The Root Apex of Arabidopsis thaliana Consists of Four Distinct Zones of Growth Activities: Meristematic Zone, Transition Zone, Fast Elongation Zone and Growth Terminating Zone

Investigation of Arabidopsis root skototropism with different distance settings

Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of Arabidopsis thaliana seedlings (atglr3.7 ko, AtGLR3.7 OE, and pin2 knockout) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root's positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.

Shaping root architecture: towards understanding the mechanisms involved in lateral root development

Plants have an amazing ability to adapt to their environment, and this extends beyond biochemical responses and includes developmental changes that help them better exploit resources and survive. The plasticity observed in individual plant morphology is associated with robust developmental pathways that are influenced by environmental factors. However, there is still much to learn about the mechanisms behind the formation of the root system. In Arabidopsis thaliana, the root system displays a hierarchical structure with primary and secondary roots. The process of lateral root (LR) organogenesis involves multiple steps, including LR pre-patterning, LR initiation, LR outgrowth, and LR emergence. The study of root developmental plasticity in Arabidopsis has led to significant progress in understanding the mechanisms governing lateral root formation. The importance of root system architecture lies in its ability to shape the distribution of roots in the soil, which affects the plant's ability to acquire nutrients and water. In Arabidopsis, lateral roots originate from pericycle cells adjacent to the xylem poles known as the xylem-pole-pericycle (XPP). The positioning of LRs along the primary root is underpinned by a repetitive pre-patterning mechanism that establishes primed sites for future lateral root formation. In a subset of primed cells, the memory of a transient priming stimulus leads to the formation of stable pre-branch sites and the establishment of founder cell identity. These founder cells undergo a series of highly organized periclinal and anticlinal cell divisions and expansion to form lateral root primordia. Subsequently, LRP emerges through three overlying cell layers of the primary root, giving rise to fully developed LRs. In addition to LRs Arabidopsis can also develop adventitious lateral roots from the primary root in response to specific stress signals such as wounding or environmental cues. Overall, this review creates an overview of the mechanisms governing root lateral root formation which can be a stepping stone to improved crop yields and a better understanding of plant adaptation to changing environments.

The Arabidopsis splicing factor PORCUPINE/SmE1 orchestrates temperature-dependent root development via auxin homeostasis maintenance

Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.

Plant chromosome polytenization contributes to suppression of root growth in high polyploids

Autopolyploidization, which refers to a polyploidization via genome duplication without hybridization, promotes growth in autotetraploids, but suppresses growth in high polyploids (autohexaploids or auto-octoploids). The mechanism underlying this growth suppression (i.e. 'high-ploidy syndrome') has not been comprehensively characterized. In this study, we conducted a kinematic analysis of the root apical meristem cells in Arabidopsis thaliana autopolyploids (diploid, tetraploid, hexaploid, and octoploid) to determine the effects of the progression of genome duplication on root growth. The results of the root growth analysis showed that tetraploidization increases the cell volume, but decreases cell proliferation. However, cell proliferation and volume growth are suppressed in high polyploids. Whole-mount fluorescence in situ hybridization analysis revealed extensive chromosome polytenization in the region where cell proliferation does not usually occur in the roots of high polyploids, which is likely to be at least partly correlated with the suppression of endoreduplication. The study findings indicate that chromosome polytenization is important for the suppressed growth of high polyploids.

Arinole, a novel auxin-stimulating benzoxazole, affects root growth and promotes adventitious root formation

The triple response phenotype is characteristic for seedlings treated with the phytohormone ethylene or its direct precursor 1-aminocyclopropane-carboxylic acid, and is often employed to find novel chemical tools to probe ethylene responses. We identified a benzoxazole-urea derivative (B2) partially mimicking ethylene effects in a triple response bioassay. A phenotypic analysis demonstrated that B2 and its closest analogue arinole (ARI) induced phenotypic responses reminiscent of seedlings with elevated levels of auxin, including impaired hook development and inhibition of seedling growth. Specifically, ARI reduced longitudinal cell elongation in roots, while promoting cell division. In contrast to other natural or synthetic auxins, ARI mostly acts as an inducer of adventitious root development, with only limited effects on lateral root development. Quantification of free auxins and auxin biosynthetic precursors as well as auxin-related gene expression demonstrated that ARI boosts global auxin levels. In addition, analyses of auxin reporter lines and mutants, together with pharmacological assays with auxin-related inhibitors, confirmed that ARI effects are facilitated by TRYPTOPHAN AMINOTRANSFERASE1 (TAA1)-mediated auxin synthesis. ARI treatment in an array of species, including Arabidopsis, pea, tomato, poplar, and lavender, resulted in adventitious root formation, which is a desirable trait in both agriculture and horticulture.

WOX11-mediated cell size control in Arabidopsis attenuates growth and fecundity of endoparasitic cyst nematodes

Cyst nematodes establish permanent feeding structures called syncytia inside the host root vasculature, disrupting the flow of water and minerals. In response, plants form WOX11-mediated adventitious lateral roots at nematode infection sites. WOX11 adventitious lateral rooting modulates tolerance to nematode infections; however, whether this also benefits nematode parasitism remains unknown. Here, we report on bioassays using a 35S::WOX11-SRDX transcriptional repressor mutant to investigate whether WOX11 adventitious lateral rooting promotes syncytium development and thereby female growth and fecundity. Moreover, we chemically inhibited cellulose biosynthesis to verify if WOX11 directly modulates cell wall plasticity in syncytia. Finally, we performed histochemical analyses to test if WOX11 mediates syncytial cell wall plasticity via reactive oxygen species (ROS). Repression of WOX11-mediated transcription specifically enhanced the radial expansion of syncytial elements, increasing both syncytium size and female offspring. The enhanced syncytial hypertrophy observed in the 35S::WOX11-SRDX mutant could be phenocopied by chemical inhibition of cellulose biosynthesis and was associated with elevated levels of ROS at nematode infection sites. We, therefore, conclude that WOX11 restricts radial expansion of nematode-feeding structures and female growth and fecundity, likely by modulating ROS-mediated cell wall plasticity mechanisms. Remarkably, this novel role of WOX11 in plant cell size control is distinct from WOX11 adventitious lateral rooting underlying disease tolerance.

CELLULOSE SYNTHASE-LIKE C proteins modulate cell wall establishment during ethylene-mediated root growth inhibition in rice

The cell wall shapes plant cell morphogenesis and affects the plasticity of organ growth. However, the way in which cell wall establishment is regulated by ethylene remains largely elusive. Here, by analyzing cell wall patterns, cell wall composition and gene expression in rice (Oryza sativa, L.) roots, we found that ethylene induces cell wall thickening and the expression of cell wall synthesis-related genes, including CELLULOSE SYNTHASE-LIKE C1, 2, 7, 9, 10 (OsCSLC1, 2, 7, 9, 10) and CELLULOSE SYNTHASE A3, 4, 7, 9 (OsCESA3, 4, 7, 9). Overexpression and mutant analyses revealed that OsCSLC2 and its homologs function in ethylene-mediated induction of xyloglucan biosynthesis mainly in the cell wall of root epidermal cells. Moreover, OsCESA-catalyzed cellulose deposition in the cell wall was enhanced by ethylene. OsCSLC-mediated xyloglucan biosynthesis likely plays an important role in restricting cell wall extension and cell elongation during the ethylene response in rice roots. Genetically, OsCSLC2 acts downstream of ETHYLENE-INSENSITIVE3-LIKE1 (OsEIL1)-mediated ethylene signaling, and OsCSLC1, 2, 7, 9 are directly activated by OsEIL1. Furthermore, the auxin signaling pathway is synergistically involved in these regulatory processes. These findings link plant hormone signaling with cell wall establishment, broadening our understanding of root growth plasticity in rice and other crops.

Physiological roles of Arabidopsis MCA1 and MCA2 based on their dynamic expression patterns

Determining the mechanisms by which plants sense and respond to mechanical stimuli is crucial for unraveling the detailed processes by which plants grow and develop. Mechanosensitive (MS) channels, including MCA1 and its paralog MCA2 in Arabidopsis thaliana, may be essential for these processes. Although significant progress has been made in elucidating the physiological roles of MS channels, comprehensive insights into their expression dynamics remain elusive. Here, we summarize recent advancements and new data on the spatiotemporal expression patterns of the MCA1 and MCA2 genes, revealing their involvement in various developmental processes. Then, we describe findings from our study, in which the expression profiles of MCA1 and MCA2 were characterized in different plant organs at various developmental stages through histochemical analyses and semiquantitative RT‒PCR. Our findings revealed that MCA1 and MCA2 are preferentially expressed in young tissues, suggesting their pivotal roles in processes such as cell division, expansion, and mechanosensing. Lastly, we discuss the differential expression patterns observed in reproductive organs and trichomes, hinting at their specialized functions in response to mechanical cues. Overall, this review provides valuable insights into the dynamic expression patterns of MCA1 and MCA2, paving the way for future research on the precise roles of these genes in planta.

ABSCISIC ACID INSENSITIVE 3 promotes auxin signalling by regulating SHY2 expression to control primary root growth in response to dehydration stress

Plants combat dehydration stress through different strategies including root architectural changes. Here we show that when exposed to varying levels of dehydration stress, primary root growth in Arabidopsis is modulated by regulating root meristem activity. Abscisic acid (ABA) in concert with auxin signalling adjust primary root growth according to stress levels. ABSCISIC ACID INSENSITIVE 3 (ABI3), an ABA-responsive transcription factor, stands at the intersection of ABA and auxin signalling and fine-tunes primary root growth in response to dehydration stress. Under low ABA or dehydration stress, induction of ABI3 expression promotes auxin signalling by decreasing expression of SHY2, a negative regulator of auxin response. This further enhances the expression of auxin transporter gene PIN1 and cell cycle gene CYCB1;1, resulting in an increase in primary root meristem size and root length. Higher levels of dehydration stress or ABA repress ABI3 expression and promote ABSCISIC ACID INSENSITIVE 5 (ABI5) expression. This elevates SHY2 expression, thereby impairing primary root meristem activity and retarding root growth. Notably, ABI5 can promote SHY2 expression only in the absence of ABI3. Such ABA concentration-dependent expression of ABI3 therefore functions as a regulatory sensor of dehydration stress levels and orchestrates primary root growth by coordinating its downstream regulation.

The hidden harmony: Exploring ROS-phytohormone nexus for shaping plant root architecture in response to environmental cues

Root system architecture, encompassing lateral roots and root hairs, plays a vital in overall plant growth and stress tolerance. Reactive oxygen species (ROS) and plant hormones intricately regulate root growth and development, serving as signaling molecules that govern processes such as cell proliferation and differentiation. Manipulating the interplay between ROS and hormones has the potential to enhance nutrient absorption, stress tolerance, and agricultural productivity. In this review, we delve into how studying these processes provides insights into how plants respond to environmental changes and optimize growth patterns to better control cellular processes and stress responses in crops. We discuss various factors and complex signaling networks that may exist among ROS and phytohormones during root development. Additionally, the review highlights possible role of reactive nitrogen species (RNS) in ROS-phytohormone interactions and in shaping root system architecture according to environmental cues.

Arabidopsis Root Development Regulation by the Endogenous Folate Precursor, Para-Aminobenzoic Acid, via Modulation of the Root Cell Cycle

The continuous growth of roots depends on their ability to maintain a balanced ratio between cell production and cell differentiation at the tip. This process is regulated by the hormonal balance of cytokinin and auxin. However, other important regulators, such as plant folates, also play a regulatory role. In this study, we investigated the impact of the folate precursor para-aminobenzoic acid (PABA) on root development. Using pharmacological, genetic, and imaging approaches, we show that the growth of Arabidopsis thaliana roots is repressed by either supplementing the growth medium with PABA or overexpressing the PABA synthesis gene GAT-ADCS. This is associated with a smaller root meristem consisting of fewer cells. Conversely, reducing the levels of free root endogenous PABA results in longer roots with extended meristems. We provide evidence that PABA represses Arabidopsis root growth in a folate-independent manner and likely acts through two mechanisms: (i) the G2/M transition of cell division in the root apical meristem and (ii) promoting premature cell differentiation in the transition zone. These data collectively suggest that PABA plays a role in Arabidopsis root growth at the intersection between cell division and cell differentiation.

Root growth of monocotyledons and dicotyledons is limited by different tissues

Plant growth and morphogenesis are determined by the mechanical properties of its cell walls. Using atomic force microscopy, we have characterized the dynamics of cell wall elasticity in different tissues in developing roots of several plant species. The elongation growth zone of roots of all species studied was distinguished by a reduced modulus of elasticity of most cell walls compared to the meristem or late elongation zone. Within the individual developmental zones of roots, there were also significant differences in the elasticity of the cell walls of the different tissues, thus identifying the tissues that limit root growth in the different species. In cereals, this is mainly the inner cortex, whereas in dicotyledons this function is performed by the outer tissues-rhizodermis and cortex. These differences result in a different behaviour of the roots of these species during longitudinal dissection. Modelling of longitudinal root dissection using measured properties confirmed the difference shown. Thus, the morphogenesis of monocotyledonous and dicotyledonous roots relies on different tissues as growth limiting, which should be taken into account when analyzing the localization of associated molecular events. At the same time, no matrix polysaccharide was found whose immunolabelling in type I or type II cell walls would predict their mechanical properties. However, assessment of the degree of anisotropy of cortical microtubules showed a striking correlation with the elasticity of the corresponding cell walls in all species studied.

Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth

Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.

PRX102 Participates in Root Hairs Tip Growth of Rice

Root hairs are extensions of epidermal cells on the root tips that increase the root contract surface area with the soil. For polar tip growth, newly synthesized proteins and other materials must be incorporated into the tips of root hairs. Here, we report the characterization of PRX102, a root hair preferential endoplasmic reticulum peroxidase. During root hair growth, PRX102 has a polar localization pattern within the tip regions of root hairs but it loses this polarity after growth termination. Moreover, PRX102 participates in root hair outgrowth by regulating dense cytoplasmic streaming toward the tip. This role is distinct from those of other peroxidases playing roles in the root hairs and regulating reactive oxygen species homeostasis. RNA-seq analysis using prx102 root hairs revealed that 87 genes including glutathione S-transferase were downregulated. Our results therefore suggest a new function of peroxidase as a player in the delivery of substances to the tips of growing root hairs.

Arabidopsis root apical meristem survival during waterlogging is determined by phytoglobin through nitric oxide and auxin

MAIN CONCLUSION

Over-expression of phytoglobin mitigates the degradation of the root apical meristem (RAM) caused by waterlogging through changes in nitric oxide and auxin distribution at the root tip. Plant performance to waterlogging is ameliorated by the over-expression of the Arabidopsis Phytoglobin 1 (Pgb1) which also contributes to the maintenance of a functional RAM. Hypoxia induces accumulation of ROS and damage in roots of wild type plants; these events were preceded by the exhaustion of the RAM resulting from the loss of functionality of the WOX5-expressing quiescent cells (QCs). These phenotypic deviations were exacerbated by suppression of Pgb1 and attenuated when the same gene was up-regulated. Genetic and pharmacological studies demonstrated that degradation of the RAM in hypoxic roots is attributed to a reduction in the auxin maximum at the root tip, necessary for the specification of the QC. This reduction was primarily caused by alterations in PIN-mediated auxin flow but not auxin synthesis. The expression and localization patterns of several PINs, including PIN1, 2, 3 and 4, facilitating the basipetal translocation of auxin and its distribution at the root tip, were altered in hypoxic WT and Pgb1-suppressing roots but mostly unchanged in those over-expressing Pgb1. Disruption of PIN1 and PIN2 signal in hypoxic roots suppressing Pgb1 initiated in the transition zone at 12 h and was specifically associated to the absence of Pgb1 protein in the same region. Exogenous auxin restored a functional RAM, while inhibition of the directional auxin flow exacerbated the degradation of the RAM. The regulation of root behavior by Pgb1 was mediated by nitric oxide (NO) in a model consistent with the recognized function of Pgbs as NO scavengers. Collectively, this study contributes to our understanding of the role of Pgbs in preserving root meristem function and QC niche during conditions of stress, and suggests that the root transition zone is most vulnerable to hypoxia.

MIZU-KUSSEI1 (MIZ1) and GNOM/MIZ2 control not only positive hydrotropism but also phototropism in Arabidopsis roots

In response to unilateral blue light illumination, roots of some plant species such as Arabidopsis thaliana exhibit negative phototropism (bending away from light), which is important for light avoidance in nature. MIZU-KUSSEI1 (MIZ1) and GNOM/MIZ2 are essential for positive hydrotropism (i.e. in the presence of a moisture gradient, root bending towards greater water availability). Intriguingly, mutations in these genes also cause a substantial reduction in phototropism. Here, we examined whether the same tissue-specific sites of expression required for MIZ1- and GNOM/MIZ2-regulated hydrotropism in Arabidopsis roots are also required for phototropism. The attenuated phototropic response of miz1 roots was completely restored when a functional MIZ1-green fluorescent protein (GFP) fusion was expressed in the cortex of the root elongation zone but not in other tissues such as root cap, meristem, epidermis, or endodermis. The hydrotropic defect and reduced phototropism of miz2 roots were restored by GNOM/MIZ2 expression in either the epidermis, cortex, or stele, but not in the root cap or endodermis. Thus, the sites in root tissues that are involved in the regulation of MIZ1- and GNOM/MIZ2-dependent hydrotropism also regulate phototropism. These results suggest that MIZ1- and GNOM/MIZ2-mediated pathways are, at least in part, shared by hydrotropic and phototropic responses in Arabidopsis roots.

The AUX1-AFB1-CNGC14 module establishes a longitudinal root surface pH profile

Plant roots navigate in the soil environment following the gravity vector. Cell divisions in the meristem and rapid cell growth in the elongation zone propel the root tips through the soil. Actively elongating cells acidify their apoplast to enable cell wall extension by the activity of plasma membrane AHA H+-ATPases. The phytohormone auxin, central regulator of gravitropic response and root development, inhibits root cell growth, likely by rising the pH of the apoplast. However, the role of auxin in the regulation of the apoplastic pH gradient along the root tip is unclear. Here, we show, by using an improved method for visualization and quantification of root surface pH, that the Arabidopsis thaliana root surface pH shows distinct acidic and alkaline zones, which are not primarily determined by the activity of AHA H+-ATPases. Instead, the distinct domain of alkaline pH in the root transition zone is controlled by a rapid auxin response module, consisting of the AUX1 auxin influx carrier, the AFB1 auxin co-receptor, and the CNCG14 calcium channel. We demonstrate that the rapid auxin response pathway is required for an efficient navigation of the root tip.

Griseofulvin Inhibits Root Growth by Targeting Microtubule-Associated Proteins Rather Tubulins in Arabidopsis

Griseofulvin was considered an effective agent for cancer therapy in past decades. Although the negative effects of griseofulvin on microtubule stability are known, the exact target and mechanism of action in plants remain unclear. Here, we used trifluralin, a well-known herbicide targeting microtubules, as a reference and revealed the differences in root tip morphology, reactive oxygen species production (ROS), microtubule dynamics, and transcriptome analysis between Arabidopsis treated with griseofulvin and trifluralin to elucidate the mechanism of root growth inhibition by griseofulvin. Like trifluralin, griseofulvin inhibited root growth and caused significant swelling of the root tip due to cell death induced by ROS. However, the presence of griseofulvin and trifluralin caused cell swelling in the transition zone (TZ) and meristematic zone (MZ) of root tips, respectively. Further observations revealed that griseofulvin first destroyed cortical microtubules in the cells of the TZ and early elongation zone (EZ) and then gradually affected the cells of other zones. The first target of trifluralin is the microtubules in the root MZ cells. Transcriptome analysis showed that griseofulvin mainly affected the expression of microtubule-associated protein (MAP) genes rather than tubulin genes, whereas trifluralin significantly suppressed the expression of αβ-tubulin genes. Finally, it was proposed that griseofulvin could first reduce the expression of MAP genes, meanwhile increasing the expression of auxin and ethylene-related genes to disrupt microtubule alignment in root tip TZ and early EZ cells, induce dramatic ROS production, and cause severe cell death, eventually leading to cell swelling in the corresponding zones and inhibition of root growth.

RootSlice-A novel functional-structural model for root anatomical phenotypes

Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes.

Novel whole-mount FISH analysis for intact root of Arabidopsis thaliana with spatial reference to 3D visualization

Whole-mount fluorescent in situ hybridization (WM-FISH) is an effective tool to observe chromosome behavior in tissues or organs. However, it is difficult to obtain a precise spatial profile of fluorescent signals in roots using conventional WM-FISH mainly because of the severe damage caused during the processing. To address this problem, we established a novel WM-FISH analysis for intact roots of Arabidopsis thaliana and successfully obtained a precise spatial profile of nuclear size and centromere signals. The two main improvements in the novel WM-FISH analysis are: (i) hybridization was performed directly on MAS-coated glass slides covered with silicon wells and (ii) conditions for enzyme treatment were optimized (37 °C, 45 s). After the WM-FISH using a centromere probe, we analyzed the results by 3D data processing to quantify the nuclear volume and number of centromere signals of the obtained cortical cell files and determined the position of each nucleus in intact roots. Then we plotted the nuclear volume and number of centromere signals versus distance from the quiescent center to evaluate the precise spatial profile of each parameter.

The large GTPase AtGBPL3 links nuclear envelope formation and morphogenesis to transcriptional repression

Guanylate binding proteins (GBPs) are prominent regulators of immunity not known to be required for nuclear envelope formation and morphogenesis. Here we identify the Arabidopsis GBP orthologue AtGBPL3 as a lamina component with essential functions in mitotic nuclear envelope reformation, nuclear morphogenesis and transcriptional repression during interphase. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with centromeric chromatin as well as with lamina components transcriptionally repressing pericentromeric chromatin. Reduced expression of AtGBPL3 or associated lamina components similarly altered nuclear morphology and caused overlapping transcriptional deregulation. Investigating the dynamics of AtGBPL3-GFP and other nuclear markers during mitosis (1) revealed that AtGBPL3 accumulation on the surface of daughter nuclei precedes nuclear envelope reformation and (2) uncovered defects in this process in roots of AtGBPL3 mutants, which cause programmed cell death and impair growth. AtGBPL3 functions established by these observations are unique among dynamin-family large GTPases.

Boron supply restores aluminum-blocked auxin transport by the modulation of PIN2 trafficking in the root apical transition zone

The supply of boron (B) alleviates the toxic effects of aluminum (Al) on root growth; however, the mechanistic basis of this process remains elusive. This study filled this knowledge gap, demonstrating that boron modifies auxin distribution and transport in Al-exposed Arabidopsis roots. In B-deprived roots, treatment with Al induced an increase in auxin content in the root apical meristem zone (MZ) and transition zone (TZ), whereas in the elongation zone (EZ) the auxin content was decreased beyond the level required for adequate growth. These distribution patterns are explained by the fact that basipetal auxin transport from the TZ to the EZ was disrupted by Al-inhibited PIN-FORMED 2 (PIN2) endocytosis. Experiments involving the modulation of protein biosynthesis by cycloheximide (CHX) and transcriptional regulation by cordycepin (COR) demonstrated that the Al-induced increase of PIN2 membrane proteins was dependent upon the inhibition of PIN2 endocytosis, rather than on the transcriptional regulation of the PIN2 gene. Experiments reporting on the profiling of Al³⁺ and PIN2 proteins revealed that the inhibition of endocytosis of PIN2 proteins was the result of Al-induced limitation of the fluidity of the plasma membrane. The supply of B mediated the turnover of PIN2 endosomes conjugated with indole-3-acetic acid (IAA), and thus restored the Al-induced inhibition of IAA transport through the TZ to the EZ. Overall, the reported results demonstrate that boron supply mediates PIN2 endosome-based auxin transport to alleviate Al toxicity in plant roots.

The overexpression of LOW PHOSPHATE ROOT 1 (LPR1) negatively regulates Arabidopsis growth in response to Cadmium (Cd) stress

Cadmium (Cd) is a highly toxic element that is easily absorbed by plant, and the mechanisms of the plant response to Cd toxicity are very complex. In this study, the role of LPR1 (LOW Phosphate Root 1) encoding a cell-wall-targeted ferroxidase in Cd stress was investigated. The results showed that the overexpression of LPR1 caused an average reduction of 23%-40% in the primary root lengths, 67%-73% in the fresh weights, 32%-46% in the lengths of the non-root hair zone (NRHZ) and 70%-71% in the chlorophyll contents in both LPR1-OX lines when compared with the wild type (WT), while there were no significant changes in these traits between the WT and mutant lpr1 lines under Cd stress (7.5 μmol/L CdSO₄). Further investigation showed that the overexpression of LPR1 triggered reactive oxygen species (ROS) bursts and reduced the entry of available iron (Fe²⁺) into the cell, which induced the expression of iron-regulated transporter 1 (IRT1). The up-regulation of IRT1 contributed to the increase of Cd accumulation and growth retardation under Cd stress. Exogenous Fe and ROS scavengers down-regulated the IRT1's expression and alleviated the growth inhibition in LPR1-OX lines, indicating that LPR1-dependent ROS up-regulated IRT1, which subsequently exacerbated the Cd influx into plants. Our findings highlight a pathway of LPR1-mediated plant responding to Cd toxicity stress through the regulation of ROS and Fe homeostasis.

ENHANCED GRAVITROPISM 2 coordinates molecular adaptations to gravistimulation in the elongation zone of barley roots

Root gravitropism includes gravity perception in the root cap, signal transduction between root cap and elongation zone, and curvature response in the elongation zone. The barley (Hordeum vulgare) mutant enhanced gravitropism 2 (egt2) displays a hypergravitropic root phenotype. We compared the transcriptomic reprogramming of the root cap, the meristem, and the elongation zone of wild-type (WT) and egt2 seminal roots upon gravistimulation in a time-course experiment and identified direct interaction partners of EGT2 by yeast-two-hybrid screening and bimolecular fluorescence complementation validation. We demonstrated that the elongation zone is subjected to most transcriptomic changes after gravistimulation. Here, 33% of graviregulated genes are also transcriptionally controlled by EGT2, suggesting a central role of this gene in controlling the molecular networks associated with gravitropic bending. Gene co-expression analyses suggested a role of EGT2 in cell wall and reactive oxygen species-related processes, in which direct interaction partners of EGT2 regulated by EGT2 and gravity might be involved. Taken together, this study demonstrated the central role of EGT2 and its interaction partners in the networks controlling root zone-specific transcriptomic reprogramming of barley roots upon gravistimulation. These findings can contribute to the development of novel root idiotypes leading to improved crop performance.

Low iron ameliorates the salinity-induced growth cessation of seminal roots in wheat seedlings

Wheat plants are ubiquitously simultaneously exposed to salinity and limited iron availability caused by soil saline-alkalisation. Through this study, we found that both low Fe and NaCl severely inhibited the growth of seminal roots in wheat seedlings; however, sufficient Fe caused greater growth cessation of seminal roots than low Fe under salt stress. Low Fe improved the root meristematic division activity, not altering the mature cell sizes compared with sufficient Fe under salt stress. Foliar Fe spray and split-root experiments showed that low Fe-alleviating the salinity-induced growth cessation of seminal roots was dependent on local low Fe signals in the roots. Ionomics combined with TEM/X-ray few differences in the root Na⁺ uptake and vacuolar Na⁺ sequestration between two Fe levels under salt stress. Phytohormone profiling and metabolomics revealed salinity-induced overaccumulation of ACC/ethylene and tryptophan/auxin in the roots under sufficient Fe than under low Fe. Differential gene expression, pharmacological inhibitor addition and the root growth performance of transgenic wheat plants revealed that the rootward auxin efflux and was responsible for the low Fe-mediated amelioration of the salinity-induced growth cessation of seminal roots. Our findings will provide novel insights into the modulation of crop root growth under salt stress.

RAV1 mediates cytokinin signaling for regulating primary root growth in Arabidopsis

Root growth dynamics is an outcome of complex hormonal crosstalk. The primary root meristem size, for example, is determined by antagonizing actions of cytokinin and auxin. Here we show that RAV1, a member of the AP2/ERF family of transcription factors, mediates cytokinin signaling in roots to regulate meristem size. The rav1 mutants have prominently longer primary roots, with a meristem that is significantly enlarged and contains higher cell numbers, compared with wild-type. The mutant phenotype could be restored on exogenous cytokinin application or by inhibiting auxin transport. At the transcript level, primary cytokinin-responsive genes like ARR1, ARR12 were significantly downregulated in the mutant root, indicating impaired cytokinin signaling. In concurrence, cytokinin induced regulation of SHY2, an Aux/IAA gene, and auxin efflux carrier PIN1 was hindered in rav1, leading to altered auxin transport and distribution. This effectively altered root meristem size in the mutant. Notably, CRF1, another member of the AP2/ERF family implicated in cytokinin signaling, is transcriptionally repressed by RAV1 to promote cytokinin response in roots. Further associating RAV1 with cytokinin signaling, our results demonstrate that cytokinin upregulates RAV1 expression through ARR1, during post-embryonic root development. Regulation of RAV1 expression is a part of secondary cytokinin response that eventually represses CRF1 to augment cytokinin signaling. To conclude, RAV1 functions in a branch pathway downstream to ARR1 that regulates CRF1 expression to enhance cytokinin action during primary root development in Arabidopsis.

A role for brassinosteroid signalling in decision-making processes in the Arabidopsis seedling

Plants often adapt to adverse conditions via differential growth, whereby limited resources are discriminately allocated to optimize the growth of one organ at the expense of another. Little is known about the decision-making processes that underly differential growth. In this study, we developed a screen to identify decision making mutants by deploying two tools that have been used in decision theory: a well-defined yet limited budget, as well as conflict-of-interest scenarios. A forward genetic screen that combined light and water withdrawal was carried out. This identified BRASSINOSTEROID INSENSITIVE 2 (BIN2) alleles as decision mutants with "confused" phenotypes. An assessment of organ and cell length suggested that hypocotyl elongation occurred predominantly via cellular elongation. In contrast, root growth appeared to be regulated by a combination of cell division and cell elongation or exit from the meristem. Gain- or loss- of function bin2 mutants were most severely impaired in their ability to adjust cell geometry in the hypocotyl or cell elongation as a function of distance from the quiescent centre in the root tips. This study describes a novel paradigm for root growth under limiting conditions, which depends not only on hypocotyl-versus-root trade-offs in the allocation of limited resources, but also on an ability to deploy different strategies for root growth in response to multiple stress conditions.

Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length

Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation. Twenty-three genes and five statistically significant SNPs were identified. The SNP with the highest score mapped to the fifth exon of NAC048 and this change makes a missense variant in only 33.3% of the accessions with a large PR, compared with the accessions with a short PR length. Moreover, we detected five more SNPs in this gene and in NAC3 that allow us to discover closely related accessions according to the phylogenetic tree analysis. We also found that the association between genetic variants among the 18 genes with the highest scores in our GWAS and the phenotypic classes into which we divided our accessions are not straightforward and likely follow historical patterns.

Advances towards understanding the responses of root cells to acidic stress

"Acid soil syndrome" is a worldwide phenomenon characterized by low pH (pH < 5.5), scarce nutrient availability (K⁺, Ca²⁺, Mg²⁺, P), and mineral toxicity such as those caused by soluble aluminium (Al) forms. Regardless of the mineral toxicity, the low pH by itself is detrimental to crop development causing striking sensitivity responses such as root growth arrest. However, low pH-induced responses are still poorly understood and underrated. Here, we review and discuss the core evidence about the action of low pH upon specific root zones, distinct cell types, and possible cellular targets (cell wall, plasma membrane, and alternative oxidase). The role of different players in signaling processes leading to low pH-induced responses, such as the STOP transcription factors, the reactive oxygen species (ROS), auxin, ethylene, and components of the antioxidant system, is also addressed. Information at the molecular level is still lacking to link the low pH targets and the subsequent actors that trigger the observed sensitivity responses. Future studies will have to combine genetic tools to identify the signaling processes triggered by low pH, unraveling not only the mechanisms by which low pH affects root cells but also finding new ways to engineer the tolerance of domesticated plants to acidic stress.

The Arabidopsis TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE (TTL) family members are involved in root system formation via their interaction with cytoskeleton and cell wall remodeling

Lateral roots (LR) are essential components of the plant edaphic interface; contributing to water and nutrient uptake, biotic and abiotic interactions, stress survival, and plant anchorage. We have identified the TETRATRICOPEPTIDE-REPEAT THIOREDOXIN-LIKE 3 (TTL3) gene as being related to LR emergence and later development. Loss of function of TTL3 leads to a reduced number of emerged LR due to delayed development of lateral root primordia (LRP). This trait is further enhanced in the triple mutant ttl1ttl3ttl4. TTL3 interacts with microtubules and endomembranes, and is known to participate in the brassinosteroid (BR) signaling pathway. Both ttl3 and ttl1ttl3ttl4 mutants are less sensitive to BR treatment in terms of LR formation and primary root growth. The ability of TTL3 to modulate biophysical properties of the cell wall was established under restrictive conditions of hyperosmotic stress and loss of root growth recovery, which was enhanced in ttl1ttl3ttl4. Timing and spatial distribution of TTL3 expression is consistent with its role in development of LRP before their emergence and subsequent growth of LR. TTL3 emerged as a component of the root system morphogenesis regulatory network.

The peptide SCOOP12 acts on reactive oxygen species homeostasis to modulate cell division and elongation in Arabidopsis primary root

Small secreted peptides have been described as key contributors to complex signalling networks that control plant development and stress responses. The Brassicaceae-specific PROSCOOP family encodes precursors of Serine riCh endOgenOus Peptides (SCOOPs). In Arabidopsis SCOOP12 has been shown to promote the defence response against pathogens and to be involved in root development. Here, we explore its role as a moderator of Arabidopsis primary root development. We show that the PROSCOOP12 null mutation leads to longer primary roots through the development of longer differentiated cells while PROSCOOP12 overexpression induces dramatic plant growth impairments. In comparison, the exogenous application of synthetic SCOOP12 peptide shortens roots through meristem size and cell length reductions. Moreover, superoxide anion (O2·-) and hydrogen peroxide (H2O2) production in root tips vary according to SCOOP12 abundance. By using reactive oxygen species scavengers that suppress the proscoop12 phenotype, we showed that root growth regulation by SCOOP12 is associated with reactive oxygen species metabolism. Furthermore, our results suggest that peroxidases act as potential SCOOP12 downstream targets to regulate H2O2 production, which in turn triggers cell wall modifications in root. Finally, a massive transcriptional reprogramming, including the induction of genes from numerous other pathways, including ethylene, salicylic acid, and glucosinolates biosynthesis, was observed, emphasizing its dual role in defence and development.

Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root

Brassinosteroids (BR) are key hormonal regulators of plant development. However, whereas the individual components of BR perception and signaling are well characterized experimentally, the question of how they can act and whether they are sufficient to carry out the critical function of cellular elongation remains open. Here, we combined computational modeling with quantitative cell physiology to understand the dynamics of the plasma membrane (PM)-localized BR response pathway during the initiation of cellular responses in the epidermis of the Arabidopsis root tip that are be linked to cell elongation. The model, consisting of ordinary differential equations, comprises the BR-induced hyperpolarization of the PM, the acidification of the apoplast and subsequent cell wall swelling. We demonstrate that the competence of the root epidermal cells for the BR response predominantly depends on the amount and activity of H+-ATPases in the PM. The model further predicts that an influx of cations is required to compensate for the shift of positive charges caused by the apoplastic acidification. A potassium channel was subsequently identified and experimentally characterized, fulfilling this function. Thus, we established the landscape of components and parameters for physiological processes potentially linked to cell elongation, a central process in plant development.

Auxin in Root Development

Root system architecture is an important determinant of below-ground resource capture and hence overall plant fitness. The plant hormone auxin plays a central role in almost every facet of root development from the cellular to the whole-root-system level. Here, using Arabidopsis as a model, we review the multiple gene signaling networks regulated by auxin biosynthesis, conjugation, and transport that underpin primary and lateral root development. We describe the role of auxin in establishing the root apical meristem and discuss how the tight spatiotemporal regulation of auxin distribution controls transitions between cell division, cell growth, and differentiation. This includes the localized reestablishment of mitotic activity required to elaborate the root system via the production of lateral roots. We also summarize recent discoveries on the effects of auxin and auxin signaling and transport on the control of lateral root gravitropic setpoint angle (GSA), a critical determinant of the overall shape of the root system. Finally, we discuss how environmental conditions influence root developmental plasticity by modulation of auxin biosynthesis, transport, and the canonical auxin signaling pathway.

Bending to auxin: fast acid growth for tropisms

The phytohormone auxin is the major growth regulator governing tropic responses including gravitropism. Auxin build-up at the lower side of stimulated shoots promotes cell expansion, whereas in roots it inhibits growth, leading to upward shoot bending and downward root bending, respectively. Yet it remains an enigma how the same signal can trigger such opposite cellular responses. In this review, we discuss several recent unexpected insights into the mechanisms underlying auxin regulation of growth, challenging several existing models. We focus on the divergent mechanisms of apoplastic pH regulation in shoots and roots revisiting the classical Acid Growth Theory and discuss coordinated involvement of multiple auxin signaling pathways. From this emerges a more comprehensive, updated picture how auxin regulates growth.

Surface-enhanced Raman scattering labeled nanoplastic models for reliable bio-nano interaction investigations

Nanoplastics (NPs) have attracted great attention as an emerging pollution. To date, their interaction with biological systems has been studied mostly by using fluorescent-labeled NPs, which suffered from serious drawbacks such as biological autofluorescence interference and false-positive results. Reliable optically labeled NP models are eagerly desired until now. Herein, a novel near-infrared (NIR) surface-enhanced Raman scattering (SERS) labeled NP model was proposed, which gained single-particle ultra-sensitivity, deep tissue detection, multiplex labeling ability, and anti-interference property. More importantly, the NP demonstrated satisfactory in vivo signal stability which completely prevented the positive-false problems. The advantages of the NPs enabled direct, dynamic in vivo behavior imaging study in living zebrafish embryo, adult zebrafish and green vegetable Brassica rapa. It was found for the first time that NPs entered blood circulation system of zebrafish larva via dermal uptake route, which only occurred in a short 48 h-window post-hatch. NPs widely distributed in roots, shoots and leaves of Brassica rapa seedlings germinating and growing in the NP-containing hydroponic culture. Different depths of one root showed varied adsorption capabilities towards NPs with fulvic acid, lipid and sodium dodecyl sulfate eco-coronas. This work provided an ideal tool for reliable bio-NP interaction study for a variety of organisms, which could promote the research of NPs.

Arabidopsis root growth and development under metal exposure presented in an adverse outcome pathway framework

Due to human activities, soils become more and more polluted with metals, which imposes risks for human health and wildlife welfare. As most of the metals end up in the food chain through accumulation in plants, we need to establish science-based environmental criteria and risk management policies. To meet these necessities, a thorough understanding is required of how these metals accumulate in and affect plants. Many studies have been conducted towards this aim, but strikingly, only a few entries can be found in ecotoxicological databases, especially on Arabidopsis thaliana, which serves as a model species for plant (cell) physiology and genetic studies. As experimental conditions seem to vary considerably throughout literature, extrapolation or comparison of data is rather difficult or should be approached with caution. Furthermore, metal-polluted soils often contain more than one metal, yet limited studies investigated the impact of metal mixtures on plants. This review aims to compile all data concerning root system architecture under Cu, Cd and Zn stress, in single or multi-metal exposure in A. thaliana, and link it to metal-induced responses at different biological levels. Global incorporation into an adverse outcome pathway framework is presented.

Live Plant Cell Tracking: Fiji plugin to analyze cell proliferation dynamics and understand morphogenesis

Arabidopsis (Arabidopsis thaliana) primary and lateral roots (LRs) are well suited for 3D and 4D microscopy, and their development provides an ideal system for studying morphogenesis and cell proliferation dynamics. With fast-advancing microscopy techniques used for live-imaging, whole tissue data are increasingly available, yet present the great challenge of analyzing complex interactions within cell populations. We developed a plugin "Live Plant Cell Tracking" (LiPlaCeT) coupled to the publicly available ImageJ image analysis program and generated a pipeline that allows, with the aid of LiPlaCeT, 4D cell tracking and lineage analysis of populations of dividing and growing cells. The LiPlaCeT plugin contains ad hoc ergonomic curating tools, making it very simple to use for manual cell tracking, especially when the signal-to-noise ratio of images is low or variable in time or 3D space and when automated methods may fail. Performing time-lapse experiments and using cell-tracking data extracted with the assistance of LiPlaCeT, we accomplished deep analyses of cell proliferation and clonal relations in the whole developing LR primordia and constructed genealogical trees. We also used cell-tracking data for endodermis cells of the root apical meristem (RAM) and performed automated analyses of cell population dynamics using ParaView software (also publicly available). Using the RAM as an example, we also showed how LiPlaCeT can be used to generate information at the whole-tissue level regarding cell length, cell position, cell growth rate, cell displacement rate, and proliferation activity. The pipeline will be useful in live-imaging studies of roots and other plant organs to understand complex interactions within proliferating and growing cell populations. The plugin includes a step-by-step user manual and a dataset example that are available at https://www.ibt.unam.mx/documentos/diversos/LiPlaCeT.zip.

Effects of Elevated Temperature on Root System Development of Two Lupine Species

The aim of this study was to assess the effect of elevated temperature on the growth, morphology and spatial orientation of lupine roots at the initial stages of development and on the formation of lupine root architecture at later stages. Two lupine species were studied-the invasive Lupinus polyphyllus Lindl. and the non-invasive L. luteus L. The plants were grown in climate chambers under 25 °C and simulated warming at 30 °C conditions. The angle of root curvature towards the vector of gravity was measured at the 48th hour of growth, and during a 4-h period after 90° reorientation. Root biometrical, histological measurements were carried out on 7-day-old and 30-day-old plants. The elevation of 5 °C affected root formation of the two lupine species differently. The initial roots of L. polyphyllus were characterized by worse spatial orientation, reduced growth and reduced mitotic index of root apical meristem at 30 °C compared with 25 °C. The length of primary roots of 30-day-old lupines and the number of lateral roots decreased by 14% and 16%, respectively. More intense root development and formation were observed in non-invasive L. luteus at 30 °C. Our results provide important information on the effect of elevated temperature on the formation of root architecture in two lupine species and suggest that global warming may impact the invasiveness of these species.

Cytoplasmic Linker Protein-Associating Protein at the Nexus of Hormone Signaling, Microtubule Organization, and the Transition From Division to Differentiation in Primary Roots

The transition from cell division to differentiation in primary roots is dependent on precise gradients of phytohormones, including auxin, cytokinins and brassinosteroids. The reorganization of microtubules also plays a key role in determining whether a cell will enter another round of mitosis or begin to rapidly elongate as the first step in terminal differentiation. In the last few years, progress has been made to establish connections between signaling pathways at distinct locations within the root. This review focuses on the different factors that influence whether a root cell remains in the division zone or transitions to elongation and differentiation using Arabidopsis thaliana as a model system. We highlight the role of the microtubule-associated protein CLASP as an intermediary between sustaining hormone signaling and controlling microtubule organization. We discuss new, innovative tools and methods, such as hormone sensors and computer modeling, that are allowing researchers to more accurately visualize the belowground growth dynamics of plants.

Microscopic Imaging of Endosomal Trafficking of ABA Receptors

The abscisic acid (ABA) is a key hormone for stress tolerance. The balance between growth/development and stress responses is crucial for the optimal course of plant life meaning that plants need to control the timing and extent of ABA pathway activation. In this regard, protein turnover regulation by means of both the ubiquitin-proteasome system (UPS) and non-26S proteasome endomembrane trafficking pathways, plays a critical role in the regulation of ABA signaling activation and deactivation. Over the last few years, the ubiquitination of ABA receptors PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR) at the plasma membrane by the RING between RING fingers (RBR)-type E3 ligase RING FINGER OF SEED LONGEVITY1 (RSL1) triggering their internalization through the clathrin-mediated endocytosis (CME) pathway, followed by their endosomal trafficking and delivery to the vacuole for degradation, was reported. For this process, the direct role of some components of the endosomal sorting complex required for transport (ESCRT) machinery, that is, FYVE DOMAIN-CONTAINING PROTEIN 1 (FYVE1)/FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1) and VACUOLAR PROTEIN SORTING23A (VPS23A) members of ESCRT-I complex, and ALG-2 INTERACTING PROTEIN-X (ALIX) associated protein of ESCRT-III, was reported. In this chapter, we will detail two methods for imaging endosomal trafficking of ABA receptor proteins by confocal microscopy: (a) colocalization of GFP-PYL4 (also known as RCAR10) and CLATHRIN LIGHT CHAIN 2 (CLC2)-mOrange in clathrin-coated vesicles in Nicotiana benthamiana leaf cells and (b) localization of GFP-PYL4 into Wortmannin (WM)-enlarged late endosomes in Arabidopsis thaliana root cells.

Hormonal orchestration of root apical meristem formation and maintenance in Arabidopsis

Plant hormones are key regulators of a number of developmental and adaptive responses in plants, integrating the control of intrinsic developmental regulatory circuits with environmental inputs. Here we provide an overview of the molecular mechanisms underlying hormonal regulation of root development. We focus on key events during both embryonic and post-embryonic development, including specification of the hypophysis as a future organizer of the root apical meristem (RAM), hypophysis asymmetric division, specification of the quiescent centre (QC) and the stem cell niche (SCN), RAM maturation and maintenance of QC/SCN activity, and RAM size. We address both well-established and newly proposed concepts, highlight potential ambiguities in recent terminology and classification criteria of longitudinal root zonation, and point to contrasting results and alternative scenarios for recent models. In the concluding remarks, we summarize the common principles of hormonal control during root development and the mechanisms potentially explaining often antagonistic outputs of hormone action, and propose possible future research directions on hormones in the root.

Morphogenic responses and biochemical alterations induced by the cover crop Urochloa ruziziensis and its component protodioscin in weed species

Urochloa ruziziensis, a cover plant used in no-till systems, can suppress weeds in the field through their chemical compounds, but the mode of action of these compounds is still unknown. The present study aimed to investigate the effects of a saponin-rich butanolic extract from U. ruziziensis straw (BfUr) and one of its components, protodioscin on an eudicot Ipomoea grandifolia and a monocot Digitaria insularis weed. The anatomy and the morphology of the root systems and several parameters related to energy metabolism and antioxidant defense systems were examined. The IC₅₀ values for the root growth inhibition by BfUr were 108 μg mL^-1 in D. insularis and 230 μg mL^-1 in I. grandifolia. The corresponding values for protodioscin were 34 μg mL^-1 and 54 μg mL^-1. I. grandifolia exhibited higher ROS-induced peroxidative damage in its roots compared with D. insularis. In the roots of both weeds, the BfUr and protodioscin induced a reduction in the meristematic and elongation zones with a precocious appearance of lateral roots, particularly in I. grandifolia. The roots also exhibited features of advanced cell differentiation in the vascular cylinder. These alterations were similar to stress-induced morphogenic responses (SIMRs), which are plant adaptive strategies to survive in the presence of toxicants. At concentrations above their IC₅₀ values, the BfUr or protodioscin strongly inhibited the development of both weeds. Such findings demonstrated that U. ruziziensis mulches may contribute to the use of natural and renewable weed control tools.

AFB1 controls rapid auxin signalling through membrane depolarization in Arabidopsis thaliana root

The membrane potential reflects the difference between cytoplasmic and apoplastic electrical potentials and is essential for cellular operation. The application of the phytohormone auxin (3-indoleacetic acid (IAA)) causes instantaneous membrane depolarization in various cell types^1-6, making depolarization a hallmark of IAA-induced rapid responses. In root hairs, depolarization requires functional IAA transport and TIR1-AFB signalling⁵, but its physiological importance is not understood. Specifically in roots, auxin triggers rapid growth inhibition^7-9 (RGI), a process required for gravitropic bending. RGI is initiated by the TIR1-AFB co-receptors, with the AFB1 paralogue playing a crucial role^10,11. The nature of the underlying rapid signalling is unknown, as well as the molecular machinery executing it. Even though the growth and depolarization responses to auxin show remarkable similarities, the importance of membrane depolarization for root growth inhibition and gravitropism is unclear. Here, by combining the DISBAC₂(3) voltage sensor with microfluidics and vertical-stage microscopy, we show that rapid auxin-induced membrane depolarization tightly correlates with RGI. Rapid depolarization and RGI require the AFB1 auxin co-receptor. Finally, AFB1 is essential for the rapid formation of the membrane depolarization gradient across the gravistimulated root. These results clarify the role of AFB1 as the central receptor for rapid auxin responses.

The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators

Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H⁺-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr³¹ phosphorylation site for growth regulation in the Arabidopsis root tip.

Inhibition of cell expansion enhances cortical microtubule stability in the root apex of Arabidopsis thaliana

Background

Cortical microtubules regulate cell expansion by determining cellulose microfibril orientation in the root apex of Arabidopsis thaliana. While the regulation of cell wall properties by cortical microtubules is well studied, the data on the influence of cell wall to cortical microtubule organization and stability remain scarce. Studies on cellulose biosynthesis mutants revealed that cortical microtubules depend on Cellulose Synthase A (CESA) function and/or cell expansion. Furthermore, it has been reported that cortical microtubules in cellulose-deficient mutants are hypersensitive to oryzalin. In this work, the persistence of cortical microtubules against anti-microtubule treatment was thoroughly studied in the roots of several cesa mutants, namely thanatos, mre1, any1, prc1-1 and rsw1, and the Cellulose Synthase Interacting 1 protein (csi1) mutant pom2-4. In addition, various treatments with drugs affecting cell expansion were performed on wild-type roots. Whole mount tubulin immunolabeling was applied in the above roots and observations were performed by confocal microscopy.

Results

Cortical microtubules in all mutants showed statistically significant increased persistence against anti-microtubule drugs, compared to those of the wild-type. Furthermore, to examine if the enhanced stability of cortical microtubules was due to reduced cellulose biosynthesis or to suppression of cell expansion, treatments of wild-type roots with 2,6-dichlorobenzonitrile (DCB) and Congo red were performed. After these treatments, cortical microtubules appeared more resistant to oryzalin, than in the control.

Conclusions

According to these findings, it may be concluded that inhibition of cell expansion, irrespective of the cause, results in increased microtubule stability in A. thaliana root. In addition, cell expansion does not only rely on cortical microtubule orientation but also plays a regulatory role in microtubule dynamics, as well. Various hypotheses may explain the increased cortical microtubule stability under decreased cell expansion such as the role of cell wall sensors and the presence of less dynamic cortical microtubules.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40709-021-00143-8.

Conditions for the emergence of circumnutations in plant roots

The plant root system shows remarkably complex behaviors driven by environmental cues and internal dynamics, whose interplay remains largely unknown. A notable example is circumnutation growth movements, which are growth oscillations from side to side of the root apex. Here we describe a model capable of replicating root growth behaviors, which we used to analyze the role of circumnuntations, revealing their emergence I) under gravitropic stress, as a combination of signal propagation and sensitivity to the signal carriers; II) as a result of the interplay between gravitropic and thigmotropic responses; and III) as a behavioral strategy to detect and react to resource gradients. The latter function requires the presence of a hypothetical internal oscillator whose parameters are regulated by the perception of environmental resources.

Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems

Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Using meristems as a test system, here, we study the major rewiring that plants undergo during cold acclimation. We performed tandem mass tag-based bottom-up quantitative proteomics of two consecutive segments of barley seminal root apexes subjected to suboptimal temperatures. After comparing changes in total and ribosomal protein (RP) fraction-enriched contents with shifts in individual protein abundances, we report ribosome accumulation accompanied by an intricate translational reprogramming in the distal apex zone. Reprogramming ranges from increases in ribosome biogenesis to protein folding factors and suggests roles for cold-specific RP paralogs. Ribosome biogenesis is the largest cellular investment; thus, the vast accumulation of ribosomes and specific translation-related proteins during cold acclimation could imply a divergent ribosomal population that would lead to a proteome shift across the root. Consequently, beyond the translational reprogramming, we report a proteome rewiring. First, triggered protein accumulation includes spliceosome activity in the root tip and a ubiquitous upregulation of glutathione production and S-glutathionylation (S-GSH) assemblage machineries in both root zones. Second, triggered protein depletion includes intrinsically enriched proteins in the tip-adjacent zone, which comprise the plant immune system. In summary, ribosome and translation-related protein accumulation happens concomitantly to a proteome reprogramming in barley root meristems during cold acclimation. The cold-accumulated proteome is functionally implicated in feedbacking transcript to protein translation at both ends and could guide cold acclimation.

Latrunculin B facilitates gravitropic curvature of Arabidopsis root by inhibiting cell elongation, especially the cells in the lower flanks of the transition and elongation zones

Gravitropism plays a critical role in the growth and development of plants. Previous reports proposed that the disruption of the actin cytoskeleton resulted in enhanced gravitropism; however, the mechanism underlying these phenomena is still unclear. In the present study, real-time observation on the effect of Latrunculin B (Lat B), a depolymerizing agent of microfilament cytoskeleton, on gravitropism of the primary root of Arabidopsis was undertaken using a vertical stage microscope. The results indicated that Lat B treatment prevented the growth of root, and the growth rates of upper and lower flanks of the horizontally placed root were asymmetrically inhibited. The growth of the lower flank was influenced by Lat B more seriously, resulting in an increased differential growth rate between the upper and lower flanks of the root. Further analysis indicated that Lat B affected cell growth mainly in the transition and elongation zones. Briefly, the current data revealed that Lat B treatment inhibited cell elongation, especially the cells in the lower flanks of the transition and elongation zones, which finally manifested as the facilitation of gravitropic curvature of the primary root.

Home sweet home: how mutualistic microbes modify root development to promote symbiosis

Post-embryonic organogenesis has uniquely equipped plants to become developmentally responsive to their environment, affording opportunities to remodel organism growth and architecture to an extent not possible in other higher order eukaryotes. It is this developmental plasticity that makes the field of plant-microbe interactions an exceptionally fascinating venue in which to study symbiosis. This review article describes the various ways in which mutualistic microbes alter the growth, development, and architecture of the roots of their plant hosts. We first summarize general knowledge of root development, and then examine how association of plants with beneficial microbes affects these processes. Working our way inwards from the epidermis to the pericycle, this review dissects the cell biology and molecular mechanisms underlying plant-microbe interactions in a tissue-specific manner. We examine the ways in which microbes gain entry into the root, and modify this specialized organ for symbiont accommodation, with a particular emphasis on the colonization of root cortical cells. We present significant advances in our understanding of root-microbe interactions, and conclude our discussion by identifying questions pertinent to root endosymbiosis that at present remain unresolved.