Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA147835 | ENA |
REPOSITORIES: ENA
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Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits. Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap
2012-05-03 | E-GEOD-32522 | biostudies-arrayexpress
Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits.
2012-05-04 | GSE32522 | GEO
Project description:Here we show that the phytochrome-less chlorophyte Chlamydomonas reinhardtii retains a functional pathway to synthesize the linear tetrapyrrole (bilin) precursor of the phytochrome chromophore. Reverse genetic, metabolic inactivation and bilin rescue experiments establish that this pathway is needed for heme iron acquisition and for the diurnal transition to phototrophic growth. RNA-Seq measurements reveal a bilin-dependent signaling network that is necessary for the heterotrophic to phototrophic transition. These results imply the presence of a novel bilin sensor pathway that may be widely distributed amongst oxygenic photosynthetic organisms. We isolated RNA from heterotrophic suspension cultures of 4A+ WT and the hmox1 mutant grown in the presence or absence of 0.1 mM BV IXM-NM-1 before and after transfer to low light.
2013-01-10 | E-GEOD-40031 | biostudies-arrayexpress
Project description:Here we show that the phytochrome-less chlorophyte Chlamydomonas reinhardtii retains a functional pathway to synthesize the linear tetrapyrrole (bilin) precursor of the phytochrome chromophore. Reverse genetic, metabolic inactivation and bilin rescue experiments establish that this pathway is needed for heme iron acquisition and for the diurnal transition to phototrophic growth. RNA-Seq measurements reveal a bilin-dependent signaling network that is necessary for the heterotrophic to phototrophic transition. These results imply the presence of a novel bilin sensor pathway that may be widely distributed amongst oxygenic photosynthetic organisms.
2013-01-10 | GSE40031 | GEO
Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures.
2013-11-01 | GSE46076 | 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
Project description:Fructose-1,6-bisphosphate aldolase, a ubiquitous metabolic enzyme with regulatory functions in pathogenic Francisella
2018-11-22 | PXD006908 | Pride
Project description:Bloodstream form African trypanosomes are thought to rely exclusively upon glycolysis, using glucose as a substrate, for ATP production. Indeed, the pathway has long been considered a potential therapeutic target to tackle the devastating and neglected tropical diseases caused by these parasites. However, plasma membrane glucose and glycerol transporters are both expressed by trypanosomes and these parasites can infiltrate tissues that contain glycerol. Here, we show that bloodstream form trypanosomes can use glycerol for gluconeogenesis and for ATP production, particularly when deprived of glucose following hexose transporter depletion. We demonstrate that Trypanosoma brucei hexose transporters 1 and 2 (THT1 and THT2) are localized to the plasma membrane and that knockdown of THT1 expression leads to a growth defect that is more severe when THT2 is also knocked down. These data are consistent with THT1 and THT2 being the primary routes of glucose supply for the production of ATP by glycolysis. However, supplementation of the growth medium with glycerol substantially rescued the growth defect caused by THT1 and THT2 knockdown. Metabolomic analyses with heavy-isotope labelled glycerol demonstrated that trypanosomes take up glycerol and use it to synthesize intermediates of gluconeogenesis, including fructose 1,6-bisphosphate and hexose 6-phosphates, which feed the pentose phosphate pathway and variant surface glycoprotein biosynthesis. We used Cas9-mediated gene knockout to demonstrate a gluconeogenesis-specific, but fructose-1,6-bisphosphatase (Tb927.9.8720)-independent activity, converting fructose 1,6-bisphosphate into fructose 6-phosphate. In addition, we observed increased flux through the tricarboxylic acid cycle and the succinate shunt. Thus, contrary to prior thinking, gluconeogenesis can operate in bloodstream form T. brucei. This pathway, using glycerol as a physiological substrate, may be required in mammalian host tissues.
2018-12-10 | MTBLS706 | MetaboLights
Project description:Genes differentially expressed in Haloferax mediterranei strains, DF50 and ΔdeoR2, with or without induction by fructose
| PRJNA175903 | ENA
Project description:Analysis of differentially expressed genes and differentially used exons in Drosophila tissues lacking PTEN and SF2 under nutrient restriction.
| PRJEB39006 | ENA