The gene expression of numerous SLC transporters is altered in the immortalized hypothalamic cell line N25/2 following amino acid starvation
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE61402 | GEO | 2015/09/30
SECONDARY ACCESSION(S): PRJNA261008
REPOSITORIES: GEO
Similar Datasets
Project description:Amino acids are known to play a key role in gene expression regulation, and in mammalian cells, amino acid signaling is mainly mediated via two pathways, the mammalian target of rapamycin complex 1 (mTORC1) pathway and the amino acid responsive (AAR) pathway. It is vital for cells to have a system to sense amino acid levels, in order to control protein and amino acid synthesis and catabolism. Amino acid transporters are crucial in these pathways, due to both their sensing and transport functions. In this large-scale study, an immortalized mouse hypothalamic cell line (N25/2) was used to study the gene expression changes following 1, 2, 3, 5 or 16 h of amino acid starvation. We focused on genes encoding solute carriers (SLCs) and putative SLCs, more specifically on amino acid transporters. The microarray contained 28 270 genes and 86.2% of the genes were expressed in the cell line. At 5 h of starvation, 1001 genes were upregulated and 848 genes were downregulated, and among these, 47 genes from the SLC superfamily or atypical SLCs were found. Of these, 15 were genes encoding amino acid transporters and 32 were genes encoding other SLCs or atypical SLCs. Increased expression was detected for genes encoding amino acid transporters from system A, ASC, L, N, T, xc-, and y+. Using GO annotations, genes involved in amino acid transport and amino acid transmembrane transporter activity were found to be most upregulated at 3 h and 5 h of starvation.
| S-EPMC5292668 | biostudies-literature
Project description:The low permeability and high selectivity of the blood vessels of the brain and central nervous system (CNS) characterize the blood-brain barrier (BBB). Tight junctions, a lack of fenestrations, and low rates of transcytosis in the endothelial cells of the vasculature prevent passive diffusion of most molecules other than water, gases and some lipid soluble molecules (Obermeier, Daneman, & Ransohoff, 2013). Any additional nutrients must be transported across the barrier with the help of transporter proteins. Two protein families account for most transporters. ABC transporters use ATP to power primary-active transport to move molecules across the BBB against an electrochemical gradient, frequently excluding drugs from entering the brain. Some SLC transporters facilitate transport of solutes along an electrochemical gradient, while others permit secondary-active transport by coupling the flow of a solute traveling down the electrochemical gradient to power another solute against its electrochemical gradient. Brain microvessel endothelial cells (BMEC) from human cerebral cortex were enriched through a homogenization and centrifugation procedure. Two BMEC and two tissue were sequenced with paired-end reads on a SOLiD 5500 Wildfire. Raw data was aligned using LifeScope Genomic Analysis, gene expression determined through Cufflinks, and splice junctions identified by aligning to a custom database of known to known and known to novel junctions. We found numerous examples of transporters with enriched expression in the isolated BMECs compared to whole brain tissue. In total, 131 transporter genes or pseudogenes (109 SLC, 22 ABC) are enriched at least 1.25 fold in BMEC enriched samples, and 57 of these are enriched over 2-fold (50 SLC, 7 ABC). Thirteen genes were found to have at least twice as many counts in BMEC enriched samples than in whole tissue for at least one alternative splice junction. Inversely, 23 genes were found to have at least one alternative splice junction with half as many counts in BMEC enriched samples than in whole tissue.
2017-01-26 | GSE94064 | GEO
Project description:Amino acid starvation during recombinant protein production (RPP) induces metabolic stress to cellular host which results in reduced productivity of the recombinant bioprocess. In present study, supplementation of amino acids in a chemically defined medium showed several folds increase in recombinant product titers in E. coli BL21 DE3 strain. To understand, the effect of amino acid supplementation in alleviating cellular stress during RPP a deep insight of cellular physiology must be studied. Here, we performed transcriptomic analysis of E. coli expressing a recombinant protein in two different conditions: with (5 mM of all 20 amino acids) as test and without supplementation of amino acids as control. RNA-seq data revealed downregulation of several genes associated with stress in test culture confirming the critical role of amino acids supplementation in improving RPP.
2020-05-18 | GSE138044 | GEO
Project description:<p>Solute carrier (SLC) transporters control fluxes of nutrients and metabolites across membranes and thereby represent a critical interface between the microenvironment and cellular and subcellular metabolism. Because of substantial functional overlap, the interplay and relative contributions of SLCs in response to environmental stresses remain poorly elucidated. To infer functional relationships between SLCs and metabolites, we developed a strategy to identify SLCs able to sustain cell viability and proliferation under growth-limiting concentrations of essential nutrients. One-by-one depletion of 13 amino acids required for cell proliferation enabled gain-of-function genetic screens using a SLC-focused CRISPR/Cas9–based transcriptional activation approach to uncover transporters relieving cells from growth-limiting metabolic bottlenecks. Among the transporters identified, we characterized the cationic amino acid transporter SLC7A3 as a gene that, when up-regulated, overcame low availability of arginine and lysine by increasing their uptake, whereas SLC7A5 was able to sustain cellular fitness upon deprivation of several neutral amino acids. Moreover, we identified metabolic compensation mediated by the glutamate/aspartate transporters SLC1A2 and SLC1A3 under glutamine-limiting conditions. Overall, this gain-of-function approach using human cells uncovered functional transporter-nutrient relationships and revealed that transport activity up-regulation may be sufficient to overcome environmental metabolic restrictions.</p>
2022-09-20 | MTBLS4268 | MetaboLights
Project description:Hundreds of genes have been associated with respiratory chain disease so far. Elimination of the respiratory electron chain by depleting the entire mitochondrial DNA (mtDNA, ��0 cells) has therefore one of the most severe impacts on the energy metabolism in eukaryotic cells. Here, we integrated proteomic data sets including the post transcriptional modifications (PTM���s) phosphorylation and ubiquitination, with metabolomic data sets and selected enzyme activities in the osteosarcoma cell line 143B.TK-. We applied a shotgun based SILAC LC-MS proteomics and a targeted metabolomics approach to elucidate the consequences of the ��0 state. Pathway analysis revealed a non-uniform down-regulation of the respiratory electron chain, the tricarboxylic acid (TCA) cycle and the pyruvate metabolism in ��0 cells. Surprisingly, some metabolites of the TCA cycle were dramatically reduced in ��0 cells, like citric acid (100-fold) and aconitic acid (6-fold), others instead increased, like succinic and fumaric acid (5-fold). Enzyme activities were xy. Exceptionally, the mitochondrial retrograde response, a pathway of communication from mitochondria to the nucleus, was up-regulated in ��0 cells, like signalling by GPCR, EGFR, G12/13 alpha cAMP and RhoGTPase. We observed a striking de-ubiquitination of 80S ribosomal proteins (3-fold) and SLC amino acid transporters (7-fold) in ��0 cells, the later might cause the observed significant increase of amino acids levels in ��0 cells. We conclude that mtDNA depletion not only leads to an uneven down-regulation of mitochondrial energy pathways, but also to a strong retrograde response. The partly collapsed TCA cycle and de-ubiquitination of SLC transporters lead to an altered amino acid metabolism.
2022-02-22 | PXD002270 | Pride
Project description:D-amino acids enrichment Raw sequence reads
| PRJNA745484 | ENA
Project description:Summary:
Amino acids (AA) support protein synthesis, and thus cell growth and proliferation. Specialized transporters mediate AA exchange across membranes and their regulation is critical for AA homeostasis. Here, we report that the DNA- and RNA-binding protein YBX3 regulates the expression of AA transporters. To investigate the functions of YBX3, we integrated proteomics and transcriptomics data with YBX3-RNA complex data to identify RNAs directly regulated by YBX3. The data revealed YBX3 as a versatile RNA-binding protein (RBP) that regulates as both a translational repressor and mRNA stabilizer. Among the direct YBX3 targets, we We identified two solute carrier (SLC) AA transporters (SLC7A5 and SLC3A2). We show that YBX3 stabilizes these SLC mRNAs and that the 3 UTR of SLC7A5 is necessary and sufficient for YBX3-mediated regulation. Further, YBX3 depletion results in diminished intracellular levels of SLC7A5/SLC3A2 substrates, large neutral AA. Importantly, expression of an exogenous SLC7A5 not susceptible to YBX3 regulation restores AA levels. Thus, YBX3 is a key post-transcriptional regulator of large neutral AA import.
2018-11-06 | MSV000083108 | MassIVE
Project description:Targeted quantification of amino acids in E. coli cells grown in standard M9 medium or M9 medium supplemented with individual amino acids.
See associated publication for details.
2023-06-13 | MSV000092152 | MassIVE
Project description:Mutant p53 can acquires oncogenic properties supporting tumor growth, metastases and chemoresistance, by reprogramming cancer cell transcriptome, proteome and metabolome. To investigate what is the gene expression network regulated by mutant p53 in condition of limited amino acids availability, we silenced mutant p53 expression in MDA-MB-231 Triple Negative Breast Cancer (TNBC) cell line, grown in medium with 100% and medium with 25% of amino acids. We performed gene expression profiling analysis using data obtained from RNA-seq of MDA-MB 231.
2023-10-06 | GSE214492 | GEO
Project description:Amino acid sensing and signaling is vital for cells, and both gene expression and protein levels of amino acid transporters are regulated in response to amino acid availability. Here, the aim was to study the regulation of all members of the SLC38 amino acid transporter family, Slc38a1-11, in mouse brain cells following amino acid starvation. We reanalyzed microarray data for the immortalized hypothalamic cell line N25/2 subjected to complete amino acid starvation for 1, 2, 3, 5, or 16 h, focusing specifically on the SLC38 family. All 11 Slc38 genes were expressed in the cell line, and Slc38a1, Slc38a2, and Slc38a7 were significantly upregulated at 5 h and most strongly at 16 h. Here, protein level changes were measured for SLC38A7 and the orphan family member SLC38A11 which has not been studied under different amino acid starvation condition at protein level. At 5 h, no significant alteration on protein level for either SLC38A7 or SLC38A11 could be detected. In addition, primary embryonic cortex cells were deprived of nine amino acids, the most common amino acids transported by the SLC38 family members, for 3 h, 7 h or 12 h, and the gene expression was measured using qPCR. Slc38a1, Slc38a2, Slc38a5, Slc38a6, Slc38a9, and Slc38a10 were upregulated, while Slc38a3 and Slc38a7 were downregulated. Slc38a8 was upregulated at 5 h and downregulated at 12 h. In conclusion, several members from the SLC38 family are regulated depending on amino acid levels and are likely to be involved in amino acid sensing and signaling in brain.
| S-EPMC5952004 | biostudies-literature