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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

Abundance and distribution of S-palmitoylated proteins in the mammalian proteome.A: Percentage of S-palmitoylation hits combined from 8 human or 6 palmitoyl proteomes in the human and mouse proteomes. The analysis was extended to human orthologs of mouse and all S-palmitoylation hits present in the dataset.B: Percentage of targeted studies present in palmitoyl-proteomes.C: Topology of human and mouse S-palmitoylation hits.D andE: Distribution of human and mouse S-palmitoylation hits in cellular compartments.F: Enrichment of amino acid nearby validated S-palmitoylated cysteines in all, only cytoplasmic or only membrane proteins.
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f5: Abundance and distribution of S-palmitoylated proteins in the mammalian proteome.A: Percentage of S-palmitoylation hits combined from 8 human or 6 palmitoyl proteomes in the human and mouse proteomes. The analysis was extended to human orthologs of mouse and all S-palmitoylation hits present in the dataset.B: Percentage of targeted studies present in palmitoyl-proteomes.C: Topology of human and mouse S-palmitoylation hits.D andE: Distribution of human and mouse S-palmitoylation hits in cellular compartments.F: Enrichment of amino acid nearby validated S-palmitoylated cysteines in all, only cytoplasmic or only membrane proteins.

Mentions: Estimation of the human palmitome. We made use of the information gathered in SwissPalm to obtain a current estimation of the human palmitoyl-proteome. We found using Uniprot annotation that 6.8% of the human (1453 proteins) and 9.5% (1747) of the mouse proteomes may undergo S-palmitoylation (Figure 5A,Supplementary table S3). Since several identified S-palmitoylation sites are conserved across species, we integrated 891 mouse orthologs that were not present in human palmitoyl proteomes. The joint dataset indicates that 11% (2339 proteins) of the human proteome may undergo S-palmitoylation. Extending the analysis to 2649 human orthologs present across all species, 12.47% of the human proteome may be subject to S-palmitoylation (Figure 5A,Supplementary table S3). Moreover, since more than half of the proteins described in published targeted studies were not identified in any of the palmitoyl proteome screens (Figure 5B), the current figure of 9 to 12% is probably an underestimate.


SwissPalm: Protein Palmitoylation database.

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

Abundance and distribution of S-palmitoylated proteins in the mammalian proteome.A: Percentage of S-palmitoylation hits combined from 8 human or 6 palmitoyl proteomes in the human and mouse proteomes. The analysis was extended to human orthologs of mouse and all S-palmitoylation hits present in the dataset.B: Percentage of targeted studies present in palmitoyl-proteomes.C: Topology of human and mouse S-palmitoylation hits.D andE: Distribution of human and mouse S-palmitoylation hits in cellular compartments.F: Enrichment of amino acid nearby validated S-palmitoylated cysteines in all, only cytoplasmic or only membrane proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Abundance and distribution of S-palmitoylated proteins in the mammalian proteome.A: Percentage of S-palmitoylation hits combined from 8 human or 6 palmitoyl proteomes in the human and mouse proteomes. The analysis was extended to human orthologs of mouse and all S-palmitoylation hits present in the dataset.B: Percentage of targeted studies present in palmitoyl-proteomes.C: Topology of human and mouse S-palmitoylation hits.D andE: Distribution of human and mouse S-palmitoylation hits in cellular compartments.F: Enrichment of amino acid nearby validated S-palmitoylated cysteines in all, only cytoplasmic or only membrane proteins.
Mentions: Estimation of the human palmitome. We made use of the information gathered in SwissPalm to obtain a current estimation of the human palmitoyl-proteome. We found using Uniprot annotation that 6.8% of the human (1453 proteins) and 9.5% (1747) of the mouse proteomes may undergo S-palmitoylation (Figure 5A,Supplementary table S3). Since several identified S-palmitoylation sites are conserved across species, we integrated 891 mouse orthologs that were not present in human palmitoyl proteomes. The joint dataset indicates that 11% (2339 proteins) of the human proteome may undergo S-palmitoylation. Extending the analysis to 2649 human orthologs present across all species, 12.47% of the human proteome may be subject to S-palmitoylation (Figure 5A,Supplementary table S3). Moreover, since more than half of the proteins described in published targeted studies were not identified in any of the palmitoyl proteome screens (Figure 5B), the current figure of 9 to 12% is probably an underestimate.

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