Null
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB74909 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In the early stages (30 days) of phosphorus deficiency stress, Epimedium pubescens leaves cope with short-term phosphorus deficiency by increasing the expression of related genes such as carbon metabolism, flavonoid synthesis and hormone signal transduction pathways, producing sufficient energy, scavenging ROS, and adjusting plant morphology. However, with the extension of stress duration to 90 days, the expression of genes related to phosphorus cycling and phosphorus recovery (PHT1-4, PHO1 homolog3, PAP) was upregulated, and transcriptional changes and post-transcriptional regulation (miRNA regulation and protein modification) were enhanced to resist long-term phosphorus deficiency stress. In addition, bHLH, MYB, NAC, WRKY and other families also play an important role in regulating gene expression and coping with phosphorus deficiency stress, especially MYB60 negatively regulates flavonoid synthesis pathway, which is significantly down-regulated in leaves treated with phosphorus deficiency for 30 days, thereby promoting the accumulation of flavonoid compounds in leaves.
2024-03-30 | GSE259444 | GEO
Project description:In the early stages (30 days) of phosphorus deficiency stress, Epimedium pubescens leaves cope with short-term phosphorus deficiency by increasing the expression of related genes such as carbon metabolism, flavonoid synthesis and hormone signal transduction pathways, producing sufficient energy, scavenging ROS, and adjusting plant morphology. However, with the extension of stress duration to 90 days, the expression of genes related to phosphorus cycling and phosphorus recovery (PHT1-4, PHO1 homolog3, PAP) was upregulated, and transcriptional changes and post-transcriptional regulation (miRNA regulation and protein modification) were enhanced to resist long-term phosphorus deficiency stress. In addition, bHLH, MYB, NAC, WRKY and other families also play an important role in regulating gene expression and coping with phosphorus deficiency stress, especially MYB60 negatively regulates flavonoid synthesis pathway, which is significantly down-regulated in leaves treated with phosphorus deficiency for 30 days, thereby promoting the accumulation of flavonoid compounds in leaves.
2024-03-30 | GSE259442 | GEO
Project description:In the present study the effect of phosphorus (P) limitation was investigated in the microalgae Nannochloropsis oceanica. Algal cultures were analysed for transcriptomic and lipidomic changes during P-limited growth, with sample time points: 24h, 48h, 53h, 58h and 70h. The transcriptome data identified unique P acquiring genes and the results were also supported by corresponding changes in the lipidome dataset, which showed a lipid class shift from phospholipids to phosphorus-free lipids under P-limitation. During the exponential growth phase a gradual 6-fold reduction of the cellular P level induced RNA transcripts encoding proteins acquiring P from inorganic and organic sources. For this process 6 novel purple acid phosphatases and 5 unique Pi transporters were identified. Additionally, increased gene expression of 2 triose-phosphate transporters (TPTs) indicated the importance of the carbon-to-phosphorus balance for the plastidial anabolic processes. Phospholipid degradation was shown to be an early response to P limitation, by overexpression of sets of 2 novel glycerophosphoryl diester phosphodiesterases (GDPDs), and 3 patatin-like phospholipases of type A. To compensate for phospholipid degradation, the transcriptome and lipidome level showed increased synthesis of sulfoquinovosyl diacylglycerol (SQDG), and diacylglyceroltrimethylhomoserine (DGTS). Phosphorus limitation triggered the lipid class shift in both the exponential growth phase and the triacylglycerol (TAG) accumulation period to release P and increase the organic C:P ratio.
2017-10-31 | GSE95774 | GEO
Project description:We propose a carbon source dependent genetic regulatory network for the budding yeast Saccharomyces cerevisiae, derived from quantitative proteomic analyses integrated with bioinformatics knowledge of regulatory pathways and protein interactions. The proposed network, comprising 1247 transcription factor interactions and 126 chaperone interactions, defines the proteome shift in the cell when growing under different carbon sources. We used a label-free proteomics strategy to quantify alterations in protein abundance for S. cerevisiae when grown on minimal media using glucose, galactose, maltose and trehalose as sole carbon sources.
2021-03-22 | PXD009420 | Pride
Project description:As part of Microme, we have been investigating the effects of single carbon sources upon Salmonella Typhimurium and Salmonella Enteritidis. These strains have been grown in a defined medium, supplemented with single carbon sources, in order to determine which genes are expressed in the presence of which carbon sources.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-08-20 | E-ERAD-227 | biostudies-arrayexpress
Project description:To cope with limiting phosphorus (P) availability, plants have evolved a series of mechanisms to recycle internal P sources and to acquire P from the soil. One of these mechanisms is the release of low-molecular weight carboxylates, such as malate, which helps to liberate phosphate desorbed to aluminum and iron oxides. As malate release into the rhizosphere and root apopplast also increases iron availability. To identity genes involved in this interaction, we investigated time-dependent changes in the transcriptome of Arabidopsis thaliana roots exposed to sufficient and deficient phoshate levels .
2023-11-15 | GSE217790 | GEO
Project description:Phosphorus is a critical nutrient controlling phytoplankton growth. Availability of this limiting factor can vary significantly in space and time, particularly in dynamic aquatic ecosystems. Diatoms are important eukaryotic phytoplankton that thrive in regions of pulsed phosphate supply, yet little is known of the sensory mechanisms enabling them to detect and rapidly respond to phosphorus availability. Here we show that phosphorus-starved diatoms utilise a novel Ca2+-dependent signalling pathway to sense and regulate cellular recovery following phosphorus resupply. This pathway, which has not previously been described in eukaryotes, is sensitive to sub-micromolar concentrations of phosphate, alongside a range of environmentally relevant phosphorus forms. Using comparative proteomics, we have characterised early adaptations governing diatom cellular recovery from phosphorus limitation. Strikingly, the dominant response was substantial enhancement of nitrogen assimilation proteins. This led to 12-fold increases in absolute nitrate uptake rates, relative to phosphorus-starved cells. Moreover, we find that the novel phosphorus-Ca2+ signalling pathway controls this primary recovery response. Our findings highlight that fundamental cross-talk between the essential nutrients phosphorus and nitrogen drive diatom recovery from phosphorus limitation. Moreover, a novel Ca2+-dependent phosphorus signalling pathway governs such ecological acclimation responses, and is thus likely critical to the success of diatoms in regions of episodic nutrient supply.
2021-02-22 | PXD022586 | Pride
Project description:Investigation of whole genome gene expression level changes in Streptomyces sp. SirexAA-E (ActE) when grown on different carbon sources. The results of this study demonstrate that ActE upregulates a small number of genes specific for the utilization of the avaliable carbon source. Cellulolytic Streptomyces sp. SirexAA-E (ActE), isolated from the pinewood-boring wasp Sirex noctilio, has a genome enriched for biomass utilization. The secreted proteomes obtained from growth on pure polysaccharides catalyzed hydrolysis of cellulose, mannan, and xylan with specific activities comparable to Spezyme CP, a commercial cellulase preparation. During reaction of an ActE secretome with cellulose, reducing sugar release was markedly stimulated in the presence of O2. ActE also expresses and secretes an expanded repertoire of enzymes during growth on natural and pre-treated biomass. These results indicate a new microbial contribution to biomass utilization that is widely distributed in natural environments by insects
2013-12-31 | GSE31748 | GEO
Project description:The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.
2017-05-24 | GSE99220 | GEO