Project ID: IPD7282

Project Title: Label-free quantitative plasma membrane proteome analysis of Candida glabrata wild-type and Cgvps34∆ (lacks phosphatidylinositol 3- phosphate kinase, CgVps34) strains. Label-free quantitative plasma membrane proteome analysis of Candida glabrata wild-type and Cgvps34∆ (lacks phosphatidylinositol 3- phosphate kinase, CgVps34) strains.

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 characterizing the effect of loss of phosphatidylinositol 3- phosphate kinase (CgVps34) on the plasma membrane proteome of Candida glabrata.

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Sample Preparation: C. glabrata wild-type and Cgvps34Δ strains were grown in YPD medium till logarithmic-phase. Next, cells were harvested and washed twice using ice-cold water. The cells were normalized to 200 OD600 and suspended in homogenization buffer [50 mM Tris (pH 7.5), EDTA (2.5 mM)] containing 1 mM PMSF, 10 mM sodium fluoride, 1 mM sodium orthovanadate and 1X protease inhibitor cocktail. The 0.5 mm acid-washed glass beads were added to the cells, and cells were lysed using mechanical force. The supernatant was collected after centrifugation at 2000 rpm for 15 min at 4°C, and an aliquot was saved as total cell lysate fraction. After ultracentrifugation (SW 41 Ti rotor) of the remainder supernatant at 25000 rpm for 35 min at 4⁰C, the pellet was suspended in protease inhibitor-containing buffer [10 mM Tris (pH 7.5), 0.5 mM EDTA, and 10% glycerol and protease inhibitors]. One aliquot was saved as total membrane fraction. Next, the discontinuous sucrose gradient [43.5 and 53.5% (w/v)] ultracentrifugation was carried out at 35000 rpm for 5 h. The plasma membrane fraction was collected from the middle ring, and ultracentrifuged at 38000 rpm for 30 min. The PM pellet was suspension in solution containing 6 M Gn-HCl and 0.1 M Tris (pH 8.8). The PM preparation quality was tested using anti-Pma1antibody. Samples were collected in two biological replicates, and sent on dry ice to Valerian Chem Pvt Ltd, New Delhi, India.

Peptide Separation: At the Valerian Chem facility, the label-free quantitative mass spectrometry analysis was conducted on Ultimate 3000 RSLCnano system coupled with an Orbitrap Eclipse.This analysis involved sample reduction with 5 mM TCEP, followed by alkylation with 50 mM iodoacetamide, and digestion with Trypsin (1:50, Trypsin/lysate ratio) for 16 h at 37°C. Samples with the search name S1 refers to C. glabrata wild-type replicate 1, S2 refers to C. glabrata wild-type replicate 2, S3 refers to Cgvps34Δ replicate 1, and S4 refers to Cgvps34Δ replicate 2.

Protein Characterization: RAW files were analysed with the Proteome Discoverer (v2.2) against the Uniprot C.glabrata reference proteome database. For Sequest search, precursor and fragment mass tolerances were set at 10 ppm and 0.5 Da, respectively. Both peptide spectrum match and protein false discovery rate were set to 0.01 FDR.

Experiment Type: Shotgun proteomics

PubMed-ID: 37490387

Species: Nakaseomyces glabratus-5478

Tissue: Unknown

Cell Type: Unknown

Disease: Unknown

Instrument Details: Orbitrap Eclipse (MS:1003029)

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