Project ID: IPD6038

Project Title: Candida glabrata GPI-anchored cell surface associated aspartyl protease CgYps1 and CgYps7 interactome analysis in the total cell extracts of A-498 human renal epithelial cell line

Principal Investigator: Dr Rupinder Kaur

PI Affiliation: Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India

Description: The project is aimed at identifying host epithelial proteins that interact with two different cell-surface associated aspartyl proteases (CgYps1 and CgYps7) in Candida glabrata cells.

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Meta Data

Sample Preparation: For identification of A-498 epithelial cell proteins that interact with CgYps1 or CgYps7, affinity-purification-mass spectrometry approach was used. Briefly, E. coli-purified CgYps1 and CgYps7 proteins (250 μg) were incubated overnight with 100 μl TALON beads at 4˚C on an end-to-end rotor. A-498 cells were grown in MEM in 10 cm culture dishes to 80% confluency, followed by cell collection and lysis in NETN buffer. Cell lysates (2 mg protein) were pre-cleared with NETN buffer-equilibrated TALON beads for 2 h at 4°C and centrifuged. The supernatants were divided into two fractions. One fraction was incubated with NETN buffer pre-equilibrated beads as control, and the other fraction was incubated with TALON beads-conjugated with CgYps1/CgYps7 proteins. After overnight incubation at 4˚C, beads were centrifuged at 1500 rpm for 2 min, and washed four times with NETN buffer containing 25 mM imidazole, followed by boiling and resolving of bead-bound proteins on 12 % SDS-PAGE. Gel was run for a short duration, till the dye front entered the resolving gel. The gel was stained with coomassie brilliant blue, and protein-containing gel bands were excised and sent to the Taplin Biological Mass Spectrometry Facility, Harvard Medical School, Boston, USA (https://taplin.med.harvard.edu) for protein identification using LC-MS/MS (liquid chromatography-mass spectrometry) analysis. Samples from two biological replicates for each condition were prepared and analyzed.

Peptide Separation: At the Taplin facility, gel pieces were subjected to in-gel trypsin digestion, followed by microcapillary LC-MS/MS (Liquid chromatography-tandem mass spectrometry) using the LTQ Orbitrap Velos Pro ion-trap mass spectrometer. Samples with the search name 86123-86124 (Search ID 66265 and 66264) refer to Talon beads control incubated with pre-cleared A-498 cell lysates; replicate 1 and 86125-86126 (Search ID 66263 and 66268) refer to Talon beads control incubated with pre-cleared A-498 cell lysates; replicate 2. Samples 86127-86129 (Search ID 66267, 66291 and 66290) were pre-cleared A-498 cell lysates incubated with rCgYps1 protein; replicate 1, while 86130-86132 (Search ID 66289, 66288 and 66287) refer to pre-cleared A-498 cell lysates incubated with rCgYps1 protein; replicate 2. Samples 86133-86135 (Search ID 66286, 66285 and 66284) refer to pre-cleared A-498 cell lysates incubated with rCgYps7 protein; replicate 1, while 86136-86138 (Search ID 66325, 66324 and 66323) indicate to pre-cleared A-498 cell lysates incubated with rCgYps7 protein; replicate 2.

Protein Characterization: All generated fragmentation patterns were acquired and searched against the UniProt Human reference proteome database using the SEQUEST software to determine the peptide sequences. 1% false discovery rate.

Experiment Type: Gel-based experiment, Affinity purification coupled with mass spectrometry proteomics

PubMed-ID:

Species: Homo sapiens-9606

Tissue: Kidney (bto:0000671)

Cell Type: Epithelial cell (cl:0000066)

Disease: Unknown

Instrument Details: Q Exactive HF (MS:1002523)

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