Light as stress factor to plant roots - case of root halotropism

Light at the end of the tunnel: integrating signaling pathways in the coordination of lateral root development

Root system architecture (RSA) encompasses a range of physical root attributes, including the lateral roots (LRs), root hairs and adventitious roots, in addition to the primary or main root. This overall structure is a crucial trait for efficient water and mineral capture alongside providing anchorage to the plant in the soil and is vital for plant productivity and fitness. RSA dynamics are dependent upon various environmental cues such as light, soil pH, water, mineral nutrition and the belowground microbiome. Among these factors, light signaling through HY5 significantly influences the flexibility of RSA by controlling different signaling pathways that converge at photoreceptors-mediated signaling, also present in the 'hidden half'. Furthermore, several phytohormones also drive the formation and emergence of LRs and are critical to harmonize intra and extracellular stimuli in this regard. This review endeavors to elucidate the impact of these interactions on RSA, with particular emphasis on LR development and to enhance our understanding of the fundamental mechanisms governing the light-regulation of LR growth and physiology.

Understanding Ameliorating Effects of Boron on Adaptation to Salt Stress in Arabidopsis

When faced with salinity stress, plants typically exhibit a slowdown in their growth patterns. Boron (B) is an essential micronutrient for plants that are known to play a critical role in controlling cell wall properties. In this study, we used the model plant Arabidopsis thaliana Col-0 and relevant mutants to explore how the difference in B availability may modulate plant responses to salt stress. There was a visible root growth suppression of Col-0 with the increased salt levels in the absence of B while this growth reduction was remarkably alleviated by B supply. Pharmacological experiments revealed that orthovanadate (a known blocker of H+-ATPase) inhibited root growth at no B condition, but had no effect in the presence of 30 μM B. Salinity stress resulted in a massive K+ loss from mature zones of A. thaliana roots; this efflux was attenuated in the presence of B. Supplemental B also increased the magnitude of net H+ pumping by plant roots. Boron availability was also essential for root halotropism. Interestingly, the aha2Δ57 mutant with active H+-ATPase protein exhibited the same halotropism response as Col-0 while the aha2-4 mutant had a stronger halotropism response (larger bending angle) compared with that of Col-0. Overall, the ameliorative effect of B on the A. thaliana growth under salt stress is based on the H+-ATPase stimulation and a subsequent K+ retention, involving auxin- and ROS-pathways.

How plant roots respond to waterlogging

Plant submergence is a major abiotic stress that impairs plant performance. Under water, reduced gas diffusion exposes submerged plant cells to an environment that is enriched in gaseous ethylene and is limited in oxygen (O2) availability (hypoxia). The capacity for plant roots to avoid and/or sustain critical hypoxia damage is essential for plants to survive waterlogging. Plants use spatiotemporal ethylene and O2 dynamics as instrumental flooding signals to modulate potential adaptive root growth and hypoxia stress acclimation responses. However, how non-adapted plant species modulate root growth behaviour during actual waterlogged conditions to overcome flooding stress has hardly been investigated. Here we discuss how changes in the root growth rate, lateral root formation, density, and growth angle of non-flood adapted plant species (mainly Arabidopsis) could contribute to avoiding and enduring critical hypoxic conditions. In addition, we discuss current molecular understanding of how ethylene and hypoxia signalling control these adaptive root growth responses. We propose that future research would benefit from less artificial experimental designs to better understand how plant roots respond to and survive waterlogging. This acquired knowledge would be instrumental to guide targeted breeding of flood-tolerant crops with more resilient root systems.

Local phytochrome signalling limits root growth in light by repressing auxin biosynthesis

In nature, plant shoots are exposed to light whereas the roots grow in relative darkness. Surprisingly, many root studies rely on in vitro systems that leave the roots exposed to light whilst ignoring the possible effects of this light on root development. Here, we investigated how direct root illumination affects root growth and development in Arabidopsis and tomato. Our results show that in light-grown Arabidopsis roots, activation of local phytochrome A and B by far-red or red light inhibits respectively PHYTOCHROME INTERACTING FACTORS 1 or 4, resulting in decreased YUCCA4 and YUCCA6 expression. As a result, auxin levels in the root apex become suboptimal, ultimately resulting in reduced growth of light-grown roots. These findings highlight once more the importance of using in vitro systems where roots are grown in darkness for studies that focus on root system architecture. Moreover, we show that the response and components of this mechanism are conserved in tomato roots, thus indicating its importance for horticulture as well. Our findings open up new research possibilities to investigate the importance of light-induced root growth inhibition for plant development, possibly by exploring putative correlations with responses to other abiotic signals, such as temperature, gravity, touch, or salt stress.

Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems

Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.

Light exposure of roots in aeroponics enhances the accumulation of phytochemicals in aboveground parts of the medicinal plants Artemisia annua and Hypericum perforatum

Light acts as a trigger to enhance the accumulation of secondary compounds in the aboveground part of plants; however, whether a similar triggering effect occurs in roots is unclear. Using an aeroponic setup, we investigated the effect of long-term exposure of roots to LED lighting of different wavelengths on the growth and phytochemical composition of two high-value medicinal plants, Artemisia annua and Hypericum perforatum. In A. annua, root exposure to white, blue, and red light enhanced the accumulation of artemisinin in the shoots by 2.3-, 2.5-, and 1.9-fold, respectively. In H. perforatum, root exposure to white, blue, red, and green light enhanced the accumulation of coumaroylquinic acid in leaves by 89, 65, 84, and 74%, respectively. Root lighting also increased flavonol concentrations. In contrast to its effects in the shoots, root illumination did not change phytochemical composition in the roots or root exudates. Thus, root illumination induces a systemic response, resulting in modulation of the phytochemical composition in distal tissues remote from the light exposure site.

Algal Ocelloids and Plant Ocelli

Vision is essential for most organisms, and it is highly variable across kingdoms and domains of life. The most known and understood form is animal and human vision based on eyes. Besides the wide diversity of animal eyes, some animals such as cuttlefish and cephalopods enjoy so-called dermal or skin vision. The most simple and ancient organ of vision is the cell itself and this rudimentary vision evolved in cyanobacteria. More complex are so-called ocelloids of dinoflagellates which are composed of endocellular organelles, acting as lens- and cornea/retina-like components. Although plants have almost never been included into the recent discussions on organismal vision, their plant-specific ocelli had already been proposed by Gottlieb Haberlandt already in 1905. Here, we discuss plant ocelli and their roles in plant-specific vision, both in the shoots and roots of plants. In contrast to leaf epidermis ocelli, which are distributed throughout leaf surface, the root apex ocelli are located at the root apex transition zone and serve the light-guided root navigation. We propose that the plant ocelli evolved from the algal ocelloids, are part of complex plant sensory systems and guide cognition-based plant behavior.

Signaling events for photomorphogenic root development

A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.

Reducing water uptake into BY-2 cells by systematically optimizing the cultivation parameters increases product yields achieved by transient expression in plant cell packs

Plant-based production systems are inexpensive and easy to handle, allowing them to complement existing platforms for the production of protein-based vaccines, therapeutics and diagnostic reagents. However, screening product candidates in whole plants requires a large facility footprint and is challenging due to natural variations in recombinant protein accumulation. In contrast, plant cell packs (PCPs) allow more than 1000 samples to be screened per day in microtiter plates. PCPs enable rapid development cycles based on transient expression in as little as 3 days, and yield milligram quantities of product for initial quality assessment and functional testing. However, this requires high-level expression in BY-2 cells and consistent cell quality across batches. We therefore used a statistical design of experiments (DoE) approach to systematically assess factors that contribute to consistent high yields of recombinant proteins in PCPs. Specifically, we tested the osmolality, pH, carbon source, light source and additives during cell cultivation, as well as cell and PCP harvest times. The careful adjustment of these factors increased overall productivity by approximately fourfold. Remarkably all cultivation conditions leading to high productivities during transient expression in PCPs were associated with limited water uptake into the central vacuole. The universal presence of a vacuole in plant cells indicates that our results should be transferrable to other cells lines. Our findings therefore support the broad application of PCPs for screening and product analysis during the development of protein-based pharmaceuticals and reagents in plants. This article is protected by copyright. All rights reserved.

Root growth direction in simulated microgravity is modulated by a light avoidance mechanism mediated by flavonols

In a microgravity environment, without any gravitropic signal, plants are not able to define and establish a longitudinal growth axis. Consequently, absorption of water and nutrients by the root and exposure of leaves to sunlight for efficient photosynthesis is hindered. In these conditions, other external cues can be explored to guide the direction of organ growth. Providing a unilateral light source can guide the shoot growth, but prolonged root exposure to light causes a stress response, affecting growth and development, and also affecting the response to other environmental factors. Here, we have investigated how the protection of the root from light exposure, while the shoot is illuminated, influences the direction of root growth in microgravity. We report that the light avoidance mechanism existing in roots guides their growth towards diminishing light and helps establish the proper longitudinal seedling axis in simulated microgravity conditions. This process is regulated by flavonols, as shown in the flavonoid-accumulating mutant transparent testa 3, which shows an increased correction of the root growth direction in microgravity, when the seedling is grown with the root protected from light. This finding may improve the efficiency of water and nutrient sourcing and photosynthesis under microgravity conditions, as they exist in space, contributing to better plant fitness and biomass production in space farming enterprises, necessary for space exploration by humans.

MSD2, an apoplastic Mn-SOD, contributes to root skotomorphogenic growth by modulating ROS distribution in Arabidopsis

Reactive oxygen species (ROS) play essential roles as a second messenger in various physiological processes in plants. Due to their oxidative nature, ROS can also be harmful. Thus, the generation and homeostasis of ROS are tightly controlled by multiple enzymes. Membrane-localized NADPH oxidases are well known to generate ROS during developmental and stress responses, but the metabolic pathways of the superoxide (O2^-) generated by them in the apoplast are poorly understood, and the identity of the apoplastic superoxide dismutase (SOD) is unknown in Arabidopsis. Here, we show that a putative manganese SOD, MSD2 is secreted and possesses a SOD activity that can be inhibited by nitration at tyrosine 68. The expression of MSD2 in roots is light condition-dependent, suggesting that MSD2 may act on ROS metabolism in roots during the light-to-dark transition. Root architecture is governed by ROS distribution that exhibits opposite gradient of H₂O₂ and O2^-, which is indeed altered in etiolated msd2 mutants and accompanied by changes in the onset of differentiation. These results provide a missing link in our understanding of ROS metabolism and suggest that MSD2 plays a role in root skotomorphogenesis by regulating ROS distribution, thereby playing a pivotal role in plant growth and development.

May the dark be with roots: a perspective on how root illumination may bias in vitro research on plant-environment interactions

Roots anchor plants to the soil, providing them with nutrients and water while creating a defence network and facilitating beneficial interactions with a multitude of living organisms and climatological conditions. To facilitate morphological and molecular studies, root research has been conducted using in vitro systems. However, under natural conditions, roots grow in the dark, mainly in the absence of illumination, except for the relatively low illumination of the upper soil surface, and this has been largely ignored. Here, we discuss the results found over the last decade on how experimental exposure of roots to light may bias root development and responses through the alteration of hormonal signalling, cytoskeleton organization, reactive oxygen species or the accumulation of flavonoids, among other factors. Illumination alters the uptake of nutrients or water, and also affects the response of the roots to abiotic stresses and root interactions with the microbiota. Furthermore, we review in vitro systems created to maintain roots in darkness, and provide a comparative analysis of root transcriptomes obtained with these devices. Finally, we identify other experimental variables that should be considered to better mimic soil conditions, whose improvement would benefit studies using in vitro cultivation or enclosed ecosystems.

Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination

The root is the below-ground organ of a plant, and it has evolved multiple signaling pathways that allow adaptation of architecture, growth rate, and direction to an ever-changing environment. Roots grow along the gravitropic vector towards beneficial areas in the soil to provide the plant with proper nutrients to ensure its survival and productivity. In addition, roots have developed escape mechanisms to avoid adverse environments, which include direct illumination. Standard laboratory growth conditions for basic research of plant development and stress adaptation include growing seedlings in Petri dishes on medium with roots exposed to light. Several studies have shown that direct illumination of roots alters their morphology, cellular and biochemical responses, which results in reduced nutrient uptake and adaptability upon additive stress stimuli. In this review, we summarize recent methods that allow the study of shaded roots under controlled laboratory conditions and discuss the observed changes in the results depending on the root illumination status.

Exogenous carbon source supplementation counteracts root and hypocotyl growth limitations under increased cotyledon shading, with glucose and sucrose differentially modulating growth curves

Plant growth is continuously modulated by endogenous and exogenous stimuli. By no means the only, but well described, signaling molecules produced in plants and distributed through the plant body to orchestrate efficient growth are photosynthates. Light is a potent exogenous stimulus that determines, first, the rate of photosynthesis, but also the rate of plant growth. Root meristem activity is reduced with direct illumination but enhanced with increased sugar levels. With reduced cotyledon illumination, the seedling increases hypocotyl elongation until adequate light exposure is again provided. If endogenous carbon sources are limited, this leads to a temporary inhibition of root growth. Experimental growth conditions include exogenous supplementation of sucrose or glucose in addition to culturing seedlings under light exposure in Petri dishes. We compared total root length and hypocotyl elongation of Arabidopsis thaliana wild type Col-0 in response to illumination status and carbon source in the growth medium. Overall, sucrose supplementation promoted hypocotyl and root length to a greater extent than glucose supplementation. Glucose promoted root length compared to non-supplemented seedlings especially when cotyledon illumination was greatly reduced.

PIN-mediated polar auxin transport regulations in plant tropic responses

Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underlie differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, as well as the crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.

Root developmental responses to phosphorus nutrition

Phosphorus is an essential macronutrient for plant growth and development. Root system architecture (RSA) affects a plant's ability to obtain phosphate, the major form of phosphorus that plants uptake. In this review, I first consider the relationship between RSA and plant phosphorus-acquisition efficiency, describe how external phosphorus conditions both induce and impose changes in the RSA of major crops and of the model plant Arabidopsis, and discuss whether shoot phosphorus status affects RSA and whether there is a universal root developmental response across all plant species. I then summarize the current understanding of the molecular mechanisms governing root developmental responses to phosphorus deficiency. I also explore the possible reasons for the inconsistent results reported by different research groups and comment on the relevance of some studies performed under laboratory conditions to what occurs in natural environments.

Anaesthetics and plants: from sensory systems to cognition-based adaptive behaviour

Plants are not only sensitive to exogenous anaesthetics, but they also produce multitudes of endogenous substances, especially when stressed, that often have anaesthetic and anelgesic properties when applied to both humans and animals. Moreover, plants rely on neurotransmitters and their receptors for cell-cell communication and integration in a similar fashion to the use of neural systems in animals and humans. Plants also use their plant-specific sensory systems and neurotransmitter-based communication, including long-distance action potentials, to manage stress via cognition-like plant-specific behaviour and adaptation.

Individuality, self and sociality of vascular plants

Vascular plants are integrated into coherent bodies via plant-specific synaptic adhesion domains, action potentials (APs) and other means of long-distance signalling running throughout the plant bodies. Plant-specific synapses and APs are proposed to allow plants to generate their self identities having unique ways of sensing and acting as agents with their own goals guiding their future activities. Plants move their organs with a purpose and with obvious awareness of their surroundings and require APs to perform and control these movements. Self-identities allow vascular plants to act as individuals enjoying sociality via their self/non-self-recognition and kin recognition. Flowering plants emerge as cognitive and intelligent organisms when the major strategy is to attract and control their animal pollinators as well as seed dispersers by providing them with food enriched with nutritive and manipulative/addictive compounds. Their goal in interactions with animals is manipulation for reproduction, dispersal and defence. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.

Dissecting Hierarchies between Light, Sugar and Auxin Action Underpinning Root and Root Hair Growth

Plant roots are very plastic and can adjust their tissue organization and cell appearance during abiotic stress responses. Previous studies showed that direct root illumination and sugar supplementation mask root growth phenotypes and traits. Sugar and light signaling where further connected to changes in auxin biosynthesis and distribution along the root. Auxin signaling underpins almost all processes involved in the establishment of root traits, including total root length, gravitropic growth, root hair initiation and elongation. Root hair plasticity allows maximized nutrient uptake and therefore plant productivity, and root hair priming and elongation require proper auxin availability. In the presence of sucrose in the growth medium, root hair emergence is partially rescued, but the full potential of root hair elongation is lost. With our work we describe a combinatory study showing to which extent light and sucrose are antagonistically influencing root length, but additively affecting root hair emergence and elongation. Furthermore, we investigated the impact of the loss of PIN-FORMED2, an auxin efflux carrier mediating shootward auxin transporter, on the establishment of root traits in combination with all growth conditions.

Effects of Light Intensity on Root Development in a D-Root Growth System

Plant development is highly affected by light quality, direction, and intensity. Under natural growth conditions, shoots are directly exposed to light whereas roots develop underground shielded from direct illumination. The photomorphogenic development strongly represses shoot elongation whereas promotes root growth. Over the years, several studies helped the elucidation of signaling elements that coordinate light perception and underlying developmental outputs. Light exposure of the shoots has diverse effects on main root growth and lateral root (LR) formation. In this study, we evaluated the phenotypic root responses of wild-type Arabidopsis plants, as well as several mutants, grown in a D-Root system. We observed that sucrose and light act synergistically to promote root growth and that sucrose alone cannot overcome the light requirement for root growth. We also have shown that roots respond to the light intensity applied to the shoot by changes in primary and LR development. Loss-of-function mutants for several root light-response genes display varying phenotypes according to the light intensity to which shoots are exposed. Low light intensity strongly impaired LR development for most genotypes. Only vid-27 and pils4 mutants showed higher LR density at 40 μmol m^-2 s^-1 than at 80 μmol m^-2 s^-1 whereas yuc3 and shy2-2 presented no LR development in any light condition, reinforcing the importance of auxin signaling in light-dependent root development. Our results support the use of D-Root systems to avoid the effects of direct root illumination that might lead to artifacts and unnatural phenotypic outputs.

Halotropism: Phytohormonal Aspects and Potential Applications

Halotropism is a sodium specific tropic movement of roots in order to obtain the optimal salt concentration for proper growth and development. Numerous results suggest that halotropic events are under the control and regulation of complex plant hormone pathway. This minireview collects some recent evidences about sodium sensing during halotropism and the hormonal regulation of halotropic responses in glycophytes. The precise hormonal mechanisms by which halophytes plant roots perceive salt stress and translate this perception into adaptive, directional growth forward increased salt concentrations are not well understood. This minireview aims to gather recently deciphered information about halotropism focusing potential hormonal aspects both in glycophytes and halophytes. Advances in our understanding of halotropic responses in different plant species could help these plants to be used for sustainable agriculture and other future applications.

Root-Apex Proton Fluxes at the Centre of Soil-Stress Acclimation

Proton (H⁺) fluxes in plant roots play critical roles in maintaining root growth and facilitating plant responses to multiple soil stresses, including fluctuations in nutrient supply, salt infiltration, and water stress. Soil mining for nutrients and water, rates of nutrient uptake, and the modulation of cell expansion all depend on the regulation of root H⁺ fluxes, particularly at the root apex, mediated primarily by the activity of plasma membrane (PM) H⁺-ATPases. Here, we summarize recent findings on the regulatory mechanisms of H⁺ fluxes at the root apex under three abiotic stress conditions - phosphate deficiency, salinity stress, and water deficiency - and present an integrated physiomolecular view of the functions of H⁺ fluxes in maintaining root growth in the acclimation to soil stress.

The platform GrowScreen-Agar enables identification of phenotypic diversity in root and shoot growth traits of agar grown plants

BACKGROUND

Root system architecture and especially its plasticity in acclimation to variable environments play a crucial role in the ability of plants to explore and acquire efficiently soil resources and ensure plant productivity. Non-destructive measurement methods are indispensable to quantify dynamic growth traits. For closing the phenotyping gap, we have developed an automated phenotyping platform, GrowScreen-Agar, for non-destructive characterization of root and shoot traits of plants grown in transparent agar medium.

RESULTS

The phenotyping system is capable to phenotype root systems and correlate them to whole plant development of up to 280 Arabidopsis plants within 15 min. The potential of the platform has been demonstrated by quantifying phenotypic differences within 78 Arabidopsis accessions from the 1001 genomes project. The chosen concept 'plant-to-sensor' is based on transporting plants to the imaging position, which allows for flexible experimental size and design. As transporting causes mechanical vibrations of plants, we have validated that daily imaging, and consequently, moving plants has negligible influence on plant development. Plants are cultivated in square Petri dishes modified to allow the shoot to grow in the ambient air while the roots grow inside the Petri dish filled with agar. Because it is common practice in the scientific community to grow Arabidopsis plants completely enclosed in Petri dishes, we compared development of plants that had the shoot inside with that of plants that had the shoot outside the plate. Roots of plants grown completely inside the Petri dish grew 58% slower, produced a 1.8 times higher lateral root density and showed an etiolated shoot whereas plants whose shoot grew outside the plate formed a rosette. In addition, the setup with the shoot growing outside the plate offers the unique option to accurately measure both, leaf and root traits, non-destructively, and treat roots and shoots separately.

CONCLUSIONS

Because the GrowScreen-Agar system can be moved from one growth chamber to another, plants can be phenotyped under a wide range of environmental conditions including future climate scenarios. In combination with a measurement throughput enabling phenotyping a large set of mutants or accessions, the platform will contribute to the identification of key genes.

Hormone profile changes occur in roots and leaves of Micro-Tom tomato plants when exposing the aerial part to low doses of UV-B radiation

During the last decades, many studies investigated the effects of UV-B on the above-ground organs of plants, directly reached by the radiation but, to the best of our knowledges, the influence of mild UV-B doses on root hormones was not explored. Consequently, this research aimed at understanding whether low, not-stressful doses of UV-B radiation applied above-ground influenced the hormone concentrations in leaves and roots of Micro-Tom tomato (Solanum lycopersicum L.) plants during 11 days of treatment and after 3 days of recovery. In particular, ethylene, abscisic acid, jasmonic acid, salicylic acid and indoleacetic acid were investigated. The unchanged levels of chlorophyll a and b, lutein, total xanthophylls and carotenoids, as well as the similar H₂O₂ concentration between control and treated groups suggest that the UV-B dose applied was well tolerated by the plants. Leaf ethylene emission decreased after 8 and 11 days of irradiation, while no effect was found in roots. Conversely, indoleacetic acid underwent a significant reduction in both organs, though in the roots the decrease occurred only at the end of the recovery period. Salicylic acid increased transiently in both leaves and roots on day 8. Changes in leaf and root hormone levels induced by UV-B radiation were not accompanied by marked alterations of plant architecture. The results show that irradiation of above-ground organs with low UV-B doses can affect the hormone concentrations also in roots, with likely implications in stress and acclimation responses mediated by these signal molecules.

Blue Light-Triggered Chemical Reactions Underlie Phosphate Deficiency-Induced Inhibition of Root Elongation of Arabidopsis Seedlings Grown in Petri Dishes

To tolerate phosphate (Pi) deficiency in the environment, plants alter their developmental and metabolic programs. In the past two decades, researchers have extensively used Petri dish-grown seedlings of the model plant Arabidopsis thaliana to study the molecular mechanisms underlying root developmental responses to Pi deficiency. A typical developmental response of the Petri dish-grown Arabidopsis seedlings to Pi deficiency is the inhibited growth of primary root (PR). This response is generally thought to enhance the production of lateral roots and root hairs, which increases the plant's ability to obtain Pi and is therefore regarded as an active cellular response. Here, we report that direct illumination of root surface with blue light is critical and sufficient for Pi deficiency-induced inhibition of PR growth in Arabidopsis seedlings. We further show that a blue light-triggered malate-mediated photo-Fenton reaction and a canonical Fenton reaction form an Fe redox cycle in the root apoplast. This Fe redox cycle results in the production of hydroxyl radicals that inhibit PR growth. In addition to revealing the molecular mechanism underlying Pi deficiency-induced inhibition of PR growth, our work demonstrated that this developmental change is not an active cellular response; instead, it is a phenotype resulting from root growth in transparent Petri dishes. This finding is significant because illuminated, transparent Petri dishes have been routinely used to study Arabidopsis root responses to environmental changes.

A perspective on ecologically relevant plant-UV research and its practical application

Plants perceive ultraviolet-B (UV-B) radiation through the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8), and initiate regulatory responses via associated signalling networks, gene expression and metabolic pathways. Various regulatory adaptations to UV-B radiation enable plants to harvest information about fluctuations in UV-B irradiance and spectral composition in natural environments, and to defend themselves against UV-B exposure. Given that UVR8 is present across plant organs and tissues, knowledge of the systemic signalling involved in its activation and function throughout the plant is important for understanding the context of specific responses. Fine-scale understanding of both UV-B irradiance and perception within tissues and cells requires improved application of knowledge about UV-attenuation in leaves and canopies, warranting greater consideration when designing experiments. In this context, reciprocal crosstalk among photoreceptor-induced pathways also needs to be considered, as this appears to produce particularly complex patterns of physiological and morphological response. Through crosstalk, plant responses to UV-B radiation go beyond simply UV-protection or amelioration of damage, but may give cross-protection over a suite of environmental stressors. Overall, there is emerging knowledge showing how information captured by UVR8 is used to regulate molecular and physiological processes, although understanding of upscaling to higher levels of organisation, i.e. organisms, canopies and communities remains poor. Achieving this will require further studies using model plant species beyond Arabidopsis, and that represent a broad range of functional types. More attention should also be given to plants in natural environments in all their complexity, as such studies are needed to acquire an improved understanding of the impact of climate change in the context of plant-UV responses. Furthermore, broadening the scope of experiments into the regulation of plant-UV responses will facilitate the application of UV radiation in commercial plant production. By considering the progress made in plant-UV research, this perspective highlights prescient topics in plant-UV photobiology where future research efforts can profitably be focussed. This perspective also emphasises burgeoning interdisciplinary links that will assist in understanding of UV-B effects across organisational scales and gaps in knowledge that need to be filled so as to achieve an integrated vision of plant responses to UV-radiation.

Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile

Arabidopsis is used as a model species in numerous physiological and genetic studies. Most of them employ parafilm-wrapped sterile culture. Here we demonstrate that this method is prone to potential artifacts and can lead to erroneous conclusions. We compared the effect of different sealing methods including air-permeable paper tape and traditional parafilm on Arabidopsis seedling growth, root development and gene expression network. Although seedlings grown in Petri dishes after 1 week sealed with paper tape showed a similar growth phenotype to that of parafilm-sealed seedlings, more than 700 differentially expressed genes (DEG) were found, including stress and nutrition-responsive genes. In addition, more H₂O₂ was accumulated in the tissues of parafilm-sealed plants. After 14 days of growth, paper tape-sealed plants grew much better than parafilm-sealed ones and accumulated higher chlorophyll content, with 490 DEGs found. After 3 weeks of growth, paper tape-sealed plants had higher chlorophyll and better growth compared to parafilm-sealed ones; and only 10 DEGs were found at this stage. Thus, the obvious phenotype observed at the latter stage was a result of differential gene expression at earlier time points, mostly of defense, abiotic stress, nutrition, and phytohormone-responsive genes. More O₂ content was detected inside paper tape-sealed Petri dishes at early growth stage (7 days), and distinct difference in the CO₂ content was observed between parafilm-sealed and paper tape-sealed Petri dishes. Furthermore, the carbon source also influenced seedlings growth with different sealing methods. In conclusion, conventional sealing using parafilm was not the optimal choice, most likely because of the limited gas exchange and a consequent stress caused to plants.

Root Tropisms: Investigations on Earth and in Space to Unravel Plant Growth Direction

Root tropisms are important responses of plants, allowing them to adapt their growth direction. Research on plant tropisms is indispensable for future space programs that envisage plant-based life support systems for long-term missions and planet colonization. Root tropisms encompass responses toward or away from different environmental stimuli, with an underexplored level of mechanistic divergence. Research into signaling events that coordinate tropistic responses is complicated by the consistent coincidence of various environmental stimuli, often interacting via shared signaling mechanisms. On Earth the major determinant of root growth direction is the gravitational vector, acting through gravitropism and overruling most other tropistic responses to environmental stimuli. Critical advancements in the understanding of root tropisms have been achieved nullifying the gravitropic dominance with experiments performed in the microgravity environment. In this review, we summarize current knowledge on root tropisms to different environmental stimuli. We highlight that the term tropism must be used with care, because it can be easily confused with a change in root growth direction due to asymmetrical damage to the root, as can occur in apparent chemotropism, electrotropism, and magnetotropism. Clearly, the use of Arabidopsis thaliana as a model for tropism research contributed much to our understanding of the underlying regulatory processes and signaling events. However, pronounced differences in tropisms exist among species, and we argue that these should be further investigated to get a more comprehensive view of the signaling pathways and sensors. Finally, we point out that the Cholodny-Went theory of asymmetric auxin distribution remains to be the central and unifying tropistic mechanism after 100 years. Nevertheless, it becomes increasingly clear that the theory is not applicable to all root tropistic responses, and we propose further research to unravel commonalities and differences in the molecular and physiological processes orchestrating root tropisms.

HY5 Contributes to Light-Regulated Root System Architecture Under a Root-Covered Culture System

Light is essential for plant organogenesis and development. Light-regulated shoot morphogenesis has been extensively studied; however, the mechanisms by which plant roots perceive and respond to aboveground light are largely unknown, particularly because the roots of most terrestrial plants are usually located underground in darkness. To mimic natural root growth conditions, we developed a root-covered system (RCS) in which the shoots were illuminated and the plant roots could be either exposed to light or cultivated in darkness. Using the RCS, we observed that root growth of wild-type plants was significantly promoted when the roots were in darkness, whereas it was inhibited by direct light exposure. This growth change seems to be regulated by ELONGATED HYPOCOTYL 5 (HY5), a master regulator of photomorphogenesis. Light was found to regulate HY5 expression in the roots, while a HY5 deficiency partially abolished the inhibition of growth in roots directly exposed to light, suggesting that HY5 expression is induced by direct light exposure and inhibits root growth. However, no differences in HY5 expression were observed between illuminated and dark-grown cop1 roots, indicating that HY5 may be regulated by COP1-mediated proteasome degradation. We confirmed the crucial role of HY5 in regulating root development in response to light under soil-grown conditions. A transcriptomic analysis revealed that light controls the expression of numerous genes involved in phytohormone signaling, stress adaptation, and metabolic processes in a HY5-dependent manner. In combination with the results of the flavonol quantification and exogenous quercetin application, these findings suggested that HY5 regulates the root response to light through a complex network that integrates flavonol biosynthesis and reactive oxygen species signaling. Collectively, our results indicate that HY5 is a master regulator of root photomorphogenesis.

Root-expressed phytochromes B1 and B2, but not PhyA and Cry2, regulate shoot growth in nature

Although photoreceptors are expressed throughout all plant organs, most studies have focused on their function in aerial parts with laboratory-grown plants. Photoreceptor function in naturally dark-grown roots of plants in their native habitats is lacking. We characterized patterns of photoreceptor expression in field- and glasshouse-grown Nicotiana attenuata plants, silenced the expression of PhyB1/B2/A/Cry2 whose root transcripts levels were greater/equal to those of shoots, and by micrografting combined empty vector transformed shoots onto photoreceptor-silenced roots, creating chimeric plants with "blind" roots but "sighted" shoots. Micrografting procedure was robust in both field and glasshouse, as demonstrated by transcript accumulation patterns, and a spatially-explicit lignin visual reporter chimeric line. Field- and glasshouse-grown plants with PhyB1B2, but not PhyA or Cry2, -blind roots, were delayed in stalk elongation compared with control plants, robustly for two field seasons. Wild-type plants with roots directly exposed to FR phenocopied the growth of irPhyB1B2-blind root grafts. Additionally, root-expressed PhyB1B2 was required to activate the positive photomorphogenic regulator, HY5, in response to aboveground light. We conclude that roots of plants growing deep into the soil in nature sense aboveground light, and possibly soil temperature, via PhyB1B2 to control key traits, such as stalk elongation.

Shoot phytochrome B modulates reactive oxygen species homeostasis in roots via abscisic acid signaling in Arabidopsis

Underground roots normally reside in darkness. However, they are often exposed to ambient light that penetrates through cracks in the soil layers which can occur due to wind, heavy rain or temperature extremes. In response to light exposure, roots produce reactive oxygen species (ROS) which promote root growth. It is known that ROS-induced growth promotion facilitates rapid escape of the roots from non-natural light. Meanwhile, long-term exposure of the roots to light elicits a ROS burst, which causes oxidative damage to cellular components, necessitating that cellular levels of ROS should be tightly regulated in the roots. Here we demonstrate that the red/far-red light photoreceptor phytochrome B (phyB) stimulates the biosynthesis of abscisic acid (ABA) in the shoots, and notably the shoot-derived ABA signals induce a peroxidase-mediated ROS detoxification reaction in the roots. Accordingly, while ROS accumulate in the roots of the phyb mutant that exhibits reduced primary root growth in the light, such an accumulation of ROS did not occur in the dark-grown phyb roots that exhibited normal growth. These observations indicate that mobile shoot-to-root ABA signaling links shoot phyB-mediated light perception with root ROS homeostasis to help roots adapt to unfavorable light exposure. We propose that ABA-mediated shoot-to-root phyB signaling contributes to the synchronization of shoot and root growth for optimal propagation and performance in plants.

Effect of light on the kinetics and equilibrium of the textile dye (Reactive Red 120) adsorption by Helianthus annuus hairy roots

The study demonstrates for the first time that light influences the adsorption equilibrium and kinetics of a dye by root culture system. The azo dye (Reactive Red 120) adsorption by the hairy roots of H. annuus followed a pseudo first-order kinetic model and the adsorption equilibrium parameters were best estimated using Langmuir isotherm. The maximum dye adsorption capacity of the roots increased 6-fold, from 0.26 mg g^-1 under complete dark conditions to 1.51 mg g^-1 under 16/8 h light/dark photoperiod. Similarly, adsorption rate of the dye and removal (%) also increased in the presence of light, irrespective of the initial concentration of the dye (20-110 mg L^-1). The degradation of the azo dye upon adsorption by the hairy roots of H. annuus was also confirmed. In addition, a strategy for simultaneous dye removal and increased alpha-tocopherol (industrially relevant) production by H. annuus hairy root cultures has been proposed and demonstrated.

Compound Synthesis or Growth and Development of Roots/Stomata Regulate Plant Drought Tolerance or Water Use Efficiency/Water Uptake Efficiency

Water is crucial to plant growth and development because it serves as a medium for all cellular functions. Thus, the improvement of plant drought tolerance or water use efficiency/water uptake efficiency is important in modern agriculture. In this review, we mainly focus on new genetic factors for ameliorating drought tolerance or water use efficiency/water uptake efficiency of plants and explore the involvement of these genetic factors in the regulation of improving plant drought tolerance or water use efficiency/water uptake efficiency, which is a result of altered stomata density and improving root systems (primary root length, hair root growth, and lateral root number) and enhanced production of osmotic protectants, which is caused by transcription factors, proteinases, and phosphatases and protein kinases. These results will help guide the synthesis of a model for predicting how the signals of genetic and environmental stress are integrated at a few genetic determinants to control the establishment of either water use efficiency or water uptake efficiency. Collectively, these insights into the molecular mechanism underpinning the control of plant drought tolerance or water use efficiency/water uptake efficiency may aid future breeding or design strategies to increase crop yield.

Sense of space: Tactile sense for exploratory behavior of roots

In soil, plant roots grow in heterogeneous environments. Plant roots are always facing the difficulty of searching effectively the patchy natural resources, such as water, oxygen, ions and mineral nutrition. Numerous studies reported that root apex navigation enables roots to explore complex environments. In this short communication, we characterize how growing maize roots explore narrow space available with two experimental settings: tactile exploration of narrow glass tube and circumnutation in free space. We also discuss root growth in the soil in terms of foraging behavior guided by the sensory root apex.

Abscisic acid-mediated phytochrome B signaling promotes primary root growth in Arabidopsis

Plant photomorphogenic responses have been studied mostly using the shoots, the core part of plant architecture that perceives light for photosynthesis and influences the overall processes of growth and development. While the roots are also known to respond to aboveground light through multiple routes of light signal transduction, root photomorphogenesis has been less highlighted until recently. A long-standing, critical question was how the underground roots are capable of sensing aerial light and how the root-sensed light signals trigger root photomorphogenesis. When the roots are directly exposed to light, reactive oxygen species (ROS) are rapidly produced to promote primary root elongation, which helps the roots to escape from the abnormal growth conditions. However, severe or long-term exposure of the roots to light causes ROS burst, which impose oxidative damages, leading to a reduction of root growth. We have recently found that phytochrome B (phyB) promotes abscisic acid (ABA) biosynthesis in the shoots and the shoot-derived ABA signals mediate ROS detoxification in the roots, lessening the detrimental effects of light on root growth. On the basis of these observations we propose that the phyB-mediated ABA signaling contributes to the shoot-root synchronization that is essential for optimal growth and performance in plants.

Dissection of HY5/HYH expression in Arabidopsis reveals a root-autonomous HY5-mediated photomorphogenic pathway

ELONGATED HYPOCOTYL 5 (HY5), a member of the bZIP gene family, is a positive regulator of the light signaling pathway in Arabidopsis thaliana. Whereas the hy5 mutant exhibits an elongated hypocotyl when grown in the light, the hy5 homolog (hyh) mutant does not. Although the functions of HY5 and HYH in light-mediated seedling development have been revealed, the tissue-specific expression patterns of HY5 and HYH and their interconnected regulation are largely unknown. Here, we report that HY5 regulates HYH expression in roots and contributes to root growth under different light conditions. We generated HY5 and HYH transcriptional and translational fusion reporter lines to investigate their expression patterns. HY5 was constitutively expressed in all root tissues, while HYH was predominantly expressed in root xylem cells. Root growth after a dark-to-light transition was perturbed in the hy5 and hy5hyh mutant lines, but not in the hyh mutant line, indicating that HY5 plays a major role in light-regulated root growth. Light-induced HY5/HYH expression occurred autonomously in roots. HYH expression in roots was decreased in the hy5 mutant, suggesting that HY5 regulates HYH expression. Collectively, these results indicate that an organ-specific HY5-mediated pathway controls root photomorphogenic development independently of light signaling in the shoot.

Predicting green: really radical (plant) predictive processing

In this article we account for the way plants respond to salient features of their environment under the free-energy principle for biological systems. Biological self-organization amounts to the minimization of surprise over time. We posit that any self-organizing system must embody a generative model whose predictions ensure that (expected) free energy is minimized through action. Plants respond in a fast, and yet coordinated manner, to environmental contingencies. They pro-actively sample their local environment to elicit information with an adaptive value. Our main thesis is that plant behaviour takes place by way of a process (active inference) that predicts the environmental sources of sensory stimulation. This principle, we argue, endows plants with a form of perception that underwrites purposeful, anticipatory behaviour. The aim of the article is to assess the prospects of a radical predictive processing story that would follow naturally from the free-energy principle for biological systems; an approach that may ultimately bear upon our understanding of life and cognition more broadly.

Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods

Roots of Arabidopsis thaliana seedlings grown in the laboratory using the traditional plant-growing culture system (TPG) were covered to maintain them in darkness. This new method is based on a dark chamber and is named the improved plant-growing method (IPG). We measured the light conditions in dark chambers, and found that the highest light intensity was dramatically reduced deeper in the dark chamber. In the bottom and side parts of dark chambers, roots were almost completely shaded. Using the high-throughput RNA sequencing method on the whole RNA extraction from roots, we compared the global gene expression levels in roots of seedlings from these two conditions and identified 141 differently expressed genes (DEGs) between them. According to the KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment, the flavone and flavonol biosynthesis and flavonoid biosynthesis pathways were most affected among all annotated pathways. Surprisingly, no genes of known plant photoreceptors were identified as DEGs by this method. Considering that the light intensity was decreased in the IPG system, we collected four sections (1.5 cm for each) of Arabidopsis roots grown in TPG and IPG conditions, and the spatial-related differential gene expression levels of plant photoreceptors and polar auxin transporters, including CRY1, CRY2, PHYA, PHYB, PHOT1, PHOT2, and UVR8 were analyzed by qRT-PCR. Using these results, we generated a map of the spatial-related expression patterns of these genes under IPG and TPG conditions. The expression levels of light-related genes in roots is highly sensitive to illumination and it provides a background reference for selecting an improved culture method for laboratory-maintained Arabidopsis seedlings.

Skewing in Arabidopsis roots involves disparate environmental signaling pathways

BACKGROUND

Skewing root patterns provide key insights into root growth strategies and mechanisms that produce root architectures. Roots exhibit skewing and waving when grown on a tilted, impenetrable surface. The genetics guiding these morphologies have been examined, revealing that some Arabidopsis ecotypes skew and wave (e.g. WS), while others skew insignificantly but still wave (e.g. Col-0). The underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing.

RESULTS

This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling.

CONCLUSIONS

This study identified 11 genes whose change in expression level is associated with root skewing behavior. These genes are involved in signaling and perception, rather than the physical restructuring of root. Future work is needed to elucidate the potential role of these candidate genes during root skewing.

A Soil-Plate Based Pipeline for Assessing Cereal Root Growth in Response to Polyethylene Glycol (PEG)-Induced Water Deficit Stress

Drought is a serious problem that causes losses in crop-yield every year, but the mechanisms underlying how roots respond to water deficit are difficult to study under controlled conditions. Methods for assaying root elongation and architecture, especially for seedlings, are commonly achieved on artificial media, such as agar, moistened filter paper, or in hydroponic systems. However, it has been demonstrated that measuring root characteristics under such conditions does not accurately mimic what is observed when plants are grown in soil. Morphological changes in root behavior occur because of differences in solute diffusion, mechanical impedance, exposure to light (in some designs), and gas exchange of roots grown under these conditions. To address such deficiencies, we developed a quantitative method for assaying seedling root lengths and germination in soil using a plate-based approach with wheat as a model crop. We also further developed the method to include defined water deficits stress levels using the osmotic properties of polyethylene glycol (PEG). Seeds were sown into soil-filled vertical plates and grown in the dark. Root length measurements were collected using digital photography through the transparent lid under green lighting to avoid effects of white light exposure on growth. Photographs were analyzed using the cross-platform ImageJ plugin, SmartRoot, which can detect root edges and partially automate root detection for extraction of lengths. This allowed for quick measurements and straightforward and accurate assessments of non-linear roots. Other measurements, such as root width or angle, can also be collected by this method. An R function was developed to collect exported root length data, process and reformat the data, and output plots depicting root/shoot growth dynamics. For water deficit experiments, seedlings were transplanted side-by-side into well-watered plates and plates containing PEG solutions to simulate precise water deficits.

Root cap-dependent gravitropic U-turn of maize root requires light-induced auxin biosynthesis via the YUC pathway in the root apex

Gravitropism refers to the growth or movement of plants that is influenced by gravity. Roots exhibit positive gravitropism, and the root cap is thought to be the gravity-sensing site. In some plants, the root cap requires light irradiation for positive gravitropic responses. However, the mechanisms regulating this phenomenon are unknown. We herein report that maize roots exposed to white light continuously for ≥1-2h show increased indole-3-acetic acid (IAA) levels in the root tips, especially in the transition zone (1-3mm from the tip). Treatment with IAA biosynthesis inhibitors yucasin and l-kynurenine prevented any increases in IAA content and root curvature under light conditions. Analyses of the incorporation of a stable isotope label from tryptophan into IAA revealed that some of the IAA in roots was synthesized in the root apex. Furthermore, Zmvt2 and Zmyuc gene transcripts were detected in the root apex. One of the Zmyuc genes (ZM2G141383) was up-regulated by light irradiation in the 0-1mm tip region. Our findings suggest that IAA accumulation in the transition zone is due to light-induced activation of Zmyuc gene expression in the 0-1mm root apex region. Light-induced changes in IAA levels and distributions mediate the maize root gravitropic U-turn.

On Having No Head: Cognition throughout Biological Systems

The central nervous system (CNS) underlies memory, perception, decision-making, and behavior in numerous organisms. However, neural networks have no monopoly on the signaling functions that implement these remarkable algorithms. It is often forgotten that neurons optimized cellular signaling modes that existed long before the CNS appeared during evolution, and were used by somatic cellular networks to orchestrate physiology, embryonic development, and behavior. Many of the key dynamics that enable information processing can, in fact, be implemented by different biological hardware. This is widely exploited by organisms throughout the tree of life. Here, we review data on memory, learning, and other aspects of cognition in a range of models, including single celled organisms, plants, and tissues in animal bodies. We discuss current knowledge of the molecular mechanisms at work in these systems, and suggest several hypotheses for future investigation. The study of cognitive processes implemented in aneural contexts is a fascinating, highly interdisciplinary topic that has many implications for evolution, cell biology, regenerative medicine, computer science, and synthetic bioengineering.

Flavonols Mediate Root Phototropism and Growth through Regulation of Proliferation-to-Differentiation Transition

Roots normally grow in darkness, but they may be exposed to light. After perceiving light, roots bend to escape from light (root light avoidance) and reduce their growth. How root light avoidance responses are regulated is not well understood. Here, we show that illumination induces the accumulation of flavonols in Arabidopsis thaliana roots. During root illumination, flavonols rapidly accumulate at the side closer to light in the transition zone. This accumulation promotes asymmetrical cell elongation and causes differential growth between the two sides, leading to root bending. Furthermore, roots illuminated for a long period of time accumulate high levels of flavonols. This high flavonol content decreases both auxin signaling and PLETHORA gradient as well as superoxide radical content, resulting in reduction of cell proliferation. In addition, cytokinin and hydrogen peroxide, which promote root differentiation, induce flavonol accumulation in the root transition zone. As an outcome of prolonged light exposure and flavonol accumulation, root growth is reduced and a different root developmental zonation is established. Finally, we observed that these differentiation-related pathways are required for root light avoidance. We propose that flavonols function as positional signals, integrating hormonal and reactive oxygen species pathways to regulate root growth direction and rate in response to light.

MES Buffer Affects Arabidopsis Root Apex Zonation and Root Growth by Suppressing Superoxide Generation in Root Apex

In plants, growth of roots and root hairs is regulated by the fine cellular control of pH and reactive oxygen species (ROS). MES, 2-(N-morpholino)ethanesulfonic acid as one of the Good's buffers has broadly been used for buffering medium, and it is thought to suit for plant growth with the concentration at 0.1% (w/v) because the buffer capacity of MES ranging pH 5.5-7.0 (for Arabidopsis, pH 5.8). However, many reports have shown that, in nature, roots require different pH values on the surface of specific root apex zones, namely meristem, transition zone, and elongation zone. Despite the fact that roots always grow on a media containing buffer molecule, little is known about impact of MES on root growth. Here, we have checked the effects of different concentrations of MES buffer using growing roots of Arabidopsis thaliana. Our results show that 1% of MES significantly inhibited root growth, the number of root hairs and length of meristem, whereas 0.1% promoted root growth and root apex area (region spanning from the root tip up to the transition zone). Furthermore, superoxide generation in root apex disappeared at 1% of MES. These results suggest that MES disturbs normal root morphogenesis by changing the ROS homeostasis in root apex.

The Arabidopsis ANGUSTIFOLIA3-YODA Gene Cascade Induces Anthocyanin Accumulation by Regulating Sucrose Levels

Anthocyanin accumulation specifically depends on sucrose (Suc) signaling/levels. However, the gene cascades specifically involved in the Suc signaling/level-mediated anthocyanin biosynthetic pathway are still unknown. Arabidopsis ANGUSTIFOLIA3 (AN3), a transcription coactivator, is involved in the regulation of leaf shape and drought tolerance. Recently, an AN3-CONSTITUTIVE PHOTOMORPHOGENIC 1 gene cascade has been reported to regulate the light signaling-mediated anthocyanin accumulation. Target gene analysis indicates that AN3 is associated with the YODA (YDA) promoter, a mitogen-activated protein kinase kinase kinase, in vivo for inducing anthocyanin accumulation. Indeed, loss-of-function mutants of YDA showed significantly increased anthocyanin accumulation. YDA mutation can also suppress the decrease in an3-4 anthocyanin accumulation. Further analysis indicates that the mutations of AN3 and YDA disrupt the normal Suc levels because of the changes of invertase activity in mutants of an3 or yda, which in turn induces the alterations of anthocyanin accumulation in mutants of an3 or yda via unknown regulatory mechanisms.

The TOR Complex: An Emergency Switch for Root Behavior

Target of rapamycin (TOR) kinase is known to be a controller of cell growth and aging, which determines the fine balance between growth rates and energy availabilities. It has been reported that many eukaryotes express TOR genes. In plants, TOR signaling modifies growth and development in response to a plant's energy status. An example of TOR action can be found in the root apices, which are active organs that explore the soil environment via vigorous growth and numerous tropisms. The exploratory nature of root apices requires a large energy supply for signaling, as well as for cell division and elongation. In the case of negative tropisms, roots must respond quickly to avoid patches of unfavorable soil conditions, again by consuming precious energy reserves. Here we review the current findings on TOR signaling in plants and animals, and propose possible roles for this important complex in driving plant root negative tropisms, particularly during light escape and salt avoidance behavior.

D-Root: a system for cultivating plants with the roots in darkness or under different light conditions

In nature roots grow in the dark and away from light (negative phototropism). However, most current research in root biology has been carried out with the root system grown in the presence of light. Here, we have engineered a device, called Dark-Root (D-Root), to grow plants in vitro with the aerial part exposed to the normal light/dark photoperiod while the roots are in the dark or exposed to specific wavelengths or light intensities. D-Root provides an efficient system for cultivating a large number of seedlings and easily characterizing root architecture in the dark. At the morphological level, root illumination shortens root length and promotes early emergence of lateral roots, therefore inducing expansion of the root system. Surprisingly, root illumination also affects shoot development, including flowering time. Our analyses also show that root illumination alters the proper response to hormones or abiotic stress (e.g. salt or osmotic stress) and nutrient starvation, enhancing inhibition of root growth. In conclusion, D-Root provides a growing system closer to the natural one for assaying Arabidopsis plants, and therefore its use will contribute to a better understanding of the mechanisms involved in root development, hormonal signaling and stress responses.