Dataset Information

YBX3 is a versatile RNA-binding protein that controls amino acid import by regulating SLC mRNA abundance

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Gertjan Kramer

PROVIDER: MSV000083108 | MassIVE | Tue Nov 06 08:30:00 GMT 2018

SECONDARY ACCESSION(S): PXD011592

REPOSITORIES: MassIVE

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Publications

The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance.

Cooke Amy A Schwarzl Thomas T Huppertz Ina I Kramer Gertjan G Mantas Panagiotis P Alleaume Anne-Marie AM Huber Wolfgang W Krijgsveld Jeroen J Hentze Matthias W MW

Cell reports 20190601 11

Sufficient amino acid supplies are critical for protein synthesis and, thus, cell growth and proliferation. Specialized transporters mediate amino acid exchange across membranes and their regulation is critical for amino acid homeostasis. Here, we report that the DNA- and RNA-binding protein YBX3 regulates the expression of amino acid transporters. To investigate the functions of YBX3, we integrated proteomic and transcriptomic data from cells depleted of YBX3 with analyses of YBX3 RNA binding s ...[more]

PMID: 31189097

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Project description:BACKGROUND & AIMS- More frequent interaction of bacteria with the colonic epithelium is associated with ulcerative colitis (UC). The identities of all proteins which promote bacterial clearance in colonic epithelial cells are unknown. Previously, we discovered that dCAP-D3 (Chromosome Associated Protein-D3), regulates responses to bacterial infection. We examined whether CAP-D3 promotes bacterial clearance in human colonic epithelium. METHODS- Clearance of Salmonella or adherent-invasive Escherichia coli LF82 was assessed by gentamycin protection assays in HT-29 and Caco-2 cells expressing CAP-D3 shRNA. CAP-D3 levels in colonic epithelial cells from healthy and UC patient tissues were analyzed by immunoblot. RNA-sequencing identified bacterially-induced CAP-D3 target genes. The role of CAP-D3 target genes in bacterial clearance was analyzed by gentamycin protection assays, immunofluorescent staining, and by using pharmacologic inhibitors. RESULTS- CAP-D3 expression was reduced in colonic epithelial cells from UC patients with active disease. Reduction of CAP-D3 expression inhibited autophagy and decreased intracellular bacterial clearance. The components of the heterodimeric SLC7A5/SLC3A2 amino acid transporter were identified as CAP-D3 target genes; their levels increased in infected, CAP-D3 deficient cell lines and in cells from UC patients. In HT-29 cells, this resulted in earlier SLC7A5 recruitment to Salmonella-containing vacuoles, increased mTOR activity, and enhanced bacterial survival. Inhibition of SLC7A5/SLC3A2 or mTOR activity rescued the bacterial clearance defect in CAP-D3 deficient cells. CONCLUSIONS- CAP-D3 attenuates amino acid transporter transcription to promote bacterial autophagy in colon epithelial cells. CAP-D3 protein levels are decreased in patients with active UC, suggesting that CAP-D3 is a potential therapeutic target to restore mucosal homeostasis in UC patients. Three RNA samples from 3 independent experiments including timepoints taken at 0, 0.5 and 7 hours post-infection were analyzed on a bioanalyzer for quality; one of the 0.5 hour post-infection samples was excluded at this time due to poor RNA purity. Directional, cDNA libraries made from cellular mRNAs were generated from the other 8 samples and sequenced (paired-end sequencing of 100 bp reads) in the Genomics Core at the University of Chicago on an Illumina HiSeq2000.

Dataset Information

YBX3 is a versatile RNA-binding protein that controls amino acid import by regulating SLC mRNA abundance

Publications

The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance.

Similar Datasets

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