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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

Ontology and network analysis of S-palmitoylated proteins.A: GO term analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies. GO terms sharing the same biological functions enriched in S-palmitoylation Hit proteins are clustered. The distance between GO terms corresponds to the inverse numbers of proteins common to the two terms and the size of the circle to the number of proteins associated with the GO term.B: Protein-protein interactions networks analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies using STRING software. The interactions (high confidence score > 0.9) are shown in evidence view (pink: experimental evidences and blue database evidences).
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f6: Ontology and network analysis of S-palmitoylated proteins.A: GO term analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies. GO terms sharing the same biological functions enriched in S-palmitoylation Hit proteins are clustered. The distance between GO terms corresponds to the inverse numbers of proteins common to the two terms and the size of the circle to the number of proteins associated with the GO term.B: Protein-protein interactions networks analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies using STRING software. The interactions (high confidence score > 0.9) are shown in evidence view (pink: experimental evidences and blue database evidences).

Mentions: Consistent with the findings reported in some targeted studies, specific biological functions/processes (Figure 6A,Supplementary figure S3 andSupplementary figure S4,Supplementary table S6, methods) are enriched in potentially S-palmitoylated proteins: membrane organisation, cytoskeleton organization, protein localization, cell localization and cell signalling. For example, proteins involved in vesicular trafficking were enriched such as subunits of the coatomer complex, clathrin as well as a significant number of SNARE proteins (Supplementary table S5). We also found 289 hit proteins associated with the GO term Cytoskeleton. These include microfilament- and microtubule-related proteins such as actin subunits, dynein and vimentin but also proteins involved in the formation and regulation of these structures: profilin I, Arp2-Arp3 related proteins. Consistent with a role of S-palmitoylated proteins in cytoskeleton dynamics, tubulin S-palmitoylation was shown to contribute to its association with membrane72 (Supplementary table S5). More recently, S-palmitoylation of LIM Kinase-1 was shown to regulate spine-specific actin polymerization and thereby morphological plasticity73. The full view of the role of S-palmitoylation in cytoskeleton organization will clearly require further studies.


SwissPalm: Protein Palmitoylation database.

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

Ontology and network analysis of S-palmitoylated proteins.A: GO term analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies. GO terms sharing the same biological functions enriched in S-palmitoylation Hit proteins are clustered. The distance between GO terms corresponds to the inverse numbers of proteins common to the two terms and the size of the circle to the number of proteins associated with the GO term.B: Protein-protein interactions networks analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies using STRING software. The interactions (high confidence score > 0.9) are shown in evidence view (pink: experimental evidences and blue database evidences).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Ontology and network analysis of S-palmitoylated proteins.A: GO term analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies. GO terms sharing the same biological functions enriched in S-palmitoylation Hit proteins are clustered. The distance between GO terms corresponds to the inverse numbers of proteins common to the two terms and the size of the circle to the number of proteins associated with the GO term.B: Protein-protein interactions networks analysis of 470 human S-palmitoylation hits found by 2 independent techniques or by targeted studies using STRING software. The interactions (high confidence score > 0.9) are shown in evidence view (pink: experimental evidences and blue database evidences).
Mentions: Consistent with the findings reported in some targeted studies, specific biological functions/processes (Figure 6A,Supplementary figure S3 andSupplementary figure S4,Supplementary table S6, methods) are enriched in potentially S-palmitoylated proteins: membrane organisation, cytoskeleton organization, protein localization, cell localization and cell signalling. For example, proteins involved in vesicular trafficking were enriched such as subunits of the coatomer complex, clathrin as well as a significant number of SNARE proteins (Supplementary table S5). We also found 289 hit proteins associated with the GO term Cytoskeleton. These include microfilament- and microtubule-related proteins such as actin subunits, dynein and vimentin but also proteins involved in the formation and regulation of these structures: profilin I, Arp2-Arp3 related proteins. Consistent with a role of S-palmitoylated proteins in cytoskeleton dynamics, tubulin S-palmitoylation was shown to contribute to its association with membrane72 (Supplementary table S5). More recently, S-palmitoylation of LIM Kinase-1 was shown to regulate spine-specific actin polymerization and thereby morphological plasticity73. The full view of the role of S-palmitoylation in cytoskeleton organization will clearly require further studies.

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