Dopamine biosynthesis in plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Brachypodium distachyon
PROVIDER: GSE284170 | GEO | 2025/12/27
REPOSITORIES: GEO
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Project description:Plant cell walls are complex structures that contain a matrix of cellulose, lignin and hemicellulose. The regulation of the biosynthesis of these components has been well-studied in the eudicot plant Arabidopsis thaliana, and a transcriptional network has been elucidated. Several NAC and MYB family transcription factors are key regulators of secondary cell wall biosynthesis, and their functional characterization provides significant insight into the complex underlying transcriptional network. Genetic and structural evidence suggests that genes controlling this process might be different between eudicots and monocots. Here, the model grass Brachypodium distachyon has been selected to characterize the function of GNRF (GRASS NAC REPRESSOR OF FLOWERING), SWAM1 (SECONDARY WALL ASSOCIATED MYB1), and SWAM4 in the regulation of secondary cell wall biosynthesis. Functional characterization was performed by using the overexpression plants GNRF-OE and SWAM4-OE; sodium azide mutant plants from a TILLING (Targeting Induced Local Lesion IN Genome) collection for gnrf-1, gnrf-2, gnrf-3, gnrf-4, gnrf-5, swam4-1, and swam4-2; a T-DNA insertional mutant plant, gnrf-6; and a dominant repressor plant, SWAM4-DR. GNRF-OE plants remained at juvenile stage and exhibited persistent vegetative growth, and some gnrf mutant plants were late flowering. SWAM4-DR plants were severely dwarfed. Stems of all genotypes mentioned above were subjected to RNA-seq analysis.
2019-08-02 | E-MTAB-8172 | biostudies-arrayexpress
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2020-06-22 | GSE145255 | GEO
Project description:A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (c3h/apx) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, c3h/apx plant shows unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a global proteomics measurement of the stem tissue of the model grass Brachypodium distachyon was used to investigate the underlying mechanism of c3h/apx-associated lignin modification and negative growth phenotype. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense response associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.
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Project description:Sulfur-deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants Glucosinolates (GSLs) in the plant order of the Brassicales are sulfur-rich secondary metabolites harboring anti-pathogenic and anti-herbivory plant-protective functions as well as possessing medicinal properties such as carcinopreventive and antibiotic activities. Plants repress GSL biosynthesis upon sulfur deficiency (–S), hence, field performance and medicinal quality are impaired by inadequate sulfate supply. The molecular mechanism linking –S to GSL biosynthesis has remained understudied. We report here the identification of the –S marker genes Sulfur deficiency induced1 and Sulfur deficiency induced2 (SDI1, SDI2) acting as major repressors controlling GSL biosynthesis in Arabidopsis under –S condition. SDI1 and SDI2 expression negatively correlated with GSL biosynthesis in both transcript and metabolite levels. Principal component analysis of transcriptome data indicated that SDI1 regulates aliphatic GSL biosynthesis as part of –S-response. SDI1 was localized to the nucleus and interacted with MYB28, a major transcription factor promoting aliphatic GSL biosynthesis, in both yeast and plant cells. SDI1 inhibited transcription of aliphatic GSL biosynthetic genes through maintaining the DNA-binding composition in a form of a SDI1-MYB28 complex, leading to down-regulate GSL biosynthesis and prioritize sulfate usage for primary metabolites under sulfur-deprived conditions.
2016-10-07 | GSE81347 | GEO
Project description:Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds and faster seed germination, whereas gene silencing by RNA interference (RNAi) caused poor fruit set and inhibited seed germination. Gene expression analysis showed that SlZFP2 represses ABA biosynthesis mainly through downregulation of the ABA biosynthetic genes SITIENS (SIT), FLACCA (FLC) and aldehyde oxidase SlAO1. SlZFP2 delays the onset of ripening through suppression of the ripening regulator COLORLESS NON-RIPENING (CNR). Using bacterial one hybrid screening and a selected amplification and binding assay we identified the (A/T)(G/C)TT repeat as the core binding sequence of SlZFP2. We further identified a large number of tomato genes containing putative SlZFP2 binding sites in their promoter regions. Chromatin immunoprecipitation and electrophoretic mobility shift assays demonstrated that SIT, FLC and SlAO1 are direct targets of SlZFP2 through binding to their promoter regions. We propose that SlZFP2 represents a novel negative regulator for fine tuning ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.To gain further insight on transcriptome changes regulated by SlZFP2, we sequenced a representative SlZFP2 RNAi line in LA1589 background and its nontransgenic sibling (WT) on a Miseq platform. The RNAi line 207 showed defected fruit set and ABA biosynthesis were chosen for profiling gene expression via RNA sequencing. Its nontransgenic sibling was served as controls. Three biological replicates were conducted.
2015-11-23 | E-GEOD-63838 | biostudies-arrayexpress
Project description:Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds and faster seed germination, whereas gene silencing by RNA interference (RNAi) caused poor fruit set and inhibited seed germination. Gene expression analysis showed that SlZFP2 represses ABA biosynthesis mainly through downregulation of the ABA biosynthetic genes SITIENS (SIT), FLACCA (FLC) and aldehyde oxidase SlAO1. SlZFP2 delays the onset of ripening through suppression of the ripening regulator COLORLESS NON-RIPENING (CNR). Using bacterial one hybrid screening and a selected amplification and binding assay we identified the (A/T)(G/C)TT repeat as the core binding sequence of SlZFP2. We further identified a large number of tomato genes containing putative SlZFP2 binding sites in their promoter regions. Chromatin immunoprecipitation and electrophoretic mobility shift assays demonstrated that SIT, FLC and SlAO1 are direct targets of SlZFP2 through binding to their promoter regions. We propose that SlZFP2 represents a novel negative regulator for fine tuning ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.To gain further insight on transcriptome changes regulated by SlZFP2, we sequenced a representative SlZFP2 RNAi line in LA1589 background and its nontransgenic sibling (WT) on a Miseq platform.
2015-11-23 | GSE63838 | GEO
Project description:Dendrobium plants are perennial herbs in the family Orchidaceae (Dendrobium Sw.). Due to protocorm can also produce plant-specific useful metabolites, protocorm is becoming a good substitute. MicroRNAs play essential roles in plant growth, development, and the response to environmental stresses, and they are widely used for prediction of molecular functions for biosynthesizing active comportments in medicinal plants. To obtain insight into the function of miRNAs in Dendrobium plants. Illumina sequencing of D. nobile protocorm, D. officinale protocorm and D. nobile leaf were conducted. A total of 439, 412 and 432 miRNAs were identified in three samples, and their expression levels were significantly different. Specially, 2, 12 and 4 specific miRNAs were identified. Through integrated GO and KEGG function annotation, miRNAs mainly involved in metabolic pathways, plant hormone signal transduction, biological regulation and protein binding. AACT, MK, DXR and HDS as important enzymes in synthesizing basic precursor isoprene pyrophosphate (IPP). were predicted controlled by 6 different miRNAs in terpenoid backbone biosynthesis pathway. 26 miRNAs participated in Auxin, Cytoklinine, Abscisic acid, Jasmonic acid and Salicylic acid signal transduction pathway. Our results could provide valuable information about miRNAs involved in terpenoid biosynthesis and plant hormone signal transduction pathway in D. nobile and candidate genes for increasing the yield of dendrobine.
2022-08-01 | GSE135444 | GEO
Project description:Purpose: We here wanted to describe the gene regulation of Gigaspora rosea in association with phyllogenetically divergent plant hosts, and compare these results with gene regulation occuring in R. irregularis, the model arbuscular mycorrhizal fungus. Methods: mRNA from Medicago truncatula (legume), Brachypodium distachyon (grass) in association with G. rosea, and extra radical mycelium of G.rosea were sequenced by Illumina. Reads were mapped on a in-house de novo transcript assembly with the software CLC workbench. Fungal gene expression in the different host plants was compared to extra radical hyphae as reference. Results: Sets of 1891 and 1566 G. rosea genes were highly overexpressed (fold change >5 ; FDR <0,05 and experimental value difference > 10) , in M. truncatula and B. distachyon respectively compared to ERM, among which 802 of them were up-regulated in both plants. Non common up-regulated genes are mainly found non statistically robust in one condition. Conclusions: Our study represents the first transcriptomic analysis on several hosts for this fungal species. These results showed that the interaction between plants and AMF is highly conserved.
2016-03-07 | GSE67911 | GEO
Project description:The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using Parallel Analysis of RNA Ends (PARE) data is lacking in B. distachyon. B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset to analyze small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.
2013-12-06 | GSE52441 | GEO
Project description:In plants, fatty acids are de novo synthesized predominantly in plastids fromacetyl-CoA. Although fatty acid biosynthesis has been biochemically well-studied, little isknown about the regulatory mechanisms of the pathway. Here, we show that overexpressionof the Arabidopsis (Arabidopsis thaliana) LEAFY COTYLEDON1 (LEC1) gene causesglobally increased expression of fatty acid biosynthetic genes, which are involved in keyreactions of condensation, chain elongation and desaturation of fatty acid biosynthesis. Inthe plastidial fatty acid synthetic pathway, over 58% of known enzyme-coding genes areupregulated in LEC1-overexpressing transgenic plants, including those encoding threesubunits of acetyl-CoA carboxylase, a key enzyme controlling the fatty acid biosynthesisflux. Moreover, genes involved in glycolysis and lipid accumulation are also upregulated.Consistent with these results, levels of major fatty acid species and lipids were substantiallyincreased in the transgenic plants. Genetic analysis indicates that the LEC1 function ispartially dependent on ABSCISIC ACID INSENSITIVE3, FUSCA3 and WRINKLED1 in theregulation of fatty acid biosynthesis. Moreover, a similar phenotype was observed intransgenic Arabidopsis plants overexpressing two LEC1-like genes of Brassica napus.These results suggest that LEC1 and LEC1-like genes act as key regulators to coordinate theexpression of fatty acid biosynthetic genes, thereby representing a promising target forgenetic improvement of oil-production plants.
2008-08-31 | GSE12137 | GEO