A gateway with a guard: how the endodermis regulates growth through hormone signaling

Not so hidden anymore: Advances and challenges in understanding root growth under water deficits

Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.

Near-Infrared Fluorescent Carbon Nanotube Sensors for the Plant Hormone Family Gibberellins

Gibberellins (GAs) are a class of phytohormones, important for plant growth, and very difficult to distinguish because of their similarity in chemical structures. Herein, we develop the first nanosensors for GAs by designing and engineering polymer-wrapped single-walled carbon nanotubes (SWNTs) with unique corona phases that selectively bind to bioactive GAs, GA₃ and GA₄, triggering near-infrared (NIR) fluorescence intensity changes. Using a new coupled Raman/NIR fluorimeter that enables self-referencing of nanosensor NIR fluorescence with its Raman G-band, we demonstrated detection of cellular GA in Arabidopsis, lettuce, and basil roots. The nanosensors reported increased endogenous GA levels in transgenic Arabidopsis mutants that overexpress GA and in emerging lateral roots. Our approach allows rapid spatiotemporal detection of GA across species. The reversible sensor captured the decreasing GA levels in salt-treated lettuce roots, which correlated remarkably with fresh weight changes. This work demonstrates the potential for nanosensors to solve longstanding problems in plant biotechnology.

Water Stress Differentially Modulates the Expression of Tomato Cell Wall Metabolism-Related Genes in Meloidogyne incognita Feeding Sites

Microscopic observations and transcriptomic RNA-Seq analyses were applied to investigate the effect of water stress during the formation of tomato galls formation 1 and 2 weeks after inoculation with the root-knot nematode Meloidogyne incognita. Water stress affected root growth and the nematode ability to mount an efficient parasitism. The effects of water stress on the feeding site development were already observed at 1 week after nematode inoculation, with smaller giant cells, delayed development, and thinner cell walls. These features suggested changes in the expression levels of genes involved in the feeding site formation and maintenance. Gene Ontology (GO) enrichment and expression patterns were used to characterize differentially expressed genes. Water stress modified the expression profile of genes involved in the synthesis, degradation, and remodeling of the cell wall during the development of nematode feeding site. A comparison of gene expression with unstressed galls revealed that water stress intensified the up or downregulation of most genes. However, it particularly influenced the expression pattern of expansin A11 (Solyc04g081870.4.1), expansin-like B1(Solyc08g077910.3.1), a pectin acetylesterase (Solyc08g005800.4.1), and the pectin methylesterase pmeu1 (Solyc03g123630.4.1) which were upregulated in unstressed galls and repressed by water stress, at both sampling times. The expression of most members of the genes involved in cell wall metabolism, i.e., those coding for Csl, fasciclin, and COBRA proteins, were negatively influenced. Interestingly, alteration in the expression profiles of most dirigent protein genes (DIRs) and upregulation of five gene coding for Casparian strip domain protein (CASP)-like proteins were found. Gene expression analysis of galls from water stressed plants allowed us to better understand the molecular basis of M. incognita parasitism in tomato. Specific genes, including those involved in regulation of cellulose synthesis and lignification process, require further study to develop defense strategies against root-knot nematodes.

Structure, Function, and Regulation of the Plasma Membrane Na+/H+ Antiporter Salt Overly Sensitive 1 in Plants

Physiological studies have confirmed that export of Na⁺ to improve salt tolerance in plants is regulated by the combined activities of a complex transport system. In the Na⁺ transport system, the Na⁺/H⁺ antiporter salt overly sensitive 1 (SOS1) is the main protein that functions to excrete Na⁺ out of plant cells. In this paper, we review the structure and function of the Na⁺/H⁺ antiporter and the physiological process of Na⁺ transport in SOS signaling pathway, and discuss the regulation of SOS1 during phosphorylation activation by protein kinase and the balance mechanism of inhibiting SOS1 antiporter at molecular and protein levels. In addition, we carried out phylogenetic tree analysis of SOS1 proteins reported so far in plants, which implied the specificity of salt tolerance mechanism from model plants to higher crops under salt stress. Finally, the high complexity of the regulatory network of adaptation to salt tolerance, and the feasibility of coping strategies in the process of genetic improvement of salt tolerance quality of higher crops were reviewed.

Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks.

Size and activity of the root meristem: A key for drought resistance and a key model of drought-related signaling

Plants make many adjustments to their growth and development in response to even small changes in water availability. Under such conditions, root elongation can be actively restricted by stress-related signaling mechanisms. Here we look at how the Arabidopsis thaliana root meristem can be affected by moderate water limitation (low water potential, ψ_w ). Recent characterization of the clade E Growth-Regulating (EGR) protein phosphatases and Microtubule Associated Stress Protein 1 (MASP1) provides an example of how active restriction of root meristem size allows the plant to downregulate root elongation during low ψ_w stress. EGR2 protein accumulation in cortex cells of the transition zone at the distal end of the root meristem illustrates how the balance of cell division versus cell expansion signals at this critical location can determine meristem size and root elongation during low ψ_w . These characteristics of EGRs also raise the question of whether they may also be involved in hydrotropism, and, more broadly, whether hydrotropism is a distinct response or a specific manifestation of more general mechanisms used to adjust root growth under moderate severity low ψ_w whether or not a gradient of water availability is present. These questions, as well as a better understanding of how specific cell layers (cortex and endodermis) seem to have an outsized role in growth regulation and better understanding the roles of plasma membrane-based signaling and polar-localized proteins in the regulation of root meristem size and cell division activity are key to elucidating the cellular mechanisms that determine root growth behavior during soil drying.

A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and stress response

Root growth relies on both cell division and cell elongation, which occur in the meristem and elongation zones, respectively. SCARECROW (SCR) and SHORT-ROOT (SHR) are GRAS family genes essential for root growth and radial patterning in the Arabidopsis root. Previous studies showed that SCR and SHR promote root growth by suppressing cytokinin response in the meristem, but there is evidence that SCR expressed beyond the meristem is also required for root growth. Here we report a previously unknown role for SCR in promoting cell elongation. Consistent with this, we found that the scr mutant accumulated a higher level of reactive oxygen species (ROS) in the elongation zone, which is probably due to decreased expression of peroxidase gene 3, which consumes hydrogen peroxide in a reaction leading to Casparian strip formation. When the oxidative stress response was blocked in the scr mutant by mutation in ABSCISIC ACID 2 (ABA2) or when the redox status was ameliorated by the upbeat 1 (upb1) mutant, the root became significantly longer, with longer cells and a larger and more mitotically active meristem. Remarkably, however, the stem cell and radial patterning defects in the double mutants still persisted. Since ROS and peroxidases are essential for endodermal differentiation, these results suggest that SCR plays a role in coordinating cell elongation, endodermal differentiation, redox homeostasis and oxidative stress response in the root. We also provide evidence that this role of SCR is independent of SHR, even though they function similarly in other aspects of root growth and development.

Functions and structure of roots and their contributions to salinity tolerance in plants

Soil salinity is an increasing threat to the productivity of glycophytic crops worldwide. The root plays vital roles under various stress conditions, including salinity, as well as has diverse functions in non-stress soil environments. In this review, we focus on the essential functions of roots such as in ion homeostasis mediated by several different membrane transporters and signaling molecules under salinity stress and describe recent advances in the impacts of quantitative trait loci (QTLs) or genetic loci (and their causal genes, if applicable) on salinity tolerance. Furthermore, we introduce important literature for the development of barriers against the apoplastic flow of ions, including Na⁺, as well as for understanding the functions and components of the barrier structure under salinity stress.

Molecular insights into the compatible and incompatible interactions between sugar beet and the beet cyst nematode

BACKGROUND

Sugar beet (Beta vulgaris subsp. vulgaris) is an economically important crop that provides nearly one third of the global sugar production. The beet cyst nematode (BCN), Heterodera schachtii, causes major yield losses in sugar beet and other crops worldwide. The most effective and economic approach to control this nematode is growing tolerant or resistant cultivars. To identify candidate genes involved in susceptibility and resistance, the transcriptome of sugar beet and BCN in compatible and incompatible interactions at two time points was studied using mRNA-seq.

RESULTS

In the susceptible cultivar, most defense-related genes were induced at 4 dai while suppressed at 10 dai but in the resistant cultivar Nemakill, induction of genes involved in the plant defense response was observed at both time points. In the compatible interaction, alterations in phytohormone-related genes were detected. The effect of exogenous application of Methyl Jasmonate and ET-generator ethephon on susceptible plants was therefore investigated and the results revealed significant reduction in plant susceptibility. Genes putatively involved in the resistance of Nemakill were identified, such as genes involved in phenylpropanoid pathway and genes encoding CYSTM domain-containing proteins, F-box proteins, chitinase, galactono-1,4-lactone dehydrogenase and CASP-like protein. Also, the transcriptome of the BCN was analyzed in infected root samples and several novel potential nematode effector genes were found.

CONCLUSIONS

Our data provides detailed insights into the plant and nematode transcriptional changes occurring during compatible and incompatible interactions between sugar beet and BCN. Many important genes playing potential roles in susceptibility or resistance of sugar beet against BCN, as well as some BCN effectors with a potential role as avr proteins were identified. In addition, our findings indicate the effective role of jasmonate and ethylene in enhancing sugar beet defense response against BCN. This research provides new molecular insights into the plant-nematode interactions that can be used to design novel management strategies against BCN.

Overexpression of Tamarix hispida ThTrx5 Confers Salt Tolerance to Arabidopsis by Activating Stress Response Signals

Salt stress inhibits normal plant growth and development by disrupting cellular water absorption and metabolism. Therefore, understanding plant salt tolerance mechanisms should provide a theoretical basis for developing salt-resistant varieties. Here, we cloned ThTrx5 from Tamarix hispida, a salt-resistant woody shrub, and generated ThTrx5-overexpressing transgenic Arabidopsis thaliana lines. Under NaCl stress, the germination rate of overexpressing ThTrx5 lines was significantly increased relative to that of the nontransgenic line; under salt stress, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione levels and root length and fresh weight values of transgenic ThTrx5 plants were significantly greater than corresponding values for wild-type plants. Moreover, with regard to the transcriptome, comparison of differential gene expression of transgenic versus nontransgenic lines at 0 h and 3 h of salt stress exposure revealed 500 and 194 differentially expressed genes (DEGs), respectively, that were mainly functionally linked to catalytic activity and binding process. Pull-down experiments showed that ThTrx bound 2-Cys peroxiredoxin BAS1-like protein that influences stress response-associated redox, hormone signal transduction, and transcription factor functions. Therefore, this work provides important insights into ThTrx5 mechanisms that promote salt tolerance in plants.

Polarized transport across root epithelia

Plant roots explore the soil to acquire water and nutrients which are often available at concentrations that drastically differ from the plant's actual need for growth and development. This stark difference between availability and requirement can be dealt with owing to the root's architecture as an inverted gut. In roots, the two epithelial characteristics (selective acquisition and diffusion barrier) are split between two cell layers: the epidermis at the root periphery and the endodermis as the innermost cortical cell layer around the vasculature. Polarized transport of nutrients across the root epithelium can be achieved through different pathways: apoplastic, symplastic, or coupled transcellular. This review highlights different features of the root that allow this polarized transport. Special emphasis is placed on the coupled transcellular pathway, facilitated by polarized nutrient carriers along root cell layers but barred by suberin lamellae in endodermal cells.

The battle of two ions: Ca2+ signalling against Na+ stress

Soil salinity adversely affects plant growth, crop yield and the composition of ecosystems. Salinity stress impacts plants by combined effects of Na⁺ toxicity and osmotic perturbation. Plants have evolved elaborate mechanisms to counteract the detrimental consequences of salinity. Here we reflect on recent advances in our understanding of plant salt tolerance mechanisms. We discuss the embedding of the salt tolerance-mediating SOS pathway in plant hormonal and developmental adaptation. Moreover, we review newly accumulating evidence indicating a crucial role of a transpiration-dependent salinity tolerance pathway, that is centred around the function of the NADPH oxidase RBOHF and its role in endodermal and Casparian strip differentiation. Together, these data suggest a unifying and coordinating role for Ca²⁺ signalling in combating salinity stress at the cellular and organismal level.

A Missing Link in Radial Ion Transport: Ion Transporters in the Endodermis

In higher plants, roots have important functions, such as the acquisition of water and ions, as well as transportation into the aerial parts of the plant via the xylem vessels. Radial ion transport in the root is strongly regulated in the endodermis, which is characterized by the presence of the Casparian strip (CS) and suberin lamellae. Although tremendous progress has been made with regard to the ion transporters and endodermal cells, little is known about the relationship between the ion transporters in the endodermis and ion homeostasis in aboveground tissues. This review summarizes the current knowledge about the location of the ion transporters (or channels) in the endodermis. We mainly discuss the effects of mutants related to the CS and/or suberin formation on the role of endodermal ion transporters in ion homeostasis. We also wish to emphasize the critical role of endodermal ion transporters in the regulation of radial ion transport in the root.

High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

BACKGROUND

Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas.

RESULT

Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana.

CONCLUSIONS

In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas.

Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo

Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.

Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation

Controlling the production of diverse cell/tissue types is essential for the development of multicellular organisms such as animals and plants. The Arabidopsis thaliana root, which contains distinct cells/tissues along longitudinal and radial axes, has served as an elegant model to investigate how genetic programs and environmental signals interact to produce different cell/tissue types. In the root, a series of asymmetric cell divisions (ACDs) give rise to three ground tissue layers at maturity (endodermis, middle cortex, and cortex). Because the middle cortex is formed by a periclinal (parallel to the axis) ACD of the endodermis around 7 to 14 days post-germination, middle cortex formation is used as a parameter to assess maturation of the root ground tissue. Molecular, genetic, and physiological studies have revealed that the control of the timing and extent of middle cortex formation during root maturation relies on the interaction of plant hormones and transcription factors. In particular, abscisic acid and gibberellin act synergistically to regulate the timing and extent of middle cortex formation, unlike their typical antagonism. The SHORT-ROOT, SCARECROW, SCARECROW-LIKE 3, and DELLA transcription factors, all of which belong to the plant-specific GRAS family, play key roles in the regulation of middle cortex formation. Recently, two additional transcription factors, SEUSS and GA- AND ABA-RESPONSIVE ZINC FINGER, have also been characterized during ground tissue maturation. In this review, we provide a detailed account of the regulatory networks that control the timing and extent of middle cortex formation during post-embryonic root development.

Environmental Control of Root System Biology

The plant root system traverses one of the most complex environments on earth. Understanding how roots support plant life on land requires knowing how soil properties affect the availability of nutrients and water and how roots manipulate the soil environment to optimize acquisition of these resources. Imaging of roots in soil allows the integrated analysis and modeling of environmental interactions occurring at micro- to macroscales. Advances in phenotyping of root systems is driving innovation in cross-platform-compatible methods for data analysis. Root systems acclimate to the environment through architectural changes that act at the root-type level as well as through tissue-specific changes that affect the metabolic needs of the root and the efficiency of nutrient uptake. A molecular understanding of the signaling mechanisms that guide local and systemic signaling is providing insight into the regulatory logic of environmental responses and has identified points where crosstalk between pathways occurs.

A Casparian strip domain-like gene, CASPL, negatively alters growth and cold tolerance

A cold-induced transcript encoding a Casparian strip membrane domain (CASP)-like protein (ClCASPL) was identified in watermelon (Citrullus lanatus). Fluorescence microscopy analysis showed that ClCASPL-GFP is localized in the plasma membrane. The orthologous gene in Arabidopsis thaliana (AtCASPL4C1) was also found to play an important role in cold tolerance. Expression analysis using a β-glucuronidase (GUS) reporter reveals that AtCASPL4C1 is widely expressed in a variety of organs and is cold inducible. Analysis of AtCASPL4C1 T-DNA knock-out plants showed altered growth dynamics, faster growth, increased biomass (dry weight) and earlier flowering compared to wild type (Col-0) and ClCASPL overexpressing plants. AtCASPL4C1 knock-out plants showed elevated tolerance to cold stress, while overexpressing CICASPL resulted in increased sensitivity to cold stress in Arabidopsis. Interestingly, AtCASPL4C1 knock-out plants did not display significant alterations in the Casparian strip formation in roots. Thus, the combination of these results suggests a role for CICASPL and AtCASPL4C1 beyond Casparian strip formation in roots, possibly indicating a more fundamental role in vascular tissue.

Traversing organizational scales in plant salt-stress responses

Modern society has developed in large part due to our ability to reliably grow plants for food and renewable resources. Predicted increases in environmental variability will impact agricultural productivity and may have extensive secondary effects on the stability of our society. Thus, a concerted effort to understand plant response strategies to stress is needed. High salinity is an agriculturally important environmental stress and generates complex effects on the physiology of the plant. The abiotic-stress-associated hormone, abscisic acid (ABA), mediates a major component of this response. I highlight recent work studying salt-stress responses at different spatial and organizational scales from the action of ABA in specific cell types to global networks of proteins that predict critical regulatory events during acclimation.

Cortex proliferation in the root is a protective mechanism against abiotic stress

Although as an organ the root plays a pivotal role in nutrient and water uptake as well anchorage, individual cell types function distinctly. Cortex is regarded as the least differentiated cell type in the root, but little is known about its role in plant growth and physiology. In recent studies, we found that cortex proliferation can be induced by oxidative stress. Since all types of abiotic stress lead to oxidative stress, this finding suggests a role for cortex in coping with abiotic stress. This hypothesis was tested in this study using the spy mutant, which has an extra layer of cortex in the root. Interestingly, the spy mutant was shown to be hypersensitive to salt and oxidizing reagent applied to the leaves, but it was as tolerant as the wild type to these compounds in the soil. This result lends support to the notion that cortex has a protective role against abiotic stress arising from the soil.