Analyses of tropistic responses using metabolomics

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.

Plant Gravitropism: From Mechanistic Insights into Plant Function on Earth to Plants Colonizing Other Worlds

Gravitropism, the growth of roots and shoots toward or away from the direction of gravity, has been studied for centuries. Such studies have not only led to a better understanding of the gravitropic process itself, but also paved new paths leading to deeper mechanistic insights into a wide range of research areas. These include hormone biology, cell signal transduction, regulation of gene expression, plant evolution, and plant interactions with a variety of environmental stimuli. In addition to contributions to basic knowledge about how plants function, there is accumulating evidence that gravitropism confers adaptive advantages to crops, particularly under marginal agricultural soils. Therefore, gravitropism is emerging as a breeding target for enhancing agricultural productivity. Moreover, research on gravitropism has spawned several studies on plant growth in microgravity that have enabled researchers to uncouple the effects of gravity from other tropisms. Although rapid progress on understanding gravitropism witnessed during the past decade continues to be driven by traditional molecular, physiological, and cell biological tools, these tools have been enriched by technological innovations in next-generation omics platforms and microgravity analog facilities. In this chapter, we review the field of gravitropism by highlighting recent landmark studies that have provided unique insights into this classic research topic while also discussing potential contributions to agriculture on Earth and beyond.

Brassinosteroids Influence Arabidopsis Hypocotyl Graviresponses through Changes in Mannans and Cellulose

The force of gravity is a constant environmental factor. Plant shoots respond to gravity through negative gravitropism and gravity resistance. These responses are essential for plants to direct the growth of aerial organs away from the soil surface after germination and to keep an upright posture above ground. We took advantage of the effect of brassinosteroids (BRs) on the two types of graviresponses in Arabidopsis thaliana hypocotyls to disentangle functions of cell wall polymers during etiolated shoot growth. The ability of etiolated Arabidopsis seedlings to grow upward was suppressed in the presence of 24-epibrassinolide (EBL) but enhanced in the presence of brassinazole (BRZ), an inhibitor of BR biosynthesis. These effects were accompanied by changes in cell wall mechanics and composition. Cell wall biochemical analyses, confocal microscopy of the cellulose-specific pontamine S4B dye and cellular growth analyses revealed that the EBL and BRZ treatments correlated with changes in cellulose fibre organization, cell expansion at the hypocotyl base and mannan content. Indeed, a longitudinal reorientation of cellulose fibres and growth inhibition at the base of hypocotyls supported their upright posture whereas the presence of mannans reduced gravitropic bending. The negative effect of mannans on gravitropism is a new function for this class of hemicelluloses. We also found that EBL interferes with upright growth of hypocotyls through their uneven thickening at the base.

Exploration of space to achieve scientific breakthroughs

Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.

Challenging current interpretation of sunflower movements

In the literature, Helianthus annuus L. (sunflower) movements are generally described as heliotropic. It is generally believed that the leaves and flowers of the growing H. annuus plant track the sun as the sun moves across the sky from east to west. This paper, however, challenges current interpretation regarding H. annuus movements, as the literature generally excludes the rotation of the earth around its own axis, gravity, and the possible role of gravitation. The general exclusion of the earth's rotation in the literature may also have resulted in flawed research design in studies conducted on H. annuus movements, which in turn may have directed researchers towards the misinterpretation of results. This paper aims to include the possible role of the Earth's rotation, gravity, and gravitation when describing H. annuus movements and to provide possible alternative explanations for the results achieved by researchers. This paper further includes concepts and examples relevant to plant movements, such as the rhythms often associated with plant movements, the physiology of plant movements, referring to turgor pressure as the main force behind plant movements, and plant rhythmic clocks and their characteristics, in order to explain the alternative views and to relate them to H. annuus movements.

A Bird's-Eye View of Molecular Changes in Plant Gravitropism Using Omics Techniques

During evolution, plants have developed mechanisms to adapt to a variety of environmental stresses, including drought, high salinity, changes in carbon dioxide levels and pathogens. Central signaling hubs and pathways that are regulated in response to these stimuli have been identified. In contrast to these well studied environmental stimuli, changes in transcript, protein and metabolite levels in response to a gravitational stimulus are less well understood. Amyloplasts, localized in statocytes of the root tip, in mesophyll cells of coleoptiles and in the elongation zone of the growing internodes comprise statoliths in higher plants. Deviations of the statocytes with respect to the earthly gravity vector lead to a displacement of statoliths relative to the cell due to their inertia and thus to gravity perception. Downstream signaling events, including the conversion from the biophysical signal of sedimentation of distinct heavy mass to a biochemical signal, however, remain elusive. More recently, technical advances, including clinostats, drop towers, parabolic flights, satellites, and the International Space Station, allowed researchers to study the effect of altered gravity conditions - real and simulated micro- as well as hypergravity on plants. This allows for a unique opportunity to study plant responses to a purely anthropogenic stress for which no evolutionary program exists. Furthermore, the requirement for plants as food and oxygen sources during prolonged manned space explorations led to an increased interest in the identi-fication of genes involved in the adaptation of plants to microgravity. Transcriptomic, proteomic, phosphoproteomic, and metabolomic profiling strategies provide a sensitive high-throughput approach to identify biochemical alterations in response to changes with respect to the influence of the gravitational vector and thus the acting gravitational force on the transcript, protein and metabolite level. This review aims at summarizing recent experimental approaches and discusses major observations.

Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development

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PREMISE OF THE STUDY

Plants will be an important component of advanced life support systems during space exploration missions. Therefore, understanding their biology in the spacecraft environment will be essential before they can be used for such systems.•

METHODS

Seedlings of Arabidopsis thaliana were grown for 2 wk in the Biological Research in Canisters (BRIC) hardware on board the second to the last mission of the space shuttle Discovery (STS-131). Transcript profiles between ground controls and space-grown seedlings were compared using stringent selection criteria.•

KEY RESULTS

Expression of transcripts associated with oxidative stress and cell wall remodeling was repressed in microgravity. These downregulated genes were previously shown to be enriched in root hairs consistent with seedling phenotypes observed in space. Mutations in genes that were downregulated in microgravity, including two uncharacterized root hair-expressed class III peroxidase genes (PRX44 and PRX57), led to defective polar root hair growth on Earth. PRX44 and PRX57 mutants had ruptured root hairs, which is a typical phenotype of tip-growing cells with defective cell walls and those subjected to stress.•

CONCLUSIONS

Long-term exposure to microgravity negatively impacts tip growth by repressing expression of genes essential for normal root hair development. Whereas changes in peroxidase gene expression leading to reduced root hair growth in space are actin-independent, root hair development modulated by phosphoinositides could be dependent on the actin cytoskeleton. These results have profound implications for plant adaptation to microgravity given the importance of tip growing cells such as root hairs for efficient nutrient capture.

Transcriptome profiling of peanut (Arachis hypogaea) gynophores in gravitropic response

Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.

Proteomic identification of gravitropic response genes in peanut gynophores

Peanut (Arachis hypogaea L.) is one of the most important oil-bearing crops in the world. The gravitropic response of peanut gynophores plays an essential role in peanut reproductive development. In this study, we developed an in vitro culture system and applied it to the study of peanut gynophore gravitropism. By comparing the proteomes of gynophores grown in vitro with the tip pointing upward (gravity stimulation sample) and downward (natural growth control) at 6h and 12h, we observed 42 and 39 with significantly altered expression pattern at 6 and 12h, respectively. Out of these proteins, 13 proteins showed same expression profiling at both 6h and 12h. They were identified by MALDI-TOF/TOF and further characterized with quantitative real time RT-PCR. Among the 13 identified proteins, two were identified as class III acidic endochitinases, two were identified as Kunitz trypsin protease inhibitors, and the remaining proteins were identified as pathogenesis-related class 10 protein, Ara h 8 allergen isoform 3, voltage-dependent anion channel, gamma carbonic anhydrase 1, germin-like protein subfamily 3 member 3 precursor, chloride channel, glycine-rich RNA-binding protein and gibberellin receptor GID1. Real time RT-PCR analysis revealed that transcriptional regulation is consistent with expression at the protein level for class III acidic endochitinase, Kunitz trypsin protease inhibitor, chloride channel and pathogenesis-related class 10 protein, while the expression of the other 7 proteins might be regulated at post-transcriptional levels. This study identified several potential gravitropic response proteins in peanut gynophores and helps to understand early gravitropic responses in peanut gynophores.

BIOLOGICAL SIGNIFICANCE

The gravitropic response of the peanut gynophores plays an essential role in peanut production. However, the molecular mechanism responsible for gravitropic responses in the peanut gynophores has not been explored yet. The result generated in this study may provide in vitro culture system for gravitropism study of plant gravitropic response and novel insights into the proteome-level response and give a more comprehensive understanding of early gravitropic response in peanut gynophores. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Plant tropisms: from Darwin to the International Space Station

Plant tropisms play a fundamental role in shaping the growth form of plants, and these fascinating movements are the focus of this thematic issue of the American Journal of Botany. The issue includes 16 reviews of the current literature and eight original manuscripts written by a diverse group of international experts in their respective fields. This special issue emphasizes tropistic responses to three fundamental stimuli governing plant growth: water, light, and gravity. We hope this issue will inform the current generation and inspire the next generation of plant biologists.