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SwissPalm: Protein Palmitoylation database.

Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG - F1000Res (2015)

Bottom Line: 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.Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

View Article: PubMed Central - PubMed

Affiliation: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

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.

No MeSH data available.


Related in: MedlinePlus

S-palmitoylation and other posttranslational modifications.A: Venn diagram displaying the strong co-occurrence of S-palmitoylation, S-nitrosylation and S-glutathionylation modifications within the same proteins. For this analysis human orthologs of mouse proteins were included.B andC: Percentage of phosphorylation and ubiquitination sites in human and mouse S-palmitoylation hits compared to the total protein population.C: Ubiquitination pattern in WT and DHHC2, 5 and 6 HAP1 cells. Total protein extracts from HAP1 cells were subject to Western blot and probe using anti-ubiquitin antibody and actin as loading control.
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f8: S-palmitoylation and other posttranslational modifications.A: Venn diagram displaying the strong co-occurrence of S-palmitoylation, S-nitrosylation and S-glutathionylation modifications within the same proteins. For this analysis human orthologs of mouse proteins were included.B andC: Percentage of phosphorylation and ubiquitination sites in human and mouse S-palmitoylation hits compared to the total protein population.C: Ubiquitination pattern in WT and DHHC2, 5 and 6 HAP1 cells. Total protein extracts from HAP1 cells were subject to Western blot and probe using anti-ubiquitin antibody and actin as loading control.

Mentions: PTMs and S-palmitoylation. S-palmitoylation is not the sole PTM that can occur on cysteine residues. They can in particular also undergo other post-translational modifications on cysteine residues such as S-nitrosylation and S-glutathionylation77,78. Site competition can thus potentially occur and has been observed77,78. To assess the potential amplitude of this competition, we compared the datasets from two available databases, Db_SNO and Db-GSH, which contain proteomic hits for S-nitrosylation and S-gluthationylation, respectively79,80. Comparison of the three datasets shows that more than 40% (1031 out of 2483) of S-palmitoylated protein hits had at least one S-nitrosylated or one S-glutathionylated site and 19% (470 proteins) had both (Figure 8A). This strong overlap suggests that either the isolation methods share the same drawbacks or there is cross-talk between these PTMs.


SwissPalm: Protein Palmitoylation database.

Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG - F1000Res (2015)

S-palmitoylation and other posttranslational modifications.A: Venn diagram displaying the strong co-occurrence of S-palmitoylation, S-nitrosylation and S-glutathionylation modifications within the same proteins. For this analysis human orthologs of mouse proteins were included.B andC: Percentage of phosphorylation and ubiquitination sites in human and mouse S-palmitoylation hits compared to the total protein population.C: Ubiquitination pattern in WT and DHHC2, 5 and 6 HAP1 cells. Total protein extracts from HAP1 cells were subject to Western blot and probe using anti-ubiquitin antibody and actin as loading control.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544385&req=5

f8: S-palmitoylation and other posttranslational modifications.A: Venn diagram displaying the strong co-occurrence of S-palmitoylation, S-nitrosylation and S-glutathionylation modifications within the same proteins. For this analysis human orthologs of mouse proteins were included.B andC: Percentage of phosphorylation and ubiquitination sites in human and mouse S-palmitoylation hits compared to the total protein population.C: Ubiquitination pattern in WT and DHHC2, 5 and 6 HAP1 cells. Total protein extracts from HAP1 cells were subject to Western blot and probe using anti-ubiquitin antibody and actin as loading control.
Mentions: PTMs and S-palmitoylation. S-palmitoylation is not the sole PTM that can occur on cysteine residues. They can in particular also undergo other post-translational modifications on cysteine residues such as S-nitrosylation and S-glutathionylation77,78. Site competition can thus potentially occur and has been observed77,78. To assess the potential amplitude of this competition, we compared the datasets from two available databases, Db_SNO and Db-GSH, which contain proteomic hits for S-nitrosylation and S-gluthationylation, respectively79,80. Comparison of the three datasets shows that more than 40% (1031 out of 2483) of S-palmitoylated protein hits had at least one S-nitrosylated or one S-glutathionylated site and 19% (470 proteins) had both (Figure 8A). This strong overlap suggests that either the isolation methods share the same drawbacks or there is cross-talk between these PTMs.

Bottom Line: 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.Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

View Article: PubMed Central - PubMed

Affiliation: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

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.

No MeSH data available.


Related in: MedlinePlus