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The Dictyostelium prestalk inducer differentiation-inducing factor-1 (DIF-1) triggers unexpectedly complex global phosphorylation changes.

Sugden C, Urbaniak MD, Araki T, Williams JG - Mol. Biol. Cell (2014)

Bottom Line: The results also provide evidence that the Ca(2+)/calmodulin-dependent phosphatase calcineurin plays a role in DIF-1 signaling to the DimB prestalk transcription factor.This accords with studies that suggest an antagonism between the two inducers and also with the rapid dephosphorylation of the cAMP receptor that we observe in response to DIF-1 and with the known inhibitory effect of DIF-1 on chemotaxis to cAMP.All MS data are available via ProteomeXchange with identifier PXD001555.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

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Analysis of class II DIF-1–regulated phosphorylation sites at each time point. (A) Chart summarizing the proportion of class II phosphorylation events vs. dephosphorylation events. Number in bars represents absolute numbers. (B–E) WebLogo sequence logo for motifs identified using Motif-X. Amino acids and color coded according to their hydrophobicity; hydrophobic, black neutral green; hydrophilic, blue. (B) RxxSxxxL motif from phosphorylation sites at 1 min; n = 15, motif score of 29, and 76-fold enrichment. (C) xSDDEx motif from dephosphorylation sites at 8 min; n = 15, motif score of 38, and 120-fold enrichment. (D) xSPRx motif from dephosphorylation sites at 8 min; n = 17, motif score of 26, and 40-fold enrichment. (E) xSPx motif from dephosphorylation sites at 8 min; n = 17, motif score of 16, and 5-fold enrichment.
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Figure 2: Analysis of class II DIF-1–regulated phosphorylation sites at each time point. (A) Chart summarizing the proportion of class II phosphorylation events vs. dephosphorylation events. Number in bars represents absolute numbers. (B–E) WebLogo sequence logo for motifs identified using Motif-X. Amino acids and color coded according to their hydrophobicity; hydrophobic, black neutral green; hydrophilic, blue. (B) RxxSxxxL motif from phosphorylation sites at 1 min; n = 15, motif score of 29, and 76-fold enrichment. (C) xSDDEx motif from dephosphorylation sites at 8 min; n = 15, motif score of 38, and 120-fold enrichment. (D) xSPRx motif from dephosphorylation sites at 8 min; n = 17, motif score of 26, and 40-fold enrichment. (E) xSPx motif from dephosphorylation sites at 8 min; n = 17, motif score of 16, and 5-fold enrichment.

Mentions: An interesting temporal pattern emerged when class I phosphorylation sites were analyzed by cluster analysis (Saeed et al., 2011) to detect groups of sites that change their phosphorylation with similar temporal profiles. Clusters showing dephosphorylation contained many more sites, indicating that DIF-1 may trigger a net dephosphorylation of cellular proteins (Figure 1C). A similar pattern emerges when class II sites are grouped into either phosphorylation or dephosphorylation events. The balance of phosphorylation versus dephosphorylation events dramatically shifts; at 1 min, just 39% of the class II sites are dephosphorylations, increasing to 94% at 15 min (Figure 2A).


The Dictyostelium prestalk inducer differentiation-inducing factor-1 (DIF-1) triggers unexpectedly complex global phosphorylation changes.

Sugden C, Urbaniak MD, Araki T, Williams JG - Mol. Biol. Cell (2014)

Analysis of class II DIF-1–regulated phosphorylation sites at each time point. (A) Chart summarizing the proportion of class II phosphorylation events vs. dephosphorylation events. Number in bars represents absolute numbers. (B–E) WebLogo sequence logo for motifs identified using Motif-X. Amino acids and color coded according to their hydrophobicity; hydrophobic, black neutral green; hydrophilic, blue. (B) RxxSxxxL motif from phosphorylation sites at 1 min; n = 15, motif score of 29, and 76-fold enrichment. (C) xSDDEx motif from dephosphorylation sites at 8 min; n = 15, motif score of 38, and 120-fold enrichment. (D) xSPRx motif from dephosphorylation sites at 8 min; n = 17, motif score of 26, and 40-fold enrichment. (E) xSPx motif from dephosphorylation sites at 8 min; n = 17, motif score of 16, and 5-fold enrichment.
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Related In: Results  -  Collection

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Figure 2: Analysis of class II DIF-1–regulated phosphorylation sites at each time point. (A) Chart summarizing the proportion of class II phosphorylation events vs. dephosphorylation events. Number in bars represents absolute numbers. (B–E) WebLogo sequence logo for motifs identified using Motif-X. Amino acids and color coded according to their hydrophobicity; hydrophobic, black neutral green; hydrophilic, blue. (B) RxxSxxxL motif from phosphorylation sites at 1 min; n = 15, motif score of 29, and 76-fold enrichment. (C) xSDDEx motif from dephosphorylation sites at 8 min; n = 15, motif score of 38, and 120-fold enrichment. (D) xSPRx motif from dephosphorylation sites at 8 min; n = 17, motif score of 26, and 40-fold enrichment. (E) xSPx motif from dephosphorylation sites at 8 min; n = 17, motif score of 16, and 5-fold enrichment.
Mentions: An interesting temporal pattern emerged when class I phosphorylation sites were analyzed by cluster analysis (Saeed et al., 2011) to detect groups of sites that change their phosphorylation with similar temporal profiles. Clusters showing dephosphorylation contained many more sites, indicating that DIF-1 may trigger a net dephosphorylation of cellular proteins (Figure 1C). A similar pattern emerges when class II sites are grouped into either phosphorylation or dephosphorylation events. The balance of phosphorylation versus dephosphorylation events dramatically shifts; at 1 min, just 39% of the class II sites are dephosphorylations, increasing to 94% at 15 min (Figure 2A).

Bottom Line: The results also provide evidence that the Ca(2+)/calmodulin-dependent phosphatase calcineurin plays a role in DIF-1 signaling to the DimB prestalk transcription factor.This accords with studies that suggest an antagonism between the two inducers and also with the rapid dephosphorylation of the cAMP receptor that we observe in response to DIF-1 and with the known inhibitory effect of DIF-1 on chemotaxis to cAMP.All MS data are available via ProteomeXchange with identifier PXD001555.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.

Show MeSH