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Metabolite and transcript profiling of VvERF045 OE transgenic lines elucidate the role of this transcription factor in the grapevine ripening physiology

ABSTRACT: We report the transcriptomic profile of L15, a transgenic line overexpressing VvERF045, and the WT as a reference. The main aim is to understand the function of this transcription factor in the overall plant though the differences in the transcript abundance (RNA-seq) and metabolite production. Total RNA from L15 and WT was sequenced with an average genome coverage of more than 100X. Transcripts representing very different biological processes were grouped into ten major categories: protein phosphorilation, wax biosynthesis process, response to andogenous stimulus, cotyledonal vascular tissue/pattern formation, drug transmembrane transport stress, jasmonic acid biosynthesis, response to salt stress, defense response to bacterium, negative regulation. This transcription factor regulates genes involved in many different responses such as drought, sanility and defense suggesting it covers a key role into the plant, moreover into those processes also typical in ripening.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE77240 | GEO | 2016/07/01

REPOSITORIES: GEO

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Metabolite and transcript profiling of VvERF045 OE transgenic lines elucidate the role of this transcription factor in the grapevine ripening physiology

Project description:We report the transcriptomic profile of L15, a transgenic line overexpressing VvERF045, and the WT as a reference. The main aim is to understand the function of this transcription factor in the overall plant though the differences in the transcript abundance (RNA-seq) and metabolite production. Total RNA from L15 and WT was sequenced with an average genome coverage of more than 100X. Transcripts representing very different biological processes were grouped into ten major categories: protein phosphorilation, wax biosynthesis process, response to andogenous stimulus, cotyledonal vascular tissue/pattern formation, drug transmembrane transport stress, jasmonic acid biosynthesis, response to salt stress, defense response to bacterium, negative regulation. This transcription factor regulates genes involved in many different responses such as drought, sanility and defense suggesting it covers a key role into the plant, moreover into those processes also typical in ripening. Total RNA profile of WT and overexpressing VvERF045 transgenic line were generated by deep sequencing, in triplicate paired end with IlluminaHiSep2000. Each biological replicate is derived from pools from five independent in vitro grapevine plants.

2016-07-01 | E-GEOD-77240 | biostudies-arrayexpress

Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing NHRGP (at4g16790) plants (OE-N6)

Project description:Microarray assays can facilitate elucidation of cellular processes and gene network functions in the processes of plant growth and development. To gain further insight into the potential molecular role of the NHRGP gene, we performed Affymetrix whole-genome microarray analysis (http://www.affymetrix.com/) on WT and OE-N6 plants to compare their genome-wide expression profiles. The differently expressed genes revealed by transcriptional profiling of an HRGP-overexpressing transgenic plant indicate that NHRGP are involved in defense response.

2017-12-30 | GSE80710 | GEO

Effect of gibberellins on metabolism during rosette growth in Arabidopsis

Project description:To understand the effect of high and low GA levels on plant metabolism and development in Arabidopsis we made use of the GA biosynthesis inhibitor paclobutrazol (PBZ) and exogenously applied GA. The whole genome response at the translation level was assessed by immunopurification of polysomes from PBZ- and GA treated plants expressing FLAG-tagged ribosomal protein L18 (RPL18B). Polysomal associated RNA was isolated and subjected to affymterix ATH1 CHIP analysis. A total of 140 genes were statistically determined to be differentially translated after GA treatment whereas 89 genes where affected PBZ treatment. Our analysis revealed that GA and PBZ have opposing effects on the expression of cell wall and wax layer biosynthesis related genes. In addition, many genes involved in secondary metabolism are upregulated upon PBZ treatment. A set of SAUR-like genes important for mediating auxin responses are downregulated by PBZ, which is of interest to coordinatian of GA levels with growth and development. Interestingly, GA treatment induces the upregulation of transcription factors related to plant defense and senescence, which is in agreement with the early flowering upon GA treatment. Our study provides a first picture of the response of Arabidopsis to altered GA levels at the translation level, and thus will be valuable for understanding gene regulation at the polysome level. Two replicates for each treatment including GA, PBZ and control samples.

2011-06-03 | E-GEOD-29699 | biostudies-arrayexpress

RNAseq transcriptome profiling of Brachypodium distachyon wildtype; GNRF-OE and gnrf mutants; and SWAM4-OE, SWAM4-DR and swam4 mutants.

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

Studies of wax genes in cotton (Gossypium arboreum)

Project description:The aim of the present study is to list the genes involved in cotton (G. arboreum) leaf epicuticular wax production and deposition. For this purpose differentially expressed genes (especially, down-regulated in wax deficient mutant plant) in wild and epicuticular wax mutant (Gawm3) plants were founded through cDNA microarray, developed from the wild plant leaves.

2015-03-08 | GSE15279 | GEO

Effect of gibberellins on metabolism during rosette growth in Arabidopsis

2011-06-03 | GSE29699 | GEO

Genome-wide analysis of coding and long non-coding RNAs involved in cabbage cuticular wax biosynthesis

Project description:We report the application of high-throughput RNA sequencing for comparing the expression levels of the coding and long noncoding RNAs (lncRNAs) in leaf samples from a glossy mutant nwgl and its wild-type (WT) in cabbage. By obtaining over 163.35 Gb cleaned data generated from six libraries (on average, more than 26.48 Gb clean data for each sample replicate), we identified 1247 differential expressed genes (DEGs) and 148 differential expressed lncRNAs in nwgl leaves relative to WT. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the DEGs and cis-regulated target genes for differential expressed lncRNAs were significantly enriched in wax and lipid biosynthetic and/or metabolic processes. Our results provide the novel foundation to explore the complex molecular basis of cuticular wax biosynthesis.

2019-07-26 | GSE130405 | GEO

Identification of DIR1-dependant cellular responses required for systemic acquired resistance in guard cells

Project description:After localized invasion by bacterial pathogens, systemic acquired resistance (SAR) is induced in uninfected plant tissues, resulting in enhanced defense against a broad range of pathogens. Although SAR requires mobilization of signaling molecules via the plant vasculature, the specific mechanisms remain elusive. The lipid transfer protein-defective in induced resistance 1-1 (DIR1-1) was identified in Arabidopsis thaliana by screening for mutants that were defective in SAR. Since then, the structure and lipid-binding properties of DIR1 have been determined, showing that its barrel structure can bind two, long-chain fatty-acid molecules. Several SAR mobile signals, including dehydroabietinal (DA), azelaic acid (AzA), and glycerol-3-phosphate (G3P) are dependent on DIR1 for transport to systemic leaves. Closure of stomata, controlled by guard cells, is a local response to bacteria. Here we demonstrate that stomatal response to pathogens is altered in systemic leaves by SAR, and this guard cell SAR defense requires DIR1. Using a multi-omics approach, we have determined potential SAR signaling mechanisms specific for guard cells in systemic leaves by profiling metabolite, lipid, and protein differences between guard cells in wild type and dir1-1 mutant during SAR. We identified two 18C fatty actyls and two 16C wax esters as putative SAR-related molecules dependent on DIR1. Proteins and metabolites related to amino acid biosynthesis and response to stimulus were altered in guard cells of dir1-1 compared to wild type. Identification of guard cell-specific SAR-related molecules will lead to new avenues of genetic modifications/molecular breeding for disease resistant plants.

2022-02-17 | PXD024991 | Pride

Expression data from WT and atrap mutant Arabidopsis rosette leaves

Project description:AtRAP, which is a bacterial-induced small RNA target gene, negatively regulate plant defense response. To identity genes that are regulated by AtRAP, we performed microarray analysis on the (Wild Type) WT and atrap mutant.

2017-05-11 | GSE98376 | GEO

Transgenic Ah24-OE vs Wild type Col 0 Arabidopsis plants

Project description:Transcriptional profiling of Arabidopsis rossette leaves comparing WT Col-0 with a transgenic line overexpressing Ah24 gene from Amaranthus hypochondriacus. One-condition experiment WT vs Ah24 OE plant leaves.

2015-06-26 | E-GEOD-70272 | biostudies-arrayexpress

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