An auxin research odyssey: 1989-2023

Active transport enables protein condensation in cells

Multiple factors drive biomolecular condensate formation. In plants, condensation of the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 attenuates response to the plant hormone auxin. Here, we report that actin-mediated movement of cytoplasmic ARF condensates enhances condensation. Coarse-grained molecular simulations of active polymers reveal that applied forces drive the associations of macromolecules to enhance phase separation while giving rise to dense phases that preferentially accumulate motile molecules. Our study highlights how molecular motility can drive phase separation, with implications for motile condensates while offering insights into cellular mechanisms that can regulate condensate dynamics.

"Shape of Cell"-An Auxin and Cell Wall Duet

Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.

Quantifying Plant Biology with Fluorescent Biosensors

Plant biology is undergoing a spatial omics revolution, but these approaches are limited to snapshots of a plant's state. Direct, genetically encoded fluorescent biosensors complement the omics approaches, giving researchers tools to assess energetic, metabolic, and signaling molecules at multiple scales, from fast subcellular dynamics to organismal patterns in living plants. This review focuses on how biosensors illuminate plant biology across these scales and the major discoveries to which they have contributed. We also discuss the core principles and common pitfalls affecting biosensor engineering, deployment, imaging, and analysis to help aspiring biosensor researchers. Innovative technologies are driving forward developments both biological and technical with implications for synergizing biosensor research with other approaches and expanding the scope of in vivo quantitative biology.

Necessity for modeling hormonal crosstalk in arabidopsis root development?

Hormones play vital roles in plant root development. Mathematical models have been employed to study hormone functions. However, models developed by different research groups focus on different aspects of hormones and therefore cannot be used to study root growth as an integrative system that involves the functions of all hormones. To use modeling to study root development, the crosstalk nature of hormones requires the further development of mathematical models to understand their interplay in the context of diverse experimental data. This opinion article discusses what new insights can be developed by modeling hormonal crosstalk beyond experimental data. We propose that one integrative model should be developed to integrate all experimental data for elucidating root growth.

Transcriptome and Metabolome Analyses Offer New Insights into Bolting Time Regulation in Broccoli

The globular buds and stems are the main edible organs of broccoli. Bolting is an important agronomic trait, and the timing of its occurrence is particularly critical when breeding and domesticating broccoli. The molecular mechanism that regulates broccoli bolting time is not well-understood. In this study, the apical flower bud and leaf tissues of two broccoli varieties with different bolting intensities were selected for metabolome and transcriptome analyses. In the apical flower buds of early-bolting B2554 and late-bolting B2557, 1094 differentially expressed genes and 206 differentially accumulated metabolites were identified. In the leaves, 487 differentially expressed genes and 40 differentially accumulated metabolites were identified. In the floral pathway, the expression of FLC (FLOWERING LOCUS C) was significantly upregulated, and that of FT (FLOWERING LOCUS T) was significantly downregulated in the late-bolting plants, indicating their possible role in suppressing bolting. In addition, significant differences were identified in the sucrose synthesis and transport, hormone synthesis, and signal transduction processes in early-bolting B2554 and late-bolting B2557. Sucrose accumulation in the leaves and apical flower buds of the early-bolting plants was about 1.3 times higher than in the late-bolting plants. Indole-3-acetic acid (IAA) and abscisic acid (ABA) accumulation in the apical flower buds of the late-bolting plants was more than twice that in the early-bolting plants. Jasmonic acid (JA) accumulation in the apical flower buds of the late-bolting plants was more than ten times higher than in the early-bolting plants. Phenolic acids may affect the bolting time of broccoli. This study offers new insights into the regulation mechanism of broccoli bolting and provides some potential molecular targets to include in breeding methods that regulate bolting time.

Effect of ethylene on bisphenol A-inhibited primary root elongation in Arabidopsis thaliana

Bisphenol A (BPA), a widespread industrial chemical, significantly inhibits root elongation, reducing it by 2%, 32%, and 64% at concentrations of 10, 20, 30, and 40 µM, respectively. This study delves into the interplay between ethylene and auxin in mediating BPA-induced primary root growth inhibition in Arabidopsis thaliana. Furthermore, ethylene modulates BPA sensitivity, as evidenced by reduced inhibition in ethylene-insensitive mutants (etr1-1, etr1-3, ein2-1) and heightened sensitivity in ethylene-overproducing lines (eto1-1, ctr1-1). Ethylene biosynthesis inhibitors (AVG, CoCl2) significantly decreased BPA-induced root inhibition. Treated plants showed increased expression of ethylene biosynthetic genes (ACS2, ACS6, ACS8, ACO1, ACO2). Auxin involvement was evident as aux1-7 mutants showed reduced sensitivity, and NPA (an auxin transport inhibitor) improved root growth. BPA and ACC treatments elevated DR5 and EBS activity, indicating enhanced ethylene and auxin signaling. AVG or NPA effects on DR5 activity under BPA stress revealed that ethylene modulates auxin accumulation and distribution. The study suggests that ethylene regulates BPA-mediated root inhibition by influencing AUX1 expression and auxin distribution, offering new insights into the interaction between ethylene, auxin, and BPA in plant growth.

Genome-Wide Analysis of Soybean Apyrase Gene Family and Functional Characterization of GmAPY1-4 Responses to Aluminum Stress

Apyrases (APYs) directly regulate intra- and extra-cellular ATP homeostasis and play a key role in the process of plants adapting to various stresses. In this study, we identified and characterized soybean APY (GmAPY) family members at the genomic level. The results identified a total of 18 APYRASE homologous genes with conserved ACR domains. We conducted a bioinformatics analysis of GmAPYs, including sequence alignment, phylogenetic relationships, and conserved motifs. According to the phylogenetic and structural characteristics, GmAPYs in soybeans are mainly divided into three groups. The characteristics of these GmAPYs were systematically evaluated, including their collinearity, gene structure, protein motifs, cis-regulatory elements, tissue expression patterns, and responses to aluminum stress. A preliminary analysis of the function of GmAPY1-4 was also conducted. The results showed that GmAPY1-4 was localized in the nucleus, presenting relatively high levels in roots and root nodules and demonstrating high sensitivity and positive responses under aluminum stress circumstances. Further functional characterization revealed that the overexpression of GmAPY1-4 in hairy roots not only induced root growth under normal growth conditions but also significantly prevented root growth inhibition under aluminum stress conditions and contributed to maintaining a relatively higher fresh root weight. By contrast, RNAi interference with the expression of GmAPY1-4 in hairy roots inhibited root growth under both normal and aluminum stress conditions, but it exerted no significant influence on the dry or fresh root weight. To sum up, these findings support the significant functional role of GmAPY1-4 in root growth and the aluminum stress response. These findings not only enhance our comprehension of the aluminum stress response mechanism by identifying and characterizing the APY gene family in the soybean genome but also provide a potential candidate gene for improving aluminum tolerance in soybeans in the future.

Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family in Lettuce (Lactuca sativa L.)

The Aux/IAA proteins are key regulators of auxin signaling transduction, mediating various physiological and developmental processes in higher plants; however, little information on Aux/IAAs is known in lettuce, an economically important vegetable. In this study, a total of 29 LsAux/IAA genes were identified from the lettuce genome. Sequence alignment and domain analyses suggested the presence of conserved Aux/IAA subdomains (Domain I-IV) in those LsIAAs, and Phylogenetic analysis indicated that members of LsAux/IAA could be classified into 10 subgroups by their homology to Arabidopsis Aux/IAAs, which is also supported by exon-intron structure, consensus motifs, and domain compositions. Transcriptome data suggested that most of the LsIAA genes were expressed in all tissues, whereas some of them were preferentially expressed in specific tissues. Analysis of cis-acting elements indicated the LsIAA genes might be regulated by hormonal treatments and abiotic stresses, which was confirmed by qRT-PCR experiments. Taken together, our study provides valuable information for further investigation of the biological roles of LsIAA genes in high-temperature conditions.

Response of Arabidopsis thaliana to Flooding with Physical Flow

Flooding causes severe yield losses worldwide, making it urgent to enhance crop tolerance to this stress. Since natural flooding often involves physical flow, we hypothesized that the effects of submergence on plants could change when combined with physical flow. In this study, we analyzed the growth and transcriptome of Arabidopsis thaliana exposed to submergence or flooding with physical flow. Plants exposed to flooding with physical flow had smaller rosette diameters, especially at faster flow rates. Transcriptome analysis revealed that "defense response" transcripts were highly up-regulated in response to flooding with physical flow. In addition, up-regulation of transcripts encoding ROS-producing enzymes, SA synthesis, JA synthesis, and ethylene signaling was more pronounced under flooding with physical flow when compared to submergence. Although H2O2 accumulation changed in response to submergence or flooding with physical flow, it did not lead to lipid peroxidation, suggesting a role for ROS as signaling molecules under these conditions. Multiple regression analysis indicated possible links between rosette diameter under flooding with physical flow and the expression of Rbohs and SA synthesis transcripts. These findings suggest that pathogen defense responses, regulated by SA and ROS signaling, play crucial roles in plant responses to flooding with physical flow.

Structure-Activity of Plant Growth Bioregulators and Their Effects on Mammals

In this review, we emphasize structure-activity and the effects on mammals of plant growth bioregulators. plant growth bioregulators can be referred to as "biochemical effectors" since they are substances having biological activity. It is possible to distinguish between "bioregulators" and "regulators" due to the significance of the compounds mentioned above in biochemistry and agrobiology. Thus, "plant growth bioregulators" (PGBRs) are the names given to naturally occurring chemical substances produced by biosynthetic processes. PGBRs affect both plant reign and animal reign. A plethora of plant growth bioregulators were described in the literature, so the structure, activity in plants, and their effects on mammals are presented.

Identification and Expression Analysis of TCP Transcription Factors Under Abiotic Stress in Phoebe bournei

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes-PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15-under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei.

Targeted Metabolites and Transcriptome Analysis Uncover the Putative Role of Auxin in Floral Sex Determination in Litchi chinensis Sonn

Litchi exhibits a large number of flowers, many flowering batches, and an inconsistent ratio of male and female flowers, frequently leading to a low fruit-setting rate. Floral sexual differentiation is a crucial phase in perennial trees to ensure optimal fruit production. However, the mechanism behind floral differentiation remains unclear. The objective of the study was to identify the role of auxin in floral differentiation at the transcriptional level. The results showed that the ratio of female flowers treated with naphthalene acetic acid (NAA) was significantly lower than that of the control stage (M0/F0). The levels of endogenous auxin and auxin metabolites were measured in male and female flowers at different stages of development. It was found that the levels of IAA, IAA-Glu, IAA-Asp, and IAA-Ala were significantly higher in male flowers compared to female flowers. Next-generation sequencing and modeling were employed to perform an in-depth transcriptome analysis on all flower buds in litchi 'Feizixiao' cultivars (Litchi chinensis Sonn.). Plant hormones were found to exert a significant impact on the litchi flowering process and flower proliferation. Specifically, a majority of differentially expressed genes (DEGs) related to the auxin pathway were noticeably increased during male flower bud differentiation. The current findings will enhance our comprehension of the process and control mechanism of litchi floral sexual differentiation. It also offers a theoretical foundation for implementing strategies to regulate flowering and enhance fruit production in litchi cultivation.

Hydrogen Peroxide Signaling in the Maintenance of Plant Root Apical Meristem Activity

Hydrogen peroxide (H2O2) is a prevalent reactive oxygen species (ROS) found in cells and takes a central role in plant development and stress adaptation. The root apical meristem (RAM) has evolved strong plasticity to adapt to complex and changing environmental conditions. Recent advances have made great progress in explaining the mechanism of key factors, such as auxin, WUSCHEL-RELATED HOMEOBOX 5 (WOX5), PLETHORA (PLT), SHORTROOT (SHR), and SCARECROW (SCR), in the regulation of RAM activity maintenance. H2O2 functions as an emerging signaling molecule to control the quiescent center (QC) specification and stem cell niche (SCN) activity. Auxin is a key signal for the regulation of RAM maintenance, which largely depends on the formation of auxin regional gradients. H2O2 regulates the auxin gradients by the modulation of intercellular transport. H2O2 also modulates the expression of WOX5, PLTs, SHR, and SCR to maintain RAM activity. The present review is dedicated to summarizing the key factors in the regulation of RAM activity and discussing the signaling transduction of H2O2 in the maintenance of RAM activity. H2O2 is a significant signal for plant development and environmental adaptation.