Effect of folate receptor depletion on gene expression in Caenorhabditis elegans
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE227272 | GEO | 2023/03/20
REPOSITORIES: GEO
Similar Datasets
Project description:cea06-02_folate - methotrexate treatment - global analysis of the folate metabolism in Arabidopsis - Treatment of cells of Arabidopsis by methotrexate which is an inhibitor of the synthesis of the folate. Consequently, the pool of folates presents a strong reduction. The goal of this project is to look at the variations of expression in the Arabidopsis genome and specifically in some genes implied in the metabolism of the folate. Keywords: time course,treated vs untreated comparison 10 dye-swap - CATMA arrays
2008-12-18 | E-GEOD-10675 | biostudies-arrayexpress
Project description:cea06-02_folate - methotrexate treatment - global analysis of the folate metabolism in Arabidopsis - Treatment of cells of Arabidopsis by methotrexate which is an inhibitor of the synthesis of the folate. Consequently, the pool of folates presents a strong reduction. The goal of this project is to look at the variations of expression in the Arabidopsis genome and specifically in some genes implied in the metabolism of the folate. Keywords: time course,treated vs untreated comparison
2008-12-19 | GSE10675 | GEO
Project description:Effect of folate receptor depletion on gene expression in Caenorhabditis elegans
| PRJNA944545 | ENA
Project description:Henry2016 Folate pathway model with induced
PanB reaction
This model is described in the article:
Experimental and Metabolic
Modeling Evidence for a Folate-Cleaving Side-Activity of
Ketopantoate Hydroxymethyltransferase (PanB).
Thiaville JJ, Frelin O,
García-Salinas C, Harrison K, Hasnain G, Horenstein NA,
Díaz de la Garza RI, Henry CS, Hanson AD, de
Crécy-Lagard V.
Front Microbiol 2016; 7: 431
Abstract:
Tetrahydrofolate (THF) and its one-carbon derivatives,
collectively termed folates, are essential cofactors, but are
inherently unstable. While it is clear that chemical oxidation
can cleave folates or damage their pterin precursors, very
little is known about enzymatic damage to these molecules or
about whether the folate biosynthesis pathway responds
adaptively to damage to its end-products. The presence of a
duplication of the gene encoding the folate biosynthesis enzyme
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (FolK) in
many sequenced bacterial genomes combined with a strong
chromosomal clustering of the folK gene with panB, encoding the
5,10-methylene-THF-dependent enzyme ketopantoate
hydroxymethyltransferase, led us to infer that PanB has a side
activity that cleaves 5,10-methylene-THF, yielding a pterin
product that is recycled by FolK. Genetic and metabolic
analyses of Escherichia coli strains showed that overexpression
of PanB leads to accumulation of the likely folate cleavage
product 6-hydroxymethylpterin and other pterins in cells and
medium, and-unexpectedly-to a 46% increase in total folate
content. In silico modeling of the folate biosynthesis pathway
showed that these observations are consistent with the in vivo
cleavage of 5,10-methylene-THF by a side-activity of PanB, with
FolK-mediated recycling of the pterin cleavage product, and
with regulation of folate biosynthesis by folates or their
damage products.
This model is hosted on
BioModels Database
and identified by:
MODEL1602280002.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000689 | BioModels
Project description:we used Caenorhabditis elegans as a model organism, to investigate the effect of mannose on the lifespan. Using nematode RNAi methods, RT-PCR, RNA-seq and other experimental method, we explored the possible mechanism for how mannose change the lifespan of Caenorhabditis elegans.
2023-09-01 | GSE192579 | GEO
Project description:Bio-electrospraying the nematode Caenorhabditis elegans
| PRJNA117707 | ENA
Project description:Henry2016 Folate pathway model with induced
PanB reaction
This model is described in the article:
Experimental and Metabolic
Modeling Evidence for a Folate-Cleaving Side-Activity of
Ketopantoate Hydroxymethyltransferase (PanB).
Thiaville JJ, Frelin O,
García-Salinas C, Harrison K, Hasnain G, Horenstein NA,
Díaz de la Garza RI, Henry CS, Hanson AD, de
Crécy-Lagard V.
Front Microbiol 2016; 7: 431
Abstract:
Tetrahydrofolate (THF) and its one-carbon derivatives,
collectively termed folates, are essential cofactors, but are
inherently unstable. While it is clear that chemical oxidation
can cleave folates or damage their pterin precursors, very
little is known about enzymatic damage to these molecules or
about whether the folate biosynthesis pathway responds
adaptively to damage to its end-products. The presence of a
duplication of the gene encoding the folate biosynthesis enzyme
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (FolK) in
many sequenced bacterial genomes combined with a strong
chromosomal clustering of the folK gene with panB, encoding the
5,10-methylene-THF-dependent enzyme ketopantoate
hydroxymethyltransferase, led us to infer that PanB has a side
activity that cleaves 5,10-methylene-THF, yielding a pterin
product that is recycled by FolK. Genetic and metabolic
analyses of Escherichia coli strains showed that overexpression
of PanB leads to accumulation of the likely folate cleavage
product 6-hydroxymethylpterin and other pterins in cells and
medium, and-unexpectedly-to a 46% increase in total folate
content. In silico modeling of the folate biosynthesis pathway
showed that these observations are consistent with the in vivo
cleavage of 5,10-methylene-THF by a side-activity of PanB, with
FolK-mediated recycling of the pterin cleavage product, and
with regulation of folate biosynthesis by folates or their
damage products.
This model is hosted on
BioModels Database
and identified by:
MODEL1602280002.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000690 | BioModels
Project description:In this study, screening efforts identified novel antifolates with potent, targeted activity against whole cell Mycobacterium tuberculosis. Liquid chromatography-mass spectrometry analysis of antifolate-treated cultures revealed unique metabolic disruption, including decreased pools of methionine and S-adenosylmethionine. Transcriptomic analysis highlighted up-regulation genes involved in the biosynthesis and utilization of methionine. Supplementation with amino acids or methionine derivatives was sufficient to rescue cultures from MIC-level antifolate treatment. Instead of the “thymineless death” that characterizes folate pathway inhibition in a wide variety of organisms, these data suggest that M. tuberculosis is vulnerable to a critical disruption of the biosynthesis of methionine-derived compounds. These arrays look at the expression profile triggered by exposure to three different anti-folates (WR99210, dimethyl and diethyl methotrexate) in three biological replicates and in a matched set of untreated samples.
2014-03-19 | E-GEOD-55979 | biostudies-arrayexpress
Project description:The nematode Caenorhabditis elegans has evolutionarily conserved EV signaling pathways. In this study, we apply a recently published method for high specificity purification of EVs from C. elegans to carry out target-independent proteomic and RNA analysis of EVs from C. elegans. Our experiments uncovered diverse coding and non-coding RNA transcripts as well as protein cargo types commonly found in human EVs.
2020-08-05 | GSE146973 | GEO
Project description:The goal of this study was to elucidate genes that are employed by the bacterivorous nematode Caenorhabditis elegans to respond to the emerging nosocomial bacterial pathogen Stenotrophomonas maltophilia.
2018-02-01 | GSE107272 | GEO