ABSTRACT: Proteomic expression analysis of Ca. Lokiarchaeum ossiferum, strain B36, grown using casein hydrolysate as the main carbon source under anaerobic conditions
Project description:Proteomic expression analysis of Ca. Lokiarchaeum ossiferum, strain B35, grown using casein hydrolysate as the main carbon source under anaerobic conditions
Project description:Peptide fingerprinting to verify the efficacy of phosphatase inhibitor beads (PIBs) for capturing Spodoptera frugiperda (Sf9) phosphatases of the PP2A family.
Project description:Muscle specific kinase (MuSK) is a receptor tyrosine kinase that plays a crucial role in development and maintenance of the neuromuscular junction (NMJ). Lack of MuSK is lethal and defective MuSK signaling causes muscle weakness. MuSK activity is tightly regulated and requires the nerve-derived heparansulphate proteoglycan Agrin. However, signal transduction induced by MuSK activation is not well understood. Here, we used proximity labeling to decipher the MuSK interactome by identifying and characterizing interaction partners of MuSK upon Agrin stimulation. To uncover the early and late events in the MuSK signaling cascade, muscle cells were stimulated with Agrin for 2 h, 4 h and 8 h. Overall, our study reveals that CrkL functions as a signaling hub to recruit different molecules for distinct signaling outcomes and contributes to a better understanding of the complex mechanisms that regulate NMJ formation.
Project description:We aimed to identify proteins that would be turned over upon artificial tethering of WIPI2 to the mitochondrial surface upon rapalog treatment, using the FIS1-FRB plus FKBP-GFP-WIPI2 tethering system. We had previously observed that this induces mitophagy based on flow cytometry analysis of the mt-mKeima probe. Here, we aimed to identify which proteins are degraded upon 24 h Rapalog treatment and verified whether there was an enrichment of mitochondrial proteins being selectively turned over by mitophagy under these conditions in wild-type and NIX/BNIP3 double-knockout HeLa cells.
Project description:We aimed to identify proteins that would be turned over upon DFP treatment, a small molecule that mimicks hypoxia treatment and which induces NIX/BNIP3 mitophagy. We aimed to identify which proteins are degraded upon 24 h DFP treatment and verified whether there was an enrichment of mitochondrial proteins being selectively turned over by mitophagy under these conditions.
Project description:Autophagy is a conserved cellular degradation pathway involving the formation of double-membrane autophagosomes that engulf cytoplasmic material for delivery to the lysosome. Autophagy-related (ATG) proteins orchestrate the steps of autophagosome formation and maturation, among which ATG9A is unique as the only integral membrane protein essential for autophagy progression. ATG9A localizes to Golgi-derived vesicles/compartments that constitute a seed for membrane nucleation. In this dataset we show proteomics analysis of mammalian ATG9A vesicles. To isolate and characterize native mammalian ATG9A-containing compartments, we generated a CRISPR/Cas9-engineered HAP1 knock-in cell line expressing ATG9A endogenously tagged ATG9A with a C-terminal GFP and FLAG tag. The FLAG-tag enabled the purification of native ATG9A vesicles via FLAG-based affinity isolation, while GFP-tag was used to submit the vesicles for mass spectrometry analysis. Both WT and ATG9A-GFP-FLAG expressing HAP1 cell lines were cultured under nutrient-rich conditions to prevent the induction of starvation-mediated autophagy.
Project description:Viable Candida glabrata cells were co-cultured with pulmonary ILCs. The culture supernatants were collected, cleared of cells and debris, and subsequently precipitated. The precipitated proteins were then analyzed using LC-MS.
Project description:IGF2BP3 is an RNA-binding protein that regulates mRNA stability, translation, and localization. IGF2BP3 binds to mRNAs encoding endoplasmic reticulum (ER) stress response proteins. To understand molecular mechanisms of its function we performed co-immunoprecipitation of the endogenous IGF2BP3 from colorectal carcinoma cell line HCT116 in control and ER stress conditions. RNase treatment was performed during washes to reveal RNA-bridged interactors.
Project description:To elucidate the mechanism responsible for the absence of p21 (protein) in homeostatic porcine skin and its rapid generation upon injury, we performed a pull-down experiment of Cdkn1a mRNA and its protein binding partners. For this, we utilized a variant of the comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS), which has been successfully used in human cells for large noncoding RNAs, but never before applied to tissues in vivo or to small targets such as Cdkn1a mRNA