Ultradeep Palmitoyl‐proteomic Analysis Uncovers Over 1,300 Novel Human Palmitoyl‐proteins

Abstract

Protein palmitoylation (more accurately known as protein S‐acylation) is a reversible lipid modification that plays critical roles in protein localization, activity, stability, and complex formation. Aberrant protein palmitoylation is associated with many human diseases such as neurodegenerative disorders and cancer. The past decade has witnessed striking progress in studying the enzymes, substrates, and functions of protein palmitoylation. However, it remains unclear whether protein palmitoylation is a widespread post‐translational modification comparable to protein phosphorylation and ubiquitination. Previously, we developed a palmitoyl‐proteomics method termed Palmitoyl‐Protein Identification and Site Characterization (PalmPISC) and applied it to profile the palmitoyl‐proteomes in human cancer cells and platelets (Yang et al., Mol Cell Proteomics, 2010; Dowal et al., Blood, 2011). Nevertheless, similar to other acyl‐biotinyl exchange (ABE)‐based palmitoyl‐proteomics methods, one shortcoming of the PalmPISC method is that many non‐palmitoylated proteins are co‐isolated with palmitoyl‐proteins, resulting in a high background that masks the detection of low‐abundance palmitoyl‐proteins and interferes with accurate quantification of palmitoyl‐proteins across different conditions. In this study, we coupled stable isotope labeling by amino acid in culture (SILAC) with PalmPISC to quantify the extent of co‐isolated proteins and found that ~65% of identified proteins were co‐isolated contaminants. To address this issue, we developed a low‐background ABE enrichment method and applied it to comprehensively profile the palmitoyl‐proteome of a human prostate cancer LNCaP cell line. Using stringent cutoffs (false discovery rate < 1% and fold change >2), a total of 2,895 proteins, including 1,571 known and 1,324 novel human palmitoyl‐proteins, were found to be significantly enriched. Western blotting analysis confirmed the palmitoylation of six novel palmitoyl‐protein candidates that play important roles in prostate cancer. In summary, our low‐background ABE enrichment method enables proteome‐wide analysis of protein palmitoylation and the study demonstrates that protein palmitoylation is more widespread than we previously thought.Support or Funding InformationThis work was supported by the Department of Defense W81XWH‐15‐1‐0167 (to W.Y.)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.