated from smoke. Among the six karrikins present in smoke, karrikin 1 (KAR₁) seems to be key for the stimulating effect of smoke. The discovery and activity of highly diluted SW and KAR₁ at extremely low concentrations (even at ca. 10^-9 M) inducing seed germination of a wide array of horticultural and agricultural plants have created tremendous opportunities for the use of these factors in pre-sowing seed treatment through smoke- or KAR₁-priming. This review presents examples of effects exerted by the two types of priming on seed germination and seedling emergence, growth, and development, as well as on the content of some compounds and enzyme activity. Seed biotechnology may involve both SW and KAR₁. Some examples demonstrate that SW and/or KAR₁ increased the efficiency of somatic embryogenesis, somatic embryo germination and conversion to plantlets. It is also possible to stimulate in vitro seed germination by SW, which allows to use in orchid propagation.

Comparative transcriptome profiling reveals the multiple levels of crosstalk in phytohormone networks in Brassica napus

Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network of synergistic, antagonistic and additive interactions has been elucidated in model plants. However, the systemic level of transcriptional responses to hormone crosstalk in Brassica napus is largely unknown. Here, we present an in-depth temporal-resolution study of the transcriptomes of the seven hormones in B. napus seedlings. Differentially expressed gene analysis revealed few common target genes that co-regulated (up- and down-regulated) by seven hormones; instead, different hormones appear to regulate distinct members of protein families. We then constructed the regulatory networks between the seven hormones side by side, which allowed us to identify key genes and transcription factors that regulate the hormone crosstalk in B. napus. Using this dataset, we uncovered a novel crosstalk between gibberellin and cytokinin in which cytokinin homeostasis was mediated by RGA-related CKXs expression. Moreover, the modulation of gibberellin metabolism by the identified key transcription factors was confirmed in B. napus. Furthermore, all data were available online from http://yanglab.hzau.edu.cn/BnTIR/hormone. Our study reveals an integrated hormone crosstalk network in Brassica napus, which also provides a versatile resource for future hormone studies in plant species.

DELLA functions evolved by rewiring of associated transcriptional networks

DELLA proteins are land-plant specific transcriptional regulators that transduce environmental information to multiple processes throughout a plant's life^1-3. The molecular basis for this critical function in angiosperms has been linked to the regulation of DELLA stability by gibberellins and to the capacity of DELLA proteins to interact with hundreds of transcription factors^4,5. Although bryophyte orthologues can partially fulfil functions attributed to angiosperm DELLA^6,7, it is not clear whether the capacity to establish interaction networks is an ancestral property of DELLA proteins or is associated with their role in gibberellin signalling^8-10. Here we show that representative DELLAs from the main plant lineages display a conserved ability to interact with multiple transcription factors. We propose that promiscuity was encoded in the ancestral DELLA protein, and that this property has been largely maintained, whereas the lineage-dependent diversification of DELLA-dependent functions mostly reflects the functional evolution of their interacting partners.

Insights into physiological and molecular mechanisms underlying efficient utilization of boron in different boron efficient Beta vulgaris L. varieties

Boron (B) deficiency and consequent limitation of plant yield and quality, particularly of sugar beet (Beta vulgaris L.) has emerged as a maior problem,which is exacerbating due to cultivar dependent variability in B deficiency tolerance. Pertinently, the current study was designed to elucidate the physiological and molecular mechanisms of B deficiency tolerance of sugar beet varieties KWS1197 (B-efficient variety) and KWS0143 (B-inefficient variety). A hydroponic experiment was conducted employing two B levels B0.1 (0.1 μM L^-1 H₃BO₃, deficiency) and B50 (50 μM L^-1 H₃BO₃, adequacy). Boron deficiency greatly inhibited root elongation and dry matter accumulation; however, formation of lateral roots stimulated and average root diameter was increased. Results exhibited that by up-regulating the expression of NIP5-1, NIP6-1, and BOR2, and suppressing the expression of BOR4, cultivar KWS1197, in contrast to KWS0143, managed to transfer sufficient amount of B to the aboveground plant parts, facilitating its effective absorption and utilization. Accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) was also mellowed in KWS1197, as well as the oxidative damage to root cells via preservation of the antioxidant enzyme system. Additionally, the expression of essential enzymes for biosynthesis of phytohormone (PYR/PYL) and lignin (COMT, POX, and CCoAOMT) were found to be highly up-regulated in KWS1197. Deductively, through effective B absorption and transportation, balanced nutrient accumulation, and an activated antioxidant enzyme system, B-efficient cultivars may cope with B deficiency while retaining a superior cellular structure to enable root development.

Die another day: phytosulfokine at the molecular trade-off between growth and defense in plants

Plants must make decisions to balance their growth versus defense against pathogens. Signaling of the plant peptide hormone phytosulfokine (PSK) has emerged as a critical stimulus for growth promotion. In this issue of The EMBO Journal, Ding et al (2022) show that PSK signaling promotes nitrogen assimilation via phosphorylation of glutamate synthase 2 (GS2). In the absence of PSK signaling, the plants growth is stunted, but its resistance to disease is reinforced.

The birth of a giant: evolutionary insights into the origin of auxin responses in plants

The plant signaling molecule auxin is present in multiple kingdoms of life. Since its discovery, a century of research has been focused on its action as a phytohormone. In land plants, auxin regulates growth and development through transcriptional and non-transcriptional programs. Some of the molecular mechanisms underlying these responses are well understood, mainly in Arabidopsis. Recently, the availability of genomic and transcriptomic data of green lineages, together with phylogenetic inference, has provided the basis to reconstruct the evolutionary history of some components involved in auxin biology. In this review, we follow the evolutionary trajectory that allowed auxin to become the "giant" of plant biology by focusing on bryophytes and streptophyte algae. We consider auxin biosynthesis, transport, physiological, and molecular responses, as well as evidence supporting the role of auxin as a chemical messenger for communication within ecosystems. Finally, we emphasize that functional validation of predicted orthologs will shed light on the conserved properties of auxin biology among streptophytes.

Gnawing pressure led to the expansion of JAZ genes in angiosperms

A long-standing problem in evolutionary biology is why some populations differentiate into many species while the majority do not. Angiosperms is an excellent group for investigating this problem because their diversity is unevenly distributed in space and phylogeny. Plant hormone participates in growth, development and defense. However, jasmonic acid (JA) was the only hormone response to bites. We first searched jasmonate ZIM-domain (JAZ), AUXIN/INDOLE ACETIC ACID (IAA / aux), PYR/PYL/RCAR (PYL), DELLA, and SUPPRESSOR OF MAX2 1-like (SMAX) in 272 plant species. We found the gene number change trends were consistent with origination rates and species numbers of angiosperms. So, 26 representative species were selected as an example for further analysis. The results showed JAZ had experienced two lineage-specific gene expansion events in angiosperms, which coincided with increases in mammalian body size and dental diversity. The proliferation of large herbivores as a results of mammalian prosperity after dinosaur extinction may be related to angiosperm evolution and bursting. The proliferation of large herbivores as the result of mammalian prosperity after the extinction of the dinosaurs was related to angiosperm evolution and bursting. Overall, our study uncovered a previously unknown co-evolution mechanism in terrestrial plants exposed to extreme environmental conditions.

Karrikin perception and signalling

Karrikins (KARs) are a class of butenolide compounds found in smoke that were first identified as seed germination stimulants for fire-following species. Early studies of KARs classified the germination and postgermination responses of many plant species and investigated crosstalk with plant hormones that regulate germination. The discovery that Arabidopsis thaliana responds to KARs laid the foundation for identifying mutants with altered KAR responses. Genetic analysis of KAR signalling revealed an unexpected link to strigolactones (SLs), a class of carotenoid-derived plant hormones. Substantial progress has since been made towards understanding how KARs are perceived and regulate plant growth, in no small part due to advances in understanding SL perception. KAR and SL signalling systems are evolutionarily related and retain a high degree of similarity. There is strong evidence that KARs are natural analogues of an endogenous signal(s), KAI2 ligand (KL), which remains unknown. KAR/KL signalling regulates many developmental processes in plants including germination, seedling photomorphogenesis, and root and root hair growth. KAR/KL signalling also affects abiotic stress responses and arbuscular mycorrhizal symbiosis. Here, we summarise the current knowledge of KAR/KL signalling and discuss current controversies and unanswered questions in this field.

Strategies to study the metabolic origins of specialized plant metabolites: The specialized 1,4-naphthoquinones

One of the hallmarks of specialized plant metabolites is that they are produced using precursors from central metabolism. Therefore, in addition to identifying and characterizing the pathway genes and enzymes involved in synthesizing a specialized compound, it is critical to study its metabolic origins. Identifying what primary metabolic pathways supply precursors to specialized metabolism and how primary metabolism has diversified to sustain fluxes to specialized metabolite pathways is imperative to optimizing synthetic biology strategies for producing high-value plant natural products in crops and microbial systems. Improved understanding of the metabolic origins of specialized plant metabolites has also revealed instances of recurrent evolution of the same compound, or nearly identical compounds, with similar ecological functions, thereby expanding knowledge about the factors driving the chemical diversity in the plant kingdom. In this chapter, we describe detailed methods for performing tracer studies, chemical inhibitor experiments, and reverse genetics. We use examples from investigations of the metabolic origins of specialized plant 1,4-naphthoquinones (1,4-NQs). The plant 1,4-NQs provide an excellent case study for illustrating the importance of investigating the metabolic origins of specialized metabolites. Over half a century of research by many groups has revealed that the pathways to synthesize plant 1,4-NQs are the result of multiple events of convergent evolution across several disparate plant lineages and that plant 1,4-NQ pathways are supported by extraordinary events of metabolic innovation and by various primary metabolic sources.

Plant Growth Hormones and Nanomaterial Interface: Exploring the connection from development to defense

The global increase in nanotechnology applications has been unprecedented and has now moved into the area of agriculture and food production. Applications with promising potential in sustainable agriculture include nanobiosensors, nanofertilizers, nanopesticides, nano-mediated remediation strategies for contaminated soils and nanoscale strategies to increase crop production and protection. Given this, the impact of nanomaterials/nanoparticles (NPs) on plant species needs to be thoroughly evaluated as this represents a critical interface between the biosphere and the environment. Importantly, phytohormones represent a critical class of biomolecules to plant health and productivity; however, the impact of NPs on these molecules is poorly understood. In addition, phytohormones, and associated pathways, are widely explored in agriculture to influence several biological processes for the improvement of plant growth and productivity under natural as well as stressed conditions. However, the impact of exogenous applications of phytohormones on NP-treated plants has not been explored. The importance of hormone signaling and cross-talk with other metabolic systems makes these biomolecules ideal candidates for a thorough assessment of NP impacts on plant species. This article presents a critical evaluation of the existing yet limited literature available on NP-phytohormone interactions in plants. In addition, the developing strategy of nano-enabled precision delivery of phytohormones via nanocarriers will be explored. Finally, directions for future research and critical knowledge gaps will be identified for this important aspect of nano-enabled agriculture.

Recent Advances in the Bacterial Phytohormone Modulation of Plant Growth

Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.

Jasmonate perception: Ligand-receptor interaction, regulation, and evolution

Phytohormones integrate external environmental and developmental signals with internal cellular responses for plant survival and multiplication in changing surroundings. Jasmonate (JA), which might originate from prokaryotes and benefit plant terrestrial adaptation, is a vital phytohormone that regulates diverse developmental processes and defense responses against various environmental stresses. In this review, we first provide an overview of ligand-receptor binding techniques used for the characterization of phytohormone-receptor interactions, then introduce the identification of the receptor COI1 and active JA molecules, and finally summarize recent advances on the regulation of JA perception and its evolution.

Organelles and phytohormones: a network of interactions in plant stress responses

Phytohormones are major signaling components that contribute to nearly all aspects of plant life. They constitute an interconnected communication network to fine-tune growth and development in response to the ever-changing environment. To this end, they have to coordinate with other signaling components, such as reactive oxygen species and calcium signals. On the one hand, the two endosymbiotic organelles, plastids and mitochondria, control various aspects of phytohormone signaling and harbor important steps of hormone precursor biosynthesis. On the other hand, phytohormones have feedback actions on organellar functions. In addition, organelles and phytohormones often act in parallel in a coordinated matter to regulate cellular functions. Therefore, linking organelle functions with increasing knowledge of phytohormone biosynthesis, perception, and signaling will reveal new aspects of plant stress tolerance. In this review, we highlight recent work on organelle-phytohormone interactions focusing on the major stress-related hormones abscisic acid, jasmonates, salicylic acid, and ethylene.

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.

The Integration of Metabolomics and Transcriptomics Provides New Insights for the Identification of Genes Key to Auxin Synthesis at Different Growth Stages of Maize

As a staple food crop, maize is widely cultivated worldwide. Sex differentiation and kernel development are regulated by auxin, but the mechanism regulating its synthesis remains unclear. This study explored the influence of the growth stage of maize on the secondary metabolite accumulation and gene expression associated with auxin synthesis. Transcriptomics and metabonomics were used to investigate the changes in secondary metabolite accumulation and gene expression in maize leaves at the jointing, tasseling, and pollen-release stages of plant growth. In total, 1221 differentially accumulated metabolites (DAMs) and 4843 differentially expressed genes (DEGs) were screened. KEGG pathway enrichment analyses of the DEGs and DAMs revealed that plant hormone signal transduction, tryptophan metabolism, and phenylpropanoid biosynthesis were highly enriched. We summarized the key genes and regulatory effects of the tryptophan-dependent auxin biosynthesis pathways, giving new insights into this type of biosynthesis. Potential MSTRG.11063 and MSTRG.35270 and MSTRG.21978 genes in auxin synthesis pathways were obtained. A weighted gene co-expression network analysis identified five candidate genes, namely TSB (Zm00001d046676 and Zm00001d049610), IGS (Zm00001d020008), AUX2 (Zm00001d006283), TAR (Zm00001d039691), and YUC (Zm00001d025005 and Zm00001d008255), which were important in the biosynthesis of both tryptophan and auxin. This study provides new insights for understanding the regulatory mechanism of auxin synthesis in maize.

The cell biology of charophytes: Exploring the past and models for the future

Charophytes (Streptophyta) represent a diverse assemblage of extant green algae that are the sister lineage to land plants. About 500-600+ million years ago, a charophyte progenitor successfully colonized land and subsequently gave rise to land plants. Charophytes have diverse but relatively simple body plans that make them highly attractive organisms for many areas of biological research. At the cellular level, many charophytes have been used for deciphering cytoskeletal networks and their dynamics, membrane trafficking, extracellular matrix secretion, and cell division mechanisms. Some charophytes live in challenging habitats and have become excellent models for elucidating the cellular and molecular effects of various abiotic stressors on plant cells. Recent sequencing of several charophyte genomes has also opened doors for the dissection of biosynthetic and signaling pathways. While we are only in an infancy stage of elucidating the cell biology of charophytes, the future application of novel analytical methodologies in charophyte studies that include a broader survey of inclusive taxa will enhance our understanding of plant evolution and cell dynamics.

Anabolism and signaling pathways of phytomelatonin

Phytomelatonin is a small multifunctional molecule found ubiquitously in plants, which plays an important role in plant growth, development, and biotic and abiotic stress responses. The classical biosynthetic and metabolic pathways of phytomelatonin have been elucidated, and uncovering alternative pathways has deepened our understanding of phytomelatonin synthesis. Phytomelatonin functions mainly via two pathways. In the direct pathway, phytomelatonin mediates the stress-induced reactive oxygen species burst through its strong antioxidant capacity. In the indirect pathway, phytomelatonin acts as a signal to activate signaling cascades and crosstalk with other plant hormones. The phytomelatonin receptor PMTR1/CAND2 was discovered in 2018, which enhanced our understanding of phytomelatonin function. This review summarizes the classical and potential pathways involved in phytomelatonin synthesis and metabolism. To elucidate the functions of phytomelatonin, we focus on the crosstalk between phytomelatonin and other phytohormones. We propose two models to explain how PMTR1 transmits the phytomelatonin signal through the G protein and MAPK cascade. This review will facilitate the identification of additional signaling molecules that function downstream of the phytomelatonin signaling pathway, thus improving our understanding of phytomelatonin signal transmission.

Molecular mechanisms and evolutionary history of phytomelatonin in flowering

Flowering is a critical stage in plant life history, which is coordinated by environmental signals and endogenous cues. Phytomelatonin is a widely distributed indoleamine present in all living organisms and plays pleiotropic roles in plant growth and development. Recent evidence has established that phytomelatonin could modulate flowering in many species, probably in a concentration-dependent manner. Phytomelatonin seems to associate with floral meristem identification and floral organ formation, and the fluctuation of phytomelatonin might be important for flowering. Regarding the underlying mechanisms, phytomelatonin interacts with the central components of floral gene regulatory networks directly or indirectly, including the MADS-box gene family, phytohormones, and reactive oxygen species (ROS). From an evolutionary point of view, the actions of phytomelatonin in flowering probably evolved during the period of the diversification of flowering plants and could be regarded as a functional extension of its primary activities. The presumed evolutionary history of phytomelatonin-modulated flowering is proposed, presented in the chronological order of the appearance of phytomelatonin and core flowering regulators, namely DELLA proteins, ROS, and phytohormones. Further efforts are needed to address some intriguing aspects, such as the exploration of the association between phytomelatonin and photoperiodic flowering, phytomelatonin-related floral MADS-box genes, the crosstalk between phytomelatonin and phytohormones, as well as its potential applications in agriculture.

Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.)

Drought is among the most serious environmental issue globally, and seriously affects the development, growth, and yield of crops. Maize (Zea mays L.), an important crop and industrial raw material, is planted on a large scale worldwide and drought can lead to large-scale reductions in maize corn production; however, few studies have focused on the maize root system mechanisms underlying drought resistance. In this study, miRNA-mRNA analysis was performed to deeply analyze the molecular mechanisms involved in drought response in the maize root system under drought stress. Furthermore, preliminary investigation of the biological function of miR408a in the maize root system was also conducted. The morphological, physiological, and transcriptomic changes in the maize variety "M8186" at the seedling stage under 12% PEG 6000 drought treatment (0, 7, and 24 h) were analyzed. With prolonged drought stress, seedlings gradually withered, the root system grew significantly, and abscisic acid, brassinolide, lignin, glutathione, and trehalose content in the root system gradually increased. Furthermore, peroxidase activity increased, while gibberellic acid and jasmonic acid gradually decreased. Moreover, 32 differentially expressed miRNAs (DEMIRs), namely, 25 known miRNAs and 7 new miRNAs, and 3,765 differentially expressed mRNAs (DEMRs), were identified in maize root under drought stress by miRNA-seq and mRNA-seq analysis, respectively. Through combined miRNA-mRNA analysis, 16 miRNA-target gene pairs, comprising 9 DEMIRs and 15 DEMRs, were obtained. In addition, four metabolic pathways, namely, "plant hormone signal transduction", "phenylpropane biosynthesis", "glutathione metabolism", and "starch and sucrose metabolism", were predicted to have important roles in the response of the maize root system to drought. MiRNA and mRNA expression results were verified by real-time quantitative PCR. Finally, miR408a was selected for functional analysis and demonstrated to be a negative regulator of drought response, mainly through regulation of reactive oxygen species accumulation in the maize root system. This study helps to elaborate the regulatory response mechanisms of the maize root system under drought stress and predicts the biological functions of candidate miRNAs and mRNAs, providing strategies for subsequent mining for, and biological breeding to select for, drought-responsive genes in the maize root system.