SwissPalm: Protein Palmitoylation database

Abstract

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species. As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites

“…26 Notably, we identified 69 proteins out of the 101 proteins previously identified as S-acylated in RAW264.7 macrophages. 26,35 …”

“…26 From the high/medium confidence hits, 322 and 347 proteins were identified by alk-16 and acyl-RAC proteomics, respectively, and 103 alk-16 labeled proteins were NH 2 OH sensitive. 83 proteins were recovered by all three analyses (acyl-RAC, alk-16 versus DMSO, alk-16 versus alk-16 + NH 2 OH), including 29 well-characterized S-fatty-acylated proteins such as CANX, IFITM3, NRas and SNAP23, and 78 proteins previously identified by S-fatty-acylation proteomic studies (Figure 2, Table S3).…”

Fatty acylation of proteins: The long and the short of it

“…Although there is no overall consensus sequence that distinctly characterizes all known S-palmitoylated proteins, algorithms have been developed to predict potential palmitoylation sites (Table 2)[56]. A recent compilation drawn from over 5,000 S-palmitoylated proteins suggests that as much as 10% of the human proteome consists of S-palmitoylated proteins[57]. …”

An outlook on protein S-acylation in plants: what are the next steps?

“…Databases -The first true database of S-acylation, SwissPalm, was recently made available 511 (Blanc et al, 2015). At the time of writing the database was being actively maintained and …”