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

A systematic review to identify target genes that modulate root system architecture in response to abiotic stress

The exposure of plant roots to soil-related stresses, including drought, high temperatures, salinization, and nutrient deficiency, is on the rise due to climate change caused by human activities. A systematic literature review was conducted, which revealed evidence for conserved genes that modulate root system architecture under specific stress conditions. A collection of Arabidopsis thaliana mutants displaying a root phenotype distinct from the wild type is available in The Arabidopsis Information Resource database. Gene expression data was gathered for specific genes in response to selected abiotic stress treatments. K-means clustering, and fold change analyses identified 118 genes that were upregulated and 185 genes that were downregulated. A dedicated phenotyping approach was used to ascertain that lack of nutrients induced the transition from a 'steep, cheap, and deep' root morphotype to a 'topsoil foraging' root morphotype in the Columbia- 0 reference genotype. The anticipated role of ISOPENTENYLTRANSFERASE 3, LIPOXYGENASE 1, and WEE1 KINASE HOMOLOG as negative regulators of root growth in response to multiple stress signals was assayed. Further research with the candidate genes identified in this study may reveal promising targets for crop improvement.

Physiological and transcriptional analyses of Arabidopsis primary root growth in response to phosphate starvation under light and dark conditions

Plants cope with Pi deficiency by triggering an array of adaptive responses, including the remodeling of root system architecture (RSA). Arabidopsis thaliana grown on a Pi-deficient (-Pi) medium in transparent Petri dishes exhibits an inhibition of primary root (PR) growth. Previous work has shown that direct illumination on roots by blue light is both required and sufficient for the Pi deficiency-induced inhibition of PR growth. However, whether light illumination on shoots of seedlings contributes to the inhibition of PR growth under -Pi condition and whether light signaling pathway is involved in this process remain largely unknown. In addition to Pi deficiency-induced inhibition of PR growth, how light affects the transcriptomic changes under -Pi also remains elusive. Here, we found that the inhibition of PR growth under -Pi condition is determined by light illumination on roots instead of shoots. Further experiments revealed that blue light receptors CRY1/CRY2 and key regulator in blue light signaling pathway HY5 play minor roles in this process. Finally, we evaluated the light effects on the transcriptomic changes during the inhibition of PR growth under -Pi condition. We found that light promotes the expression of many genes involved in stress and phytohormones-related processes and has both upregulated and downregulated effects on the expression of typical phosphate starvation-induced (PSI) genes. Taken together, our work further demonstrates our previous hypothesis that the inhibition of PR growth under -Pi condition is caused by blue light-triggered chemical reactions, rather than blue light signaling pathways. Apart from the inhibition of PR growth under -Pi, light exposure also results in substantial alterations of transcriptome under -Pi condition, encouraging us to carefully evaluate the phenotype under illuminated, transparent Petri dishes.

Two antagonistic gene regulatory networks drive Arabidopsis root hair growth at low temperature linked to a low-nutrient environment

Root hair (RH) cells can elongate to several hundred times their initial size, and are an ideal model system for investigating cell size control. Their development is influenced by both endogenous and external signals, which are combined to form an integrative response. Surprisingly, a low-temperature condition of 10°C causes increased RH growth in Arabidopsis and in several monocots, even when the development of the rest of the plant is halted. Previously, we demonstrated a strong correlation between RH growth response and a significant decrease in nutrient availability in the growth medium under low-temperature conditions. However, the molecular basis responsible for receiving and transmitting signals related to the availability of nutrients in the soil, and their relation to plant development, remain largely unknown. We have discovered two antagonic gene regulatory networks (GRNs) controlling RH early transcriptome responses to low temperature. One GNR enhances RH growth and it is commanded by the transcription factors (TFs) ROOT HAIR DEFECTIVE 6 (RHD6), HAIR DEFECTIVE 6-LIKE 2 and 4 (RSL2-RSL4) and a member of the homeodomain leucine zipper (HD-Zip I) group I 16 (AtHB16). On the other hand, a second GRN was identified as a negative regulator of RH growth at low temperature and it is composed by the trihelix TF GT2-LIKE1 (GTL1) and the associated DF1, a previously unidentified MYB-like TF (AT2G01060) and several members of HD-Zip I group (AtHB3, AtHB13, AtHB20, AtHB23). Functional analysis of both GRNs highlights a complex regulation of RH growth response to low temperature, and more importantly, these discoveries enhance our comprehension of how plants synchronize RH growth in response to variations in temperature at the cellular level.

Proteomic and metabolomic insights into the impact of topping treatment on cigar tobacco

Top removal is a widely utilized method in production process of tobacco, but little is known regarding the way it impacts protein and metabolic regulation. In this study, we investigated the underlying processes of alterations in cigar tobacco leaves with and without top removal, using a combined proteomic and metabolomic approach. The results revealed that: (1) Topping significantly affected superoxide anion (O2 -) levels, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content, (2) In the cigar tobacco proteome, 385 differentially expressed proteins (DEPs) were identified, with 228 proteins upregulated and 156 downregulated. Key pathways enriched included flavonoid biosynthesis, porphyrin and chlorophyll metabolism, cysteine and methionine metabolism, and amino acid biosynthesis and metabolism. A network of 161 nodes interconnected by 102 significantly altered proteins was established, (3) In the cigar tobacco metabolome, 247 significantly different metabolites (DEMs) were identified, with 120 upregulated and 128 downregulated metabolites, mainly comprising lipids and lipid-like molecules, phenylpropanoids and polyketides, organic acids and derivatives, and organic heterocyclic compounds, (4) KEGG pathway enrichment revealed upregulation of proteins such as chalcone synthase (CHS), chalcone isomerase (CHI), naringenin 3-dioxygenase (F3H), and flavonoid 3'-monooxygenase (F3'H), along with metabolites like pinocembrin, kaempferol, trifolin, rutin, and quercetin, enhancing the pathways of 'flavonoid' and 'flavone and flavonol' biosynthesis. This study sheds light on the metabolic and proteomic responses of cigar tobacco after topping.

The E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 and transcription factors ELONGATED HYPOCOTYL 5 and ROOT HAIR DEFECTIVE6 integrate light signaling and root hair development

Light signaling plays a substantial role in regulating plant development, including the differentiation and elongation of single-celled tissue. However, the identity of the regulatory machine that affects light signaling on root hair cell (RHC) development remains unclear. Here, we investigated how darkness inhibits differentiation and elongation of RHC in Arabidopsis (Arabidopsis thaliana). We found that light promotes the growth and development of RHC. RNA-seq analysis showed that light signaling regulates the differentiation of RHC by promoting the expression of specific genes in the root epidermis associated with cell wall remodeling, jasmonic acid, auxin, and ethylene signaling pathways. Together, these genes integrate light and phytohormone signals with root hair (RH) development. Our investigation also revealed that the core light signal factor ELONGATED HYPOCOTYL 5 (HY5) directly interacts with the key RH development factor ROOT HAIR DEFECTIVE6 (RHD6), which promotes the transcription of RSL4. However, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) repressed the RHD6 function through the COP1-HY5 complex. Our genetic studies confirm associations between RHD6, HY5, and COP1, indicating that RHD6 largely depends on HY5 for RH development. Ultimately, our work suggests a central COP1-HY5-RHD6 regulatory module that integrates light signaling and RH development with several downstream pathways, offering perspectives to decipher single-celled RH development.

Adaptable Alchemy: Exploring the Flexibility of Specialized Metabolites to Environmental Perturbations Through Post-Translational Modifications (PTMs)

Plants are subjected to various stresses during the growth process, including biotic stresses, as well as abiotic stresses such as temperature, drought, salt, and heavy metals. To cope with these biotic and abiotic adversities, plants have evolved complex regulatory mechanisms during their long-term environmental adaptations. In a suddenly changing environment, protein modifiers target other proteins to induce post-translational modification (PTM) in order to maintain cell homeostasis and protein biological activity in plants. PTMs modulate the activity of enzymes and transcription factors in their respective metabolic pathways, enabling plants to produce essential compounds for their survival under stress conditions. Examples of post-translational mechanisms include phosphorylation, ubiquitination, glycosylation, acetylation, protein-protein interactions, and targeted protein degradation. Furthermore, the role of histone modifications in regulating secondary metabolism deserves attention due to its potential impact on heritability and its contribution to stress tolerance. Understanding the epigenetic aspect of these modifications can provide valuable insights into the mechanisms underlying stress response. In this context, also examining PTMs that impact the biosynthesis of secondary metabolites is meaningful. Secondary metabolites encompass a wide range of compounds such as flavonoids, alkaloids, and terpenoids. These secondary metabolites play a crucial role in plant defense against herbivores, pathogens, and oxidative stress. In this context, it is imperative to understand the contribution of secondary metabolism to plant tolerance to abiotic stresses and how this understanding can be leveraged to improve long-term survival. While many studies have focused on the transcriptional regulation of these metabolites, there is a growing interest in understanding various changes in PTMs, such as acetylation, glycosylation, and phosphorylation, that are able to modulate plants' response to environmental conditions. In conclusion, a comprehensive exploration of post-translational mechanisms in secondary metabolism can enhance our understanding of plant responses to abiotic stress. This knowledge holds promise for future applications in genetic improvement and breeding strategies aimed at increasing plant resilience to environmental challenges.

Metabolomic and Transcriptomic Analysis Reveals Flavonoid-Mediated Regulation of Seed Antioxidant Properties in Peanut Seed Vigor

Peanut (Arachis hypogaea L.) is an oilseed crop grown worldwide. Flavonoids have profound benefits for plant growth and development because of their powerful antioxidant properties. Seed vigor is an important indicator of seed quality. However, how flavonoids impact seed vigor formation in large-seed peanuts is still poorly understood. Here, we profiled flavonoids, phytohormones, and transcriptomes of developing seeds of large-seed peanut varieties with low (ZP06) and high (H8107) seed vigor. A total of 165 flavonoids were identified, 51 of which were differentially accumulated in ZP06 and H8107. Lower levels of dihydromyricetin (0.28 times) and hesperetin-7-O-glucoside (0.26 times) were observed in ZP06 seeds than in H8107. All flavonoid biosynthesis structural genes were down-regulated in ZP06. The different hormone levels found in ZP06 and H8107 seeds could be associated with the expression of flavonoid biosynthesis genes via MYB and bHLH transcription factors. Dihydromyricetin could relate to ZP06's poor seed vigor by impacting its seed antioxidant properties. Thus, the presence of flavonoids in large-seed peanuts could contribute to their physiological quality and germination potential through controlling the accumulation of reactive oxygen species to improve seed antioxidant properties.

Filling the gaps on root hair development under salt stress and phosphate starvation using current evidence coupled with a meta-analysis approach

Population expansion is a global issue, especially for food production. Meanwhile, global climate change is damaging our soils, making it difficult for crops to thrive and lowering both production and quality. Poor nutrition and salinity stress affect plant growth and development. Although the impact of individual plant stresses has been studied for decades, the real stress scenario is more complex due to the exposure to multiple stresses at the same time. Here we investigate using existing evidence and a meta-analysis approach to determine molecular linkages between 2 contemporaneous abiotic stimuli, phosphate (Pi) deficiency and salinity, on a single plant cell model, the root hairs (RHs), which is the first plant cell exposed to them. Understanding how these 2 stresses work molecularly in RHs may help us build super-adaptable crops and sustainable agriculture in the face of global climate change.

Crystal structure and function of a phosphate starvation responsive protein phosphatase, GmHAD1-2 regulating soybean root development and flavonoid metabolism

Phosphate (Pi) availability is well known to regulate plant root growth. However, it remains largely unknown how flavonoid synthesis participates in affecting plant root growth in response to Pi starvation. In the study, the crystal structure of a plant protein phosphatase, GmHAD1-2, was dissected using X-ray crystallography for the first time. It was revealed that GmHAD1-2 contained a modified Rossmannoid class of α/β folds with three layered α/β sandwich. Transcripts of GmHAD1-2 were increased by Pi starvation in soybean roots, especially in lateral root tips. GmHAD1-2 suppression or overexpression significantly influenced soybean lateral root length and number, as well as phosphorus (P) content. Furthermore, GmHAD1-2 was found to interact with a chalcone reductase, GmCHR1. Suppression of GmHAD1-2 significantly changed the flavonoid biosynthesis pathway in soybean roots. Taken together, the results highlight that GmHAD1-2 can regulate soybean root growth by influencing flavonoid metabolism.

Transcription factor NtMYB59 targets NtMYB12 to negatively regulate the biosynthesis of polyphenols in Nicotiana tabacum

MYB12 is a key regulator that has been shown to promote the accumulation of various phenylpropanoid compounds in plants. However, the regulation of MYB12 gene is largely unknown. In this study, we found that overexpression of the NtMYB59 gene significantly inhibited the accumulation of chlorogenic acid (CGA), flavonols, and anthocyanins in tobacco, while knock-down and knock-out of NtMYB59 significantly increased the contents of these polyphenol compounds. Transcriptome analysis between WT and NtMYB59-OE plants revealed several differentially expressed genes (DEGs) encoding crucial enzymes in the phenylpropanoid pathway and the transcription factor NtMYB12. ChIP-seq assay further indicated that NtMYB12 might be a direct target of NtMYB59. Subsequent yeast one-hybrid, electrophoretic mobility shift assay, and Dual-Luciferase assays confirmed that NtMYB59 directly binds to the promoter of NtMYB12 to inhibit its expression. Moreover, loss-function of NtMYB59 significantly promoted the accumulation of flavonols and anthocyanins in ntmyb59, but their contents in ntmyb59/ntmyb12 double mutants were significantly lower than that of WT and ntmyb59 plants, indicating that the regulation of NtMYB59 on flavonoids biosynthesis depends on the activity of NtMYB12. Our study revealed that NtMYB59 regulates the expression of NtMYB12, and provided new potential strategies for modulating phenylpropanoids biosynthesis in tobacco.

Bacterial bioluminescence is an important regulator of multitrophic interactions in the soil

Enormous efforts have been made to understand the functions of bioluminescence; however, its relevance in soil ecosystems has barely been investigated. In addition, our understanding of the biological relevance of bioluminescence is hampered by the scarcity of tools to genetically manipulate this trait. Using the symbionts of entomopathogenic nematodes, Photorhabdus bacteria, we show that bioluminescence plays important regulatory roles in multitrophic interactions in the soil. Through genetic modifications and exploiting natural variability, we provide direct evidence for the multifunctional nature of bioluminescence. It regulates abiotic and biotic stress resistance, impacts other trophic levels, including nematodes, insects, and plants, and contributes to symbiosis. Our study contributes to understanding the factors that have driven the evolution and maintenance of this trait in belowground ecosystems.

Two pyridoxal phosphate homeostasis proteins are essential for management of the coenzyme pyridoxal 5'-phosphate in Arabidopsis

Coenzyme management is important for homeostasis of the pool of active metabolic enzymes. The coenzyme pyridoxal 5'-phosphate (PLP) is involved in diverse enzyme reactions including amino acid and hormone metabolism. Regulatory proteins that contribute to PLP homeostasis remain to be explored in plants. Here, we demonstrate the importance of proteins annotated as PLP homeostasis proteins (PLPHPs) for controlling PLP in Arabidopsis (Arabidopsis thaliana). A systematic analysis indicates that while most organisms across kingdoms have a single PLPHP homolog, Angiosperms have two. PLPHPs from Arabidopsis bind PLP and exist as monomers, in contrast to reported PLP-dependent enzymes, which exist as multimers. Disrupting the function of both PLPHP homologs perturbs vitamin B6 (pyridoxine) content, inducing a PLP deficit accompanied by light hypersensitive root growth, unlike PLP biosynthesis mutants. Micrografting studies show that the PLP deficit can be relieved distally between shoots and roots. Chemical treatments probing PLP-dependent reactions, notably those for auxin and ethylene, provide evidence that PLPHPs function in the dynamic management of PLP. Assays in vitro show that Arabidopsis PLPHP can coordinate PLP transfer and withdrawal from other enzymes. This study thus expands our knowledge of vitamin B6 biology and highlights the importance of PLP coenzyme homeostasis in plants.

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.

Intrinsic Mechanism of CaCl2 Alleviation of H2O2 Inhibition of Pea Primary Root Gravitropism

Normal root growth is essential for the plant uptake of soil nutrients and water. However, exogenous H2O2 inhibits the gravitropic growth of pea primary roots. It has been shown that CaCl2 application can alleviate H2O2 inhibition, but the exact alleviation mechanism is not clear. Therefore, the present study was carried out by combining the transcriptome and metabolome with a view to investigate in depth the mechanism of action of exogenous CaCl2 to alleviate the inhibition of pea primordial root gravitropism by H2O2. The results showed that the addition of CaCl2 (10 mmol·L-1) under H2O2 stress (150 mmol·L-1) significantly increased the H2O2 and starch content, decreased peroxidase (POD) activity, and reduced the accumulation of sugar metabolites and lignin in pea primary roots. Down-regulated genes regulating peroxidase, respiratory burst oxidase, and lignin synthesis up-regulated PGM1, a key gene for starch synthesis, and activated the calcium and phytohormone signaling pathways. In summary, 10 mmol·L-1 CaCl2 could alleviate H2O2 stress by modulating the oxidative stress response, signal transduction, and starch and lignin accumulation within pea primary roots, thereby promoting root gravitropism. This provides new insights into the mechanism by which CaCl2 promotes the gravitropism of pea primary roots under H2O2 treatment.

Four glycosyltransferase genes are responsible for synthesis and accumulation of different flavonol glycosides in apple tissues

Flavonols are widely synthesized throughout the plant kingdom, playing essential roles in plant physiology and providing unique health benefits for humans. Their glycosylation plays significant role in improving their stability and solubility, thus their accumulation and function. However, the genes encoding the enzymes catalyze this glycosylation remain largely unknown in apple. This study utilized a combination of methods to identify genes encoding such enzymes. Initially, candidate genes were selected based on their potential to encode UDP-dependent glycosyltransferases (UGTs) and their expression patterns in response to light induction. Subsequently, through testing the in vitro enzyme activity of the proteins produced in Escherichia coli cells, four candidates were confirmed to encode a flavonol 3-O-galactosyltransferase (UGT78T6), flavonol 3-O-glucosyltransferase (UGT78S1), flavonol 3-O-xylosyltransferase/arabinosyltransferase (UGT78T5), and flavonol 3-O-rhamnosyltransferase (UGT76AE22), respectively. Further validation of these genes' functions was conducted by modulating their expression levels in stably transformed apple plants. As anticipated, a positive correlation was observed between the expression levels of these genes and the content of specific flavonol glycosides corresponding to each gene. Moreover, overexpression of a flavonol synthase gene, MdFLS, resulted in increased flavonol glycoside content in apple roots and leaves. These findings provide valuable insights for breeding programs aimed at enriching apple flesh with flavonols and for identifying flavonol 3-O-glycosyltransferases of other plant species.

Synthetically derived BiAux modulates auxin co-receptor activity to stimulate lateral root formation

The root system plays an essential role in plant growth and adaptation to the surrounding environment. The root clock periodically specifies lateral root prebranch sites (PBS), where a group of pericycle founder cells (FC) is primed to become lateral root founder cells and eventually give rise to lateral root primordia or lateral roots (LRs). This clock-driven organ formation process is tightly controlled by modulation of auxin content and signaling. Auxin perception entails the physical interaction of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) or AUXIN SIGNALING F-BOX (AFBs) proteins with AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressors to form a co-receptor system. Despite the apparent simplicity, the understanding of how specific auxin co-receptors are assembled remains unclear. We identified the compound bis-methyl auxin conjugated with N-glucoside, or BiAux, in Arabidopsis (Arabidopsis thaliana) that specifically induces the formation of PBS and the emergence of LR, with a slight effect on root elongation. Docking analyses indicated that BiAux binds to F-box proteins, and we showed that BiAux function depends on TIR1 and AFB2 F-box proteins and AUXIN RESPONSE FACTOR 7 activity, which is involved in FC specification and LR formation. Finally, using a yeast (Saccharomyces cerevisiae) heterologous expression system, we showed that BiAux favors the assemblage of specific co-receptors subunits involved in LR formation and enhances AUXIN/INDOLE-3-ACETIC ACID 28 protein degradation. These results indicate that BiAux acts as an allosteric modulator of specific auxin co-receptors. Therefore, BiAux exerts a fine-tune regulation of auxin signaling aimed to the specific formation of LR among the many development processes regulated by auxin.

Interplay between secondary metabolites and plant hormones in silver nitrate-elicited Arabidopsis thaliana plants

Plants produce a myriad of specialized compounds in response to threats such as pathogens or pests and different abiotic factors. The stress-related induction of specialized metabolites can be mimicked using silver nitrate (AgNO3) as an elicitor, which application in conservation agriculture has gained interest. In Arabidopsis thaliana, AgNO3 triggers the accumulation of indole glucosinolates (IGs) and the phytoalexin camalexin as well as pheylpropanoid-derived defensive metabolites such as coumaroylagmatins and scopoletin through a yet unknown mechanism. In this work, the role of jasmonic (JA) and salicylic acid (SA) signaling in the AgNO3-triggered specialized metabolite production was investigated. To attain this objective, AgNO3, MeJA and SA were applied to A. thaliana lines impaired in JA or SA signaling, or affected in the endogenous levels of IGs and AGs. Metabolomics data indicated that AgNO3 elicitation required an intact JA and SA signaling to elicit the metabolic response, although mutants impaired in hormone signaling retained certain capacity to induce specialized metabolites. In turn, plants overproducing or abolishing IGs production had also an altered hormonal signaling response, both in the accumulation of signaling molecules and the molecular response mechanisms (ORA59, PDF1.2, VSP2 and PR1 gene expression), which pointed out to a crosstalk between defense hormones and specialized metabolites. The present work provides evidence of a crosstalk mechanism between JA and SA underlying AgNO3 defense metabolite elicitation in A. thaliana. In this mechanism, IGs would act as retrograde feedback signals dampening the hormonal response; hence, expanding the signaling molecule concept.

Tyrosine-sulfated peptide hormone induces flavonol biosynthesis to control elongation and differentiation in Arabidopsis primary root

In Arabidopsis roots, growth initiation and cessation are organized into distinct zones. How regulatory mechanisms are integrated to coordinate these processes and maintain proper growth progression over time is not well understood. Here, we demonstrate that the peptide hormone PLANT PEPTIDE CONTAINING SULFATED TYROSINE 1 (PSY1) promotes root growth by controlling cell elongation. Higher levels of PSY1 lead to longer differentiated cells with a shootward displacement of characteristics common to mature cells. PSY1 activates genes involved in the biosynthesis of flavonols, a group of plant-specific secondary metabolites. Using genetic and chemical approaches, we show that flavonols are required for PSY1 function. Flavonol accumulation downstream of PSY1 occurs in the differentiation zone, where PSY1 also reduces auxin and reactive oxygen species (ROS) activity. These findings support a model where PSY1 signals the developmental-specific accumulation of secondary metabolites to regulate the extent of cell elongation and the overall progression to maturation.

Changes in root metabolites and soil microbial community structures in rhizospheres of sugarcanes under different propagation methods

Root metabolites and soil microbial community structure in the rhizosphere play critical roles in crop growth. Here, we assessed the efficiency of conventional and tissue culture propagation methods in modulating the soil health and microbiota in the rhizosphere of sugarcane (Saccharum officinarum L.) plants. The seeding canes were obtained using newly planted and two-year ratooned canes propagated by conventional (CSN and CSR) or tissue culture (TCN and TCR) methods. Changes in soil fertility, root metabolites and soil microbial community structure in the rhizosphere of sugarcane plants obtained using these canes were assessed. The activities of soil β-glucosidase and aminopeptidase, soil microbial biomass nitrogen, and abundances of soil beneficial microbes, both at phyla and genera levels, were significantly higher in the rhizosphere of sugarcane plants in TCN and TCR treatments than those in that of plants in CSN and CSR treatments. Furthermore, flavonoid and flavonol biosynthesis and alanine, aspartate and glutamate metabolism were significantly upregulated in the roots of TCR and TCN plants compared with those in the roots of CSN and CSR plants. These results suggest that the tissue culture propagation method is a sustainable method for sugarcane cultivation to improve soil fertility and health in sugarcane rhizosphere.

Mutation of MYB36 affects isoflavonoid metabolism, growth, and stress responses in Lotus japonicus

Isoflavonoids are mostly produced by legumes although little is known about why and how legumes are able to regulate the biosynthesis of these particular compounds. Understanding the role of potential regulatory genes of the isoflavonoid biosynthetic pathway constitutes an important topic of research. The LORE1 mutation of the gene encoding the transcription factor MYB36 allowed the identification of this gene as a regulator of isoflavonoid biosynthesis in Lotus japonicus plants. The levels of several isoflavonoid compounds were considerably lower in two lines of Ljmyb36 mutant plants compared to the WT. In addition, we found that Ljmyb36 mutant plants were significantly smaller and showed a substantial decrease in the chlorophyll levels under normal growth conditions. The analysis of plants subjected to different types of abiotic stress conditions further revealed that mutant plants presented a higher sensitivity than WT plants, indicating that the MYB36 transcription factor is also involved in the stress response in L. japonicus plants.

How metabolism and development are intertwined in space and time

Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.

Anthocyanins and reactive oxygen species: a team of rivals regulating plant development?

Anthocyanins are a family of water-soluble vacuolar pigments present in almost all flowering plants. The chemistry, biosynthesis and functions of these flavonoids have been intensively studied, in part due to their benefit for human health. Given that they are efficient antioxidants, intense research has been devoted to studying their possible roles against damage caused by reactive oxygen species (ROS). However, the redox homeostasis established between antioxidants and ROS is important for plant growth and development. On the one hand, high levels of ROS can damage DNA, proteins, and lipids, on the other, they are also required for cell signaling, plant development and stress responses. Thus, a balance is needed in which antioxidants can remove excessive ROS, while not precluding ROS from triggering important cellular signaling cascades. In this article, we discuss how anthocyanins and ROS interact and how a deeper understanding of the balance between them could help improve plant productivity, nutritional value, and resistance to stress, while simultaneously maintaining proper cellular function and plant growth.

A bench-top Dark-Root device built with LEGO® bricks enables a non-invasive plant root development analysis in soil conditions mirroring nature

Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

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.

Integrated metabolomic and transcriptomic study unveils the gene regulatory mechanisms of sugarcane growth promotion during interaction with an endophytic nitrogen-fixing bacteria

BACKGROUND

Sugarcane growth and yield are complex biological processes influenced by endophytic nitrogen-fixing bacteria, for which the molecular mechanisms involved are largely unknown. In this study, integrated metabolomic and RNA-seq were conducted to investigate the interaction between an endophytic bacterial strain, Burkholderia GXS16, and sugarcane tissue culture seedlings.

RESULTS

During treatment, the colonization of GXS16 in sugarcane roots were determined, along with the enhanced activities of various antioxidant enzymes. Accordingly, 161, 113, and 37 differentially accumulated metabolites (DAMs) were found in the pairwise comparisons of adjacent stages. In addition, transcriptomic analyses obtained 1,371 (IN-vs-CN), 1,457 (KN-vs-IN), and 365 (LN-vs-KN) differentially expressed genes (DEGs), which were mainly involved in the pathways of glutathione metabolism and carbon metabolism. We then assessed the pattern of metabolite accumulation and gene expression in sugarcane during GXS16 colonization. The results showed that both DAMs and DGEs in the upregulated expression profiles were involved in the flavonoid biosynthesis pathway. Overall, p-coumaroyl-CoA in sugarcane roots transferred into homoeriodictyol chalcone and 5-deoxyleucopelargonidin due to the upregulation of the expression of genes shikimate O-hydroxycinnamoyltransferase (HCT), chalcone synthase (CHS), and phlorizin synthase (PGT1).

CONCLUSIONS

This study provides insights into the gene regulatory mechanisms involved in the interaction between GXS16 and sugarcane roots, which will facilitate future applications of endophytic nitrogen-fixing bacteria to promote crop growth.

Friends in Arms: Flavonoids and the Auxin/Cytokinin Balance in Terrestrialization

Land plants survive the challenges of new environments by evolving mechanisms that protect them from excess irradiation, nutrient deficiency, and temperature and water availability fluctuations. One such evolved mechanism is the regulation of the shoot/root growth ratio in response to water and nutrient availability by balancing the actions of the hormones auxin and cytokinin. Plant terrestrialization co-occurred with a dramatic expansion in secondary metabolism, particularly with the evolution and establishment of the flavonoid biosynthetic pathway. Flavonoid biosynthesis is responsive to a wide range of stresses, and the numerous synthesized flavonoid species offer two main evolutionary advantages to land plants. First, flavonoids are antioxidants and thus defend plants against those adverse conditions that lead to the overproduction of reactive oxygen species. Second, flavonoids aid in protecting plants against water and nutrient deficiency by modulating root development and establishing symbiotic relations with beneficial soil fungi and bacteria. Here, we review different aspects of the relationships between the auxin/cytokinin module and flavonoids. The current body of knowledge suggests that whereas both auxin and cytokinin regulate flavonoid biosynthesis, flavonoids act to fine-tune only auxin, which in turn regulates cytokinin action. This conclusion agrees with the established master regulatory function of auxin in controlling the shoot/root growth ratio.

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.

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.

FT-IR and FT-Raman fingerprints of flavonoids - A review

Flavonoids are secondary metabolites commonly found in plants. They are known for their antioxidant properties, are part of the defense mechanisms of plants and are responsible for the pigmentation of fruit and flowers petals. Consumption foods rich in flavonoids in the daily diet brings a number of pro-health benefits - for example blood pressure regulation, delaying the aging process or anti-cancer effect. These compounds in synthetic or natural form are also used in pharmacy. The profile of flavonoid compounds can be quickly, accurately and easy determine in the test sample by using the infrared and Raman spectroscopy. Those methods are successfully used in the food and pharmaceutical industries. Spectroscopy methods allow us to determine the chemical structure of these compounds. This review describes and compares differences between the spectroscopic spectra of individual compounds with the chemical structure for the flavonoids subgroups: flavones, isoflavones, flavanones, flavonols and anthocyanins.

Two homeologous MATE transporter genes, NtMATE21 and NtMATE22, are involved in the modulation of plant growth and flavonol transport in Nicotiana tabacum

The multidrug and toxic compound extrusion (MATE) protein family has been implicated in the transport of a diverse range of molecules, including specialized metabolites. In tobacco (Nicotiana tabacum), only a limited number of MATE transporters have been functionally characterized, and no MATE transporter has been studied in the context of flavonoid transport in this plant species so far. In the present study, we characterize two homeologous tobacco MATE genes, NtMATE21 and NtMATE22, and demonstrate their role in flavonol transport and in plant growth and development. The expression of these two genes was reported to be up-regulated in trichomes as compared with the trichome-free leaf. The transcript levels of NtMATE21 and NtMATE22 were found to be higher in flavonol overproducing tobacco transgenic lines as compared with wild type tobacco. The two transporters were demonstrated to be localized to the plasma membrane. Genetic manipulation of NtMATE21 and NtMATE22 led to altered growth phenotypes and modulated flavonol contents in N. tabacum. The β-glucuronidase and green fluorescent protein fusion transgenic lines of promoter regions suggested that NtMATE21 and NtMATE22 are exclusively expressed in the trichome heads in the leaf tissue and petals. Moreover, in a transient transactivation assay, NtMYB12, a flavonol-specific MYB transcription factor, was found to transactivate the expression of NtMATE21 and NtMATE22 genes. Together, our results strongly suggest the involvement of NtMATE21 and NtMATE22 in flavonol transport as well as in the regulation of plant growth and development.

Flavonoids in vegetables: improvement of dietary flavonoids by metabolic engineering to promote health

Flavonoids are the most abundant polyphenols in plants, and have antioxidant effects as well as other bioactivities (e.g., anti-inflammatory, anti-cancer, anti-allergic, and neuroprotective effects). Vegetables are rich in flavonoids and are indispensable in our daily diet. Moreover, the vegetables as chassis for producing natural products would emerge as a promising means for cost-effective and sustainable production of flavonoids. Understanding the metabolic engineering of flavonoids in vegetables allows us to improve their nutrient composition. In this review, a comprehensive overview of flavonoids in vegetables, including the characterized types and distribution, health-promoting effects, associated metabolic pathways, and applied metabolic engineering are provided. We also introduce breakthroughs in multi-omics approaches that pertain to the elucidation of flavonoids metabolism in vegetables, as well as prospective and potential genome-editing technologies. Based on the varied composition and content of flavonoids among vegetables, dietary suggestions are further provided for human health.

Growth and Development Responses of the Rhizome-Root System in Pleioblastus pygmaeus to Light Intensity

Light, as a primary source of energy, directly or indirectly influences virtually all morphological modifications occurring in both shoots and roots. A pot experiment was conducted to assess the growth patterns of one-year-old Pleioblastus pygmaeus plants’ rhizome-root systems and their responses to different light intensities from 11 March to 26 December 2016. The experiment design scheme was 3.87% (L1), 11.25% (L2), 20.25% (L3), 38.76% (L4), 60.70% (L5), and 100% full sunlight (control CK). The results indicated that along the growing period from March to December, eight of the eleven studied parameters of the rhizome-root system showed significant variability and diverse growth patterns. In addition, light intensity is a key factor for determining P. pygmaeus plants’ rhizome and root growth. Specifically, the light intensity had a significant, positive, and linear/or almost linear impact on the number of old and new rhizomes, old rhizome length, new rhizome diameter, as well as the culm root diameter. A nonlinear and positive relationship was found between light intensity and the listed three parameters, i.e., new rhizome length, new rhizome internode length, and rhizome root length. The value of the above-mentioned three parameters significantly increased when affected from 0% to 40–60% of full sunlight and then gradually increased until 100% of full sunlight. The ratio of aboveground dry weight to underground dry weight (A/U ratio) showed a single peak curve with increasing light intensity and presented the highest value under ca. 55% full sunlight. Furthermore, 40% full sunlight (equal to an average light of 2232 lux) might be the threshold for P. pygmaeus rhizome-root system growth. When the light intensity was below 40%, the generalized additive models (GAMs) predicted value of most studied parameters decreased to lower than zero. In conclusion, current study provides a solid basis for understanding the dynamic growth and development of P. pygmaeus rhizome-root system, and its responses to different light conditions, which could be used as inputs to P. pygmaeus plant cultivation.

Unravelling the consecutive glycosylation and methylation of flavonols in peach in response to UV-B irradiation

Flavonol glycosides are bioactive compounds important for plant defence and human nutrition. Glycosylation and methylation play an important role in enriching the diversity of flavonols in response to the environment. Peach flowers and fruit are rich in flavonol diglycosides such as isorhamnetin 3-O-rutinoside (I3Rut), kaempferol 3-O-rutinoside and quercetin 3-O-rutinoside, and flavonol monoglycosides such as I 3-O-glucoside and Q 3-O-galactoside. UV-B irradiation of fruit significantly induced accumulation of all these flavonol glycosides. Candidate biosynthetic genes induced by UV-B were identified by genome homology searches and the in vitro catalytic activities of purified recombinant proteins determined. PpUGT78T3 and PpUGT78A2 were identified as flavonol 3-O-glucosyltransferase and 3-O-galactosyltransferase, respectively. PpUGT91AK6 was identified as flavonol 1,6-rhamnosyl trasferase catalysing the formation of flavonol rutinosides and PpFOMT1 was identified as a flavonol O-methyltransferase that methylated Q at the 3'-OH-OH to form isorhamnetin derivatives. Transient expression in Nicotiana benthamiana confirmed the specificity of PpUGT78T3 as a flavonol 3-O-glucosyltransferase, PpUGT78A2 as a 3-O-galactosyltransferase, PpUGT91AK6 as a 1,6-rhamnosyltrasferase and PpFOMT1 as an O-methyltransferase. This study provides new insights into the mechanisms of glycosylation and methylation of flavonols, especially the formation of flavonol diglycosides such as I3Rut, and will also be useful for future potential metabolic engineering of complex flavonols.

Ethylene positively regulates Cd tolerance via reactive oxygen species scavenging and apoplastic transport barrier formation in rice

Ethylene regulates plant root growth and resistance to environment stress. However, the role and mechanism of ethylene signaling in response to Cd stress in rice remains unclear. Here, we revealed that ethylene signaling plays a positive role in the resistance of rice to Cd toxicity. Blocking the ethylene signal facilitated root elongation under normal conditions, but resulted in severe oxidative damage and inhibition of root growth under Cd stress. Conversely, ethylene signal enhancement by EIN2 overexpression caused root bending, similar to the response of roots to Cd stress, and displayed higher Cd tolerance than the wildtype (WT) plants. Comparative transcriptome analysis indicated EIN2-mediated upregulation of genes involved in flavonoid biosynthesis and peroxidase activity under Cd stress. The synthesis of phenolic acids and flavonoids were positively regulated by ethylene. Thus, the ein2 (ethylene insensitive 2) mutants displayed lower ROS scavenging capacity than the WT. Moreover, a significant increase in Cd accumulation and relatively increased apoplastic flow were observed in the root apex of the ein2 mutant compared with the WT plants. Overall, EIN2-mediated Cd resistance in rice is mediated by the upregulation of flavonoid biosynthesis and peroxidase activity to induce ROS scavenging, and apoplastic transport barrier formation reduces Cd uptake.

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.

Kaempferol as a precursor for ubiquinone (coenzyme Q) biosynthesis: An atypical node between specialized metabolism and primary metabolism

Ubiquinone (coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. Studies have shown that plants derive approximately a quarter of 4-hydroxybenzoate, which serves as the direct ring precursor of ubiquinone, from the catabolism of kaempferol. Biochemical and genetic evidence suggests that the release of 4-hydroxybenzoate from kaempferol is catalyzed by heme-dependent peroxidases and that 3-O-glycosylations of kaempferol act as a negative regulator of this process. These findings not only represent an atypical instance of primary metabolite being derived from specialized metabolism but also raise the question as to whether ubiquinone contributes to the ROS scavenging and signaling functions already established for flavonols.

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.

Root dynamic growth strategies in response to salinity

Increasing soil salinization largely impacts crop yield worldwide. To deal with salinity stress, plants exhibit an array of responses, including root system architecture remodelling. Here, we review recent progress in physiological, developmental and cellular mechanisms of root growth responses to salinity. Most recent research in modulation of root branching, root tropisms, as well as in root cell wall modifications under salinity stress, is discussed in the context of the contribution of these responses to overall plant performance. We highlight the power of natural variation approaches revealing novel potential pathways responsible for differences in root salt stress responses. Together, these new findings promote our understanding of how salt shapes the root phenotype, which may provide potential avenues for engineering crops with better yield and survival in saline soils.

Genome-Wide Identification and Expression Profiles of 13 Key Structural Gene Families Involved in the Biosynthesis of Rice Flavonoid Scaffolds

Flavonoids are a class of key polyphenolic secondary metabolites with broad functions in plants, including stress defense, growth, development and reproduction. Oryza sativa L. (rice) is a well-known model plant for monocots, with a wide range of flavonoids, but the key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. Here, we identified 85 key structural gene candidates associated with flavonoid biosynthesis in the rice genome. They belong to 13 families potentially encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), leucoanthocyanidin dioxygenase (LDOX), anthocyanidin synthase (ANS), flavone synthase II (FNSII), flavanone 2-hydroxylase (F2H), flavonoid 3′-hydroxylase (F3′H), flavonoid 3′,5′-hydroxylase (F3′5′H), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR). Through structural features, motif analyses and phylogenetic relationships, these gene families were further grouped into five distinct lineages and were examined for conservation and divergence. Subsequently, 22 duplication events were identified out of a total of 85 genes, among which seven pairs were derived from segmental duplication events and 15 pairs were from tandem duplications, demonstrating that segmental and tandem duplication events play important roles in the expansion of key flavonoid biosynthesis-related genes in rice. Furthermore, these 85 genes showed spatial and temporal regulation in a tissue-specific manner and differentially responded to abiotic stress (including six hormones and cold and salt treatments). RNA-Seq, microarray analysis and qRT-PCR indicated that these genes might be involved in abiotic stress response, plant growth and development. Our results provide a valuable basis for further functional analysis of the genes involved in the flavonoid biosynthesis pathway in rice.

Gnotobiotic Plant Systems for Reconstitution and Functional Studies of the Root Microbiota

Healthy plants host a multi-kingdom community of microbes, which is known as the plant microbiota. Amplicon sequencing technologies for microbial genomic markers were a milestone in revealing the taxonomic composition of the microbiota and its variation associated with a plant host in natural environments. However, this method alone does not allow conclusions to be drawn about functions of these microbial assemblages for the plant. The development of culture collections, which recapitulate natural microbial communities in their diversity, and multiple gnotobiotic plant systems therefore represent a breakthrough in plant-microbiota research such that plants can be inoculated with defined communities to study proposed microbiota functions. These systems provided, for the root microbiota, first insights into mechanisms underlying microbial community establishment and contributions of its microbial members to indirect pathogen protection and mineral nutrition of the host. We argue that the choice of a gnotobiotic system for microbiota reconstitution and subsequent functional analysis depends on the particular plant trait that is influenced by the microbiota. We start by discussing the advantages and limitations of using individual gnotobiotic systems and then describe the general procedures for preparing bacterial cultures from the Arabidopsis thaliana At-R-SPHERE culture collection for inoculation and cocultivation in two gnotobiotic plant growth systems using agar and perlite matrix. Additionally, a protocol for inoculation of plants with opportunistic Pseudomonas pathogens is provided. Lastly, we describe a high-throughput system for visual assessment of roots after inoculation with individual mutants of a transposon library generated from a root-derived bacterial commensal. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of bacterial cultures from At-R-SPHERE Support Protocol 1: Validation of strains by sequencing hypervariable regions of the 16S rRNA gene Basic Protocol 2: Coinoculation of plants grown on an agar matrix with microbial elicitor and a defined microbial community Alternate Protocol: Inoculation of plants cultivated in a perlite-based growth system Support Protocol 2: Surface sterilization of Arabidopsis thaliana seeds Basic Protocol 3: Inoculation using a Pseudomonas opportunistic pathogen Basic Protocol 4: Assessment of commensal-mediated root phenotypes using phytostrips.

Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators that Link rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density

The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.

Identification of UDP-rhamnosyltransferases and UDP-galactosyltransferase involved in flavonol glycosylation in Morella rubra

Flavonol glycosides are health-promoting phytochemicals important for human nutrition and plant defense against environmental stresses. Glycosylation modification greatly enriches the diversity of flavonols. Morella rubra, a member of the Myricaceae, contains high amounts of myricetin 3-O-rhamnoside (M3Rha), quercetin 3-O-rhamnoside (Q3Rha), and quercetin 3-O-galactoside (Q3Gal). In the present study, MrUGT78R1 and MrUGT78R2 were identified as two functional UDP-rhamnosyltransferases, while MrUGT78W1 was identified as a UDP-galactosyltransferase. Site-directed mutagenesis identified Pro143 and Asn386 as important residues for rhamnosyl transfer activity of MrUGT78R1, while the two corresponding positions in MrUGT78W1 (i.e. Ser147 and Asn370) also play important roles in galactosyl transfer activity. Transient expression data for these three MrUGTs in Nicotiana benthamiana tested the function of MrUGT78R1 and MrUGT78R2 as rhamnosyltransferases and MrUGT78W1 as a galactosyltransferase in glycosylation of flavonols. This work enriches knowledge of the diversity of UDP-rhamnosyltransferase in planta and identifies two amino acid positions important for both rhamnosyltransferase and galactosyltransferase.

Specialized metabolism and development: An unexpected friendship

Plants produce a myriad of metabolites. Some of them have been regarded for a long time as secondary or specialized metabolites and are considered to have functions mostly in defense and the adaptation of plants to their environment. However, in the last years, new research has shown that these metabolites can also have roles in the regulation of plant growth and development, some acting as signals, through the interaction with hormonal pathways, and some independently of them. These reports provide a glimpse of the functional possibilities that specialized metabolites present in the modulation of plant development and encourage more research in this direction.

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.

Plants Metabolome Study: Emerging Tools and Techniques

Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense responses to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted methods. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) matrix-assisted laser desorption/ionization (MALDI), ion mobility spectrometry (IMS) and nuclear magnetic resonance (NMR) have speed up precise metabolic profiling in plants. Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.

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.

Elucidation of myricetin biosynthesis in Morella rubra of the Myricaceae

Flavonols are health-promoting bioactive compounds important for plant defense and human nutrition. Quercetin (Q) and kaempferol (K) biosynthesis have been studied extensively while little is known about myricetin (M) biosynthesis. The roles of flavonol synthases (FLSs) and flavonoid 3',5'-hydroxylase (F3'5'H) in M biosynthesis in Morella rubra, a member of the Myricaceae rich in M-based flavonols, were investigated. The level of MrFLS transcripts alone did not correlate well with the accumulation of M-based flavonols. However, combined transcript data for MrFLS1 and MrF3'5'H showed a good correlation with the accumulation of M-based flavonols in different tissues of M. rubra. Recombinant MrFLS1 and MrFLS2 proteins showed strong activity with dihydroquercetin (DHQ), dihydrokaempferol (DHK), and dihydromyricetin (DHM) as substrates, while recombinant MrF3'5'H protein preferred converting K to M, amongst a range of substrates. Tobacco (Nicotiana tabacum) overexpressing 35S::MrFLSs produced elevated levels of K-based and Q-based flavonols without affecting M-based flavonol levels, while tobacco overexpressing 35S::MrF3'5'H accumulated significantly higher levels of M-based flavonols. We conclude that M accumulation in M. rubra is affected by gene expression and enzyme specificity of FLS and F3'5'H as well as substrate availability. In the metabolic grid of flavonol biosynthesis, the strong activity of MrF3'5'H with K as substrate additionally promotes metabolic flux towards M in M. rubra.

Light signals counteract alterations caused by simulated microgravity in proliferating plant cells

PREMISE

Light and gravity are fundamental cues for plant development. Our understanding of the effects of light stimuli on plants in space, without gravity, is key to providing conditions for plants to acclimate to the environment. Here we tested the hypothesis that the alterations caused by the absence of gravity in root meristematic cells can be counteracted by light.

METHODS

Seedlings of wild-type Arabidopsis thaliana and two mutants of the essential nucleolar protein nucleolin (nuc1, nuc2) were grown in simulated microgravity, either under a white light photoperiod or under continuous darkness. Key variables of cell proliferation (cell cycle regulation), cell growth (ribosome biogenesis), and auxin transport were measured in the root meristem using in situ cellular markers and transcriptomic methods and compared with those of a 1 g control.

RESULTS

The incorporation of a photoperiod regime was sufficient to attenuate or suppress the effects caused by gravitational stress at the cellular level in the root meristem. In all cases, values for variables recorded from samples receiving light stimuli in simulated microgravity were closer to values from the controls than values from samples grown in darkness. Differential sensitivities were obtained for the two nucleolin mutants.

CONCLUSIONS

Light signals may totally or partially replace gravity signals, significantly improving plant growth and development in microgravity. Despite that, molecular alterations are still compatible with the expected acclimation mechanisms, which need to be better understood. The differential sensitivity of nuc1 and nuc2 mutants to gravitational stress points to new strategies to produce more resilient plants to travel with humans in new extraterrestrial endeavors.