Arabidopsis CDF3 transcription factor increases carbon and nitrogen assimilation and yield in trans-grafted tomato plants.

Grafting in tomato (Solanum lycopersicum L.) has mainly been used to prevent damage by soil-borne pathogens and the negative effects of abiotic stresses, although productivity and fruit quality can also be enhanced using high vigor rootstocks. In the context of a low nutrients input agriculture, the grafting of elite cultivars onto rootstocks displaying higher Nitrogen Use Efficiency (NUE) supports a direct strategy for yield maximization. In this study we assessed the use of plants overexpressing the Arabidopsis (AtCDF3) or tomato (SlCDF3) CDF3 genes, previously reported to increase NUE in tomato, as rootstocks to improve yield in the grafted scion under low N inputs. We found that the AtCDF3 gene induced greater production of sugars and amino acids, which allowed for greater biomass and fruit yield under both sufficient and limiting N supplies. Conversely, no positive impact was found with the SlCDF3 gene. Hormone analyses suggest that gibberellins (GA4), auxin and cytokinins (tZ) might be involved in the AtCDF3 responses to N. The differential responses triggered by the two genes could be related, at least in part, to the mobility of the AtCDF3 transcript through the phloem to the shoot. Consistently, a higher expression of the target genes of the transcription factor, such as glutamine synthase 2 (SlGS2) and GA oxidase 3 (SlGA3ox), involved in amino acid and gibberellin biosynthesis, respectively, was observed in the leaves of this graft combination. Altogether, our results provided further insights into the mode of action of CDF3 genes and their biotechnology potential for transgrafting approaches.

Polymeric Inclusion Membranes Based on Ionic Liquids for Selective Separation of Metal Ions.

In this work, poly(vinyl chloride)-based polymeric ionic liquid inclusion membranes were used in the selective separation of Fe(III), Zn(II), Cd(II), and Cu(II) from hydrochloride aqueous solutions. The ionic liquids under study were 1-octyl-3-methylimidazolium hexafluorophosphate, [omim+][PF6-] and methyl trioctyl ammonium chloride, [MTOA+][Cl-]. For this purpose, stability studies of different IL/base polymer compositions against aqueous phases were carried out. Among all polymer inclusion membranes studied, [omim+][PF6-]/PVC membranes at a ratio of 30/70 and [MTOA+][Cl-]/PVC membranes at a ratio of 70/30 were able to retain up to 82% and 48% of the weight of the initial ionic liquid, respectively, after being exposed to a solution of metal ions in 1 M HCl for 2048 h (85 days). It was found that polymer inclusion membranes based on the ionic liquid methyl trioctyl ammonium chloride allowed the selective separation of Zn(II)/Cu(II) and Zn(II)/Fe(III) mixtures with separation factors of 1996, 606 and, to a lesser extent but also satisfactorily, Cd(II)/Cu(II) mixtures, with a separation factor of 112. Therefore, selecting the appropriate ionic liquid/base polymer mixture makes it possible to create polymeric inclusion membranes capable of selectively separating target metal ions.

Ectopic expression of the AtCDF1 transcription factor in potato enhances tuber starch and amino acid contents and yield under open field conditions.

Introduction: Cycling Dof transcription factors (CDFs) have been involved in different aspects of plant growth and development. In Arabidopsis and tomato, one member of this family (CDF1) has recently been associated with the regulation of primary metabolism and abiotic stress responses, but their roles in crop production under open field conditions remain unknown. Methods: In this study, we compared the growth, and tuber yield and composition of plants ectopically expressing the CDF1 gene from Arabidopsis under the control of the 35S promoter with wild-type (WT) potato plants cultured in growth chamber and open field conditions. Results: In growth chambers, the 35S::AtCDF1 plants showed a greater tuber yield than the WT by increasing the biomass partition for tuber development. Under field conditions, the ectopic expression of CDF1 also promoted the sink strength of the tubers, since 35S::AtCDF1 plants exhibited significant increases in tuber size and weight resulting in higher tuber yield. A metabolomic analysis revealed that tubers of 35S::AtCDF1 plants cultured under open field conditions accumulated higher levels of glucose, starch and amino acids than WT tubers. A comparative proteomic analysis of tubers of 35S::AtCDF1 and WT plants cultured under open field conditions revealed that these changes can be accounted for changes in the expression of proteins involved in energy production and different aspects of C and N metabolism. Discussion: The results from this study advance our collective understanding of the role of CDFs and are of great interest for the purposes of improving the yield and breeding of crop plants.

Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert.

BACKGROUND: Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400-4500 m a.s.l.) of the Talabre-Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities. RESULTS: Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT. CONCLUSIONS: In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.

A Revised View of the LSU Gene Family: New Functions in Plant Stress Responses and Phytohormone Signaling.

LSUs (RESPONSE TO LOW SULFUR) are plant-specific proteins of unknown function that were initially identified during transcriptomic studies of the sulfur deficiency response in Arabidopsis. Recent functional studies have shown that LSUs are important hubs of protein interaction networks with potential roles in plant stress responses. In particular, LSU proteins have been reported to interact with members of the brassinosteroid, jasmonate signaling, and ethylene biosynthetic pathways, suggesting that LSUs may be involved in response to plant stress through modulation of phytohormones. Furthermore, in silico analysis of the promoter regions of LSU genes in Arabidopsis has revealed the presence of cis-regulatory elements that are potentially responsive to phytohormones such as ABA, auxin, and jasmonic acid, suggesting crosstalk between LSU proteins and phytohormones. In this review, we summarize current knowledge about the LSU gene family in plants and its potential role in phytohormone responses.

Evolutionary and Gene Expression Analyses Reveal New Insights into the Role of LSU Gene-Family in Plant Responses to Sulfate-Deficiency.

LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein-protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU genomic organization, expression and function comes from studies in Arabidopsis and tobacco, while little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole-genome sequences available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Protein sequence analyses showed four new motifs that further support the subgroup classification by phylogenetic analyses. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S deficiency, suggesting that these genes might play a key role in S stress responses. In summary, our results indicate that LSU genes belong to the Spermatophyta-specific gene family and their response to S deficiency is conserved in angiosperms.

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

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

Magneto-Transport in Flexible 3D Networks Made of Interconnected Magnetic Nanowires and Nanotubes.

Electrochemical deposition of interconnected nanowires and nanotubes made of ferromagnetic metals into track-etched polycarbonate templates with crossed nanochannels has been revealed suitable for the fabrication of mechanically stable three-dimensional magnetic nanostructures with large surface area. These 3D networks embedded into flexible polymer membranes are also planar and lightweight. This fabrication technique allows for the control of the geometric characteristics and material composition of interconnected magnetic nanowire or nanotube networks, which can be used to fine-tune their magnetic and magneto-transport properties. The magnetostatic contribution to the magnetic anisotropy of crossed nanowire networks can be easily controlled using the diameter, packing density, or angle distribution characteristics. Furthermore, the fabrication of Co and Co-rich NiCo alloy crossed nanowires with textured hcp phases leads to an additional significant magnetocrystalline contribution to the magnetic anisotropy that can either compete or add to the magnetostatic contribution. The fabrication of an interconnected nanotube network has also been demonstrated, where the hollow core and the control over the tube wall thickness add another degree of freedom to control the magnetic properties and magnetization reversal mechanisms. Finally, three-dimensional networks made of interconnected multilayered nanowire with a succession of ferromagnetic and non-magnetic layers have been successfully fabricated, leading to giant magnetoresistance responses measured in the current-perpendicular-to-plane configuration. These interconnected nanowire networks have high potential as integrated, reliable, and stable magnetic field sensors; magnetic devices for memory and logic operations; or neuromorphic computing.

Control of the asymmetric growth of nanowire arrays with gradient profiles.

A novel electrochemical methodology for the growth of arrays of Ni and Co nanowires (NWs) with linear and non-linear varying micro-height gradient profiles (µHGPs), has been developed. The growth mechanism of these microstructures consists of a three-dimensional growth originating from the allowed electrical contact between the electrolyte and the edges of the cathode at the bottom side of porous alumina membranes. It has been shown that the morphology of these microstructures strongly depends on electrodeposition parameters like the cation material and concentration and the reduction potential. At constant reduction potentials, linear Ni µHGPs with trapezoid-like geometry are obtained, whereas deviations from this simple morphology are observed for Co µHGPs. In this regime, the µHGPs average inclination angle decreases for more negative reduction potential values, leading as a result to more laterally extended microstructures. Besides, more complex morphologies have been obtained by varying the reduction potential using a simple power function of time. Using this strategy allows us to accelerate or decelerate the reduction potential in order to change the µHGPs morphology, so to obtain convex- or concave-like profiles. This methodology is a novel and reliable strategy to synthesize µHGPs into porous alumina membranes with controlled and well-defined morphologies. Furthermore, the synthesized low dimensional asymmetrically loaded nanowired substrates with µHGPs are interesting for their application in micro-antennas for localized electromagnetic radiation, magnetic stray field gradients in microfluidic systems, non-reciprocal microwave absorption, and super-capacitive devices for which a very large surface area and controlled morphology are key requirements.

Arabidopsis thaliana transcription factors MYB28 and MYB29 shape ammonium stress responses by regulating Fe homeostasis.

Although ammonium (NH4+ ) is a key intermediate of plant nitrogen metabolism, high concentrations of NH4+ in the soil provoke physiological disorders that lead to the development of stress symptoms. Ammonium nutrition was shown to induce the accumulation of glucosinolates (GSLs) in leaves of different Brassicaceae species. To further understand the link between ammonium nutrition and GSLs, we analysed the ammonium stress response of Arabidopsis mutants impaired in GSL metabolic pathway. We showed that the MYB28 and MYB29 double mutant (myb28myb29), which is almost deprived of aliphatic GSLs, is highly hypersensitive to ammonium nutrition. Moreover, we evidenced that the stress symptoms developed were not a consequence of the lack of aliphatic GSLs. Transcriptomic analysis highlighted the induction of an iron (Fe) deficiency response in myb28myb29 under ammonium nutrition. Consistently, ammonium-grown myb28myb29 plants showed altered Fe accumulation and homeostasis. Interestingly, we showed overall that growing Arabidopsis with increased Fe availability relieved ammonium stress symptoms and that this was associated with MYB28 and MYB29 expression. Taken together, our data indicated that the control of Fe homeostasis was crucial for the Arabidopsis response to ammonium nutrition and evidenced that MYB28 and MYB29 play a role in this control.

Predicting microbiomes through a deep latent space.

MOTIVATION: Microbial communities influence their environment by modifying the availability of compounds, such as nutrients or chemical elicitors. Knowing the microbial composition of a site is therefore relevant to improve productivity or health. However, sequencing facilities are not always available, or may be prohibitively expensive in some cases. Thus, it would be desirable to computationally predict the microbial composition from more accessible, easily-measured features. RESULTS: Integrating deep learning techniques with microbiome data, we propose an artificial neural network architecture based on heterogeneous autoencoders to condense the long vector of microbial abundance values into a deep latent space representation. Then, we design a model to predict the deep latent space and, consequently, to predict the complete microbial composition using environmental features as input. The performance of our system is examined using the rhizosphere microbiome of Maize. We reconstruct the microbial composition (717 taxa) from the deep latent space (10 values) with high fidelity (>0.9 Pearson correlation). We then successfully predict microbial composition from environmental variables, such as plant age, temperature or precipitation (0.73 Pearson correlation, 0.42 Bray-Curtis). We extend this to predict microbiome composition under hypothetical scenarios, such as future climate change conditions. Finally, via transfer learning, we predict microbial composition in a distinct scenario with only 100 sequences, and distinct environmental features. We propose that our deep latent space may assist microbiome-engineering strategies when technical or financial resources are limited, through predicting current or future microbiome compositions. AVAILABILITY AND IMPLEMENTATION: Software, results and data are available at https://github.com/jorgemf/DeepLatentMicrobiome. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The Arabidopsis Transcription Factor CDF3 Is Involved in Nitrogen Responses and Improves Nitrogen Use Efficiency in Tomato.

Nitrate is an essential macronutrient and a signal molecule that regulates the expression of multiple genes involved in plant growth and development. Here, we describe the participation of Arabidopsis DNA binding with one finger (DOF) transcription factor CDF3 in nitrate responses and shows that CDF3 gene is induced under nitrate starvation. Moreover, knockout cdf3 mutant plants exhibit nitrate-dependent lateral and primary root modifications, whereas CDF3 overexpression plants show increased biomass and enhanced root development under both nitrogen poor and rich conditions. Expression analyses of 35S::CDF3 lines reveled that CDF3 regulates the expression of an important set of nitrate responsive genes including, glutamine synthetase-1, glutamate synthase-2, nitrate reductase-1, and nitrate transporters NRT2.1, NRT2.4, and NRT2.5 as well as carbon assimilation genes like PK1 and PEPC1 in response to N availability. Consistently, metabolite profiling disclosed that the total amount of key N metabolites like glutamate, glutamine, and asparagine were higher in CDF3-overexpressing plants, but lower in cdf3-1 in N limiting conditions. Moreover, overexpression of CDF3 in tomato increased N accumulation and yield efficiency under both optimum and limiting N supply. These results highlight CDF3 as an important regulatory factor for the nitrate response, and its potential for improving N use efficiency in crops.

Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum.

BACKGROUND: Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale. RESULTS: Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis. CONCLUSIONS: Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.

Protein quantification by bicinchoninic acid (BCA) assay follows complex kinetics and can be performed at short incubation times.

Amongst the available methodologies for protein determination, the bicinchoninic acid (BCA) assay highlights for its simplicity, sensitivity, repeatability and reproducibility. Nevertheless, in spite that the general principle behind this methodology is known, there are still unanswered questions regarding the chemistry behind the assay and the experimental conditions commonly employed. The present work explored the kinetics, and the analytical response of the assay to free amino acids, peptides (containing tryptophan and tyrosine), and proteins. Results revealed kinetic profiles characterized by the absence of plateaus, with behaviors depending on the type of the sample. The latter, along with contribution to the BCA index elicited by oxidation products generated at the side chain of tryptophan and tyrosine, as well as pre-oxidized ß-casein, evidenced the presence of complex reaction mechanisms. In spite of such complexity, our results showed that the BCA index is not modulated by the incubation time. This applies for responses producing absorbance intensities (at 562 nm) higher than 0.1. Therefore, we propose that the assay can be applied at shorter incubation times (15 min) than those indicated in manufactures specifications, and usually used by researches and industry (30 min at 37 °C).

The targeted overexpression of SlCDF4 in the fruit enhances tomato size and yield involving gibberellin signalling.

Tomato is one of the most widely cultivated vegetable crops and a model for studying fruit biology. Although several genes involved in the traits of fruit quality, development and size have been identified, little is known about the regulatory genes controlling its growth. In this study, we characterized the role of the tomato SlCDF4 gene in fruit development, a cycling DOF-type transcription factor highly expressed in fruits. The targeted overexpression of SlCDF4 gene in the fruit induced an increased yield based on a higher amount of both water and dry matter accumulated in the fruits. Accordingly, transcript levels of genes involved in water transport and cell division and expansion during the fruit enlargement phase also increased. Furthermore, the larger amount of biomass partitioned to the fruit relied on the greater sink strength of the fruits induced by the increased activity of sucrose-metabolising enzymes. Additionally, our results suggest a positive role of SlCDF4 in the gibberellin-signalling pathway through the modulation of GA4 biosynthesis. Finally, the overexpression of SlCDF4 also promoted changes in the profile of carbon and nitrogen compounds related to fruit quality. Overall, our results unveil SlCDF4 as a new key factor controlling tomato size and composition.

Science production of pesticide residues in honey research: A descriptive bibliometric study.

This work aims to provide a comprehensive study of the available research information on pesticide residues in honey through literature analysis. The research advancements within this research field from 1948 to 2019 are addressed using the Web of Science database. The results from the 685 articles analyzed indicate that this research field is in the focus of interest nowadays (Price index: 47.5%). The yearly production increased steadily from 2001 on, and authors, journals, and institutions followed Lotka's law. On the other hand, Pico, Y (Spain) (2.5%), Journal of Chromatography A (5.8%), the USA (15.0%) and Agricultural Research Service (USA) (4.0%) were the most productive author, journal, country and institution, respectively. The research hotspots of this field, according to keyword analysis, are related to the chromatographic techniques for the determination of pesticides such as imidacloprid, neonicotinoids, or coumaphos in honey and derivate products such as propolis and wax.

A descriptive bibliometric study on bioavailability of pesticides in vegetables, food or wine research (1976-2018).

A bibliometric analysis based on the Web of Science© (WOS) database was performed on bioavailability of pesticides in vegetables, food or wine related studies published from inception to 2018. A total of 1202 articles were subjected to examination. The results reveal that yearly production of scientific articles increased steadily. Journal and institution production, and author's keywords frequencies followed the Lotka's Law. Khan SU and White JC were the most productive authors. The most productive journals were Journal of Agricultural and Food Chemistry (55), and Journal of Ethnopharmacology (48), and the most common WOS subject category was Pharmacology & Pharmacy (419). USA (h-index of 40) produced 21.7 % of all articles, closely followed by China (20.6 %). Chinese Academy of Sciences (34) was the most productive research institutions. Finally, current and future trends in this area should focus on keywords such as pharmacokinetics, curcumin, in-vitro, nanoparticles, oral (bioavailability) and cell.

CDF transcription factors: plant regulators to deal with extreme environmental conditions.

In terrestrial environments, water and nutrient availabilities and temperature conditions are highly variable, and especially in extreme environments limit survival, growth, and reproduction of plants. To sustain growth and maintain cell integrity under unfavourable environmental conditions, plants have developed a variety of biochemical and physiological mechanisms, orchestrated by a large set of stress-responsive genes and a complex network of transcription factors. Recently, cycling DOF factors (CDFs), a group of plant-specific transcription factors (TFs), were identified as components of the transcriptional regulatory networks involved in the control of abiotic stress responses. The majority of the members of this TF family are activated in response to a wide range of adverse environmental conditions in different plant species. CDFs regulate different aspects of plant growth and development such as photoperiodic flowering-time control and root and shoot growth. While most of the functional characterization of CDFs has been reported in Arabidopsis, recent data suggest that their diverse roles extend to other plant species. In this review, we integrate information related to structure and functions of CDFs in plants, with special emphasis on their role in plant responses to adverse environmental conditions.

Bioreactor Membranes for Laccase Immobilization Optimized by Ionic Liquids and Cross-Linking Agents.

A novel concept of membrane bioreactor based on polymeric ionic liquids laccase membrane has been implemented in batch process for decolorization of the anthraquinonic dye Remazol Brillant Blue R (RBBR). New laccase immobilization strategy has been optimized by casting the enzyme into a polymeric inclusion membrane (PIM) using ionic liquids (ILs) and polyvinyl chloride (PVC) leading to laccase polymeric IL membrane (PILM). Four different ILs (1-octyl-3-metylimidazolium bis(trifluoromethylsulfonyl)imide, [OMIM][NTF2]; cholinium bis(trifluoromethylsulfonyl)imide, [Ch ol][NTF2]; cholinium dihydrogenphosphate, [Chol][H2PO4] and hydroxyethylammonium formate, [HEA][Fo]) have been screened and mixed to constitute the active phase of the support of PIM. This strategy has been fully succeeded since high laccase immobilization rates were recorded (about 98%) when using the optimal mixture containing three ILs (45% [OMIM][NTf2]/5% [Chol][NTf2]/2.5% [HEA][Fo]) and supplemented by 0.5% glutaraldehyde. It was found that such mixture contributes to increase the stability and reusability of laccase-PILM during eight successive assays in a batch discontinued stirred reactor. Decolorization rate of 75% has been reached in the batch decolorization process of RBBR with high reusability yield. Graphical Abstract Decolorization of RBBR by PILM_laccase.

Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots.

Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.