Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of HeLa cells upon deprivation of methionine and cysteine (Met/Cys)

ABSTRACT: We have previously shown that deprivation of essential amino acids, namely methionine/cysteine or tyrosine, leads to the transcriptional reactivation of integrated silenced transgenes, and latent HIV-1 provirus. In an effort to understand the underlying mechanisms, here we investigate the overall transcriptional profile of HeLa cells upon Met/Cys starvation for different time points, including the expression of repeated and transposable elements. HeLa cells carrying a stably integrated and silenced plasmid expressing the OA1/GPR143 gene (pcDNA3.1-OA1) were cultured in regular DMEM medium for 6-30-120 hours, or in absence of Met/Cys for 6-15-30-72-120 hours, and the changes in the expression of genes and repeated elements was evaluated by RNAseq

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Ilaria Palmisano

PROVIDER: E-MTAB-6452 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Cysteine is a rare and conserved amino acid involved in most cellular functions. The thiol group of cysteine can be subjected to diverse oxidative modifications that regulate most physio-pathological states. Here, a Cysteine-specific Phosphonate Adaptable Tag (CysPAT) was synthesized to selectively label cysteine-containing peptides (Cys peptides) followed by enrichment with titanium dioxide (TiO2) and mass spectrometric analysis. The CysPAT strategy was developed using a synthetic peptide, a standard protein and subsequently the strategy was applied to Hela cells lysate, achieving high specificity and enrichment efficiency. In particular,From 500µg of Hela cell lysate, the method led to the identification of 9229 unique Cys peptides starting from 500µg of Hela cell lysate . the CysPAT labelled Cys peptides showed increased hydrophobicity. Finally, the method was further developed to simultaneously enrich Cys peptides and phosphorylated peptidesThe method was further developed to simultaneously enrich Cys peptides and phosphorylated peptides from SILAC labelled Hela cells subjected to 5 min epidermal growth factor (EGF) stimulation. In total, of 22972 unique reversibly modified Cys peptides (3886 proteins) and 18549 unique phosphopeptides (2257 proteins) were simultaneously identified by Orbitrap Fusion. Significant regulation was observed in both phosphorylation and reversible Cys modification of proteins interacted with EGF receptor (EGFR)-binding proteins and proteins involved in EGFR signaling pathway. EGF stimulation can activate the phosphorylation of EGFR and downstream signaling molecules, such as mitogen-activated protein kinases (MAPK1 and MAPK3), meanwhile, it also leads to the activation of multiple protein tyrosine phosphatases (PTPs) by reduction of the catalytic Cys site in the conserved putative phosphatase HC(X)5R motif, Llater the activated PTPs would dephosphorylate and inactivate the molecules activated by EGF stimulation. Overall, the CysPAT strategy is a promising tool for studying redox proteomics and the simultaneous enrichment strategy offers an excellent solution for characterization of cross-talk between phosphorylation and redox induced cysteine modifications.

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Transcriptome analysis of HeLa cells upon deprivation of methionine and cysteine (Met/Cys)

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