Extended Data Fig. 5: Proteome and phosphoproteome adaptation to sustained change in temperature or external osmotic potential.
From: Macromolecular condensation buffers intracellular water potential
(a) Representative examples of proteins whose relative abundance correlates or inversely correlates with temperature or external osmolarity after two weeks adaptation. The adjusted p-value of linear fit by LIMMA was used to determine significance (with threshold p < 0.05), and is reported for the representative examples; Lamc1 is shown as an example of a protein whose abundance does not change with either osmolarity or temperature. Corresponds to Fig. 2b. (b) Examples of proteins whose abundance both increases with increasing temperature and decreases with increasing osmolarity, i.e. could be Ψπ-regulated. (c) Gene Ontology compartment enrichment for the 344 proteins that are oppositely regulated by temperature and osmolarity, against the background of all detected proteins. Number on the bars represents fold-change enrichment, colour of the bars highlights semantically close terms. (d) Validation of enrichment for ribosomal subunits in (c), strongly indicates a co-ordinated change in ribosomal subunit expression that is oppositely affected by temperature vs osmolarity during long-term adaptation, consistent with previous findings96. (e, f) Corresponding to Fig. 2d: representative examples of phosphopeptides whose relative abundance correlates or inversely correlates with temperature or osmolarity (e), as well as phosphopeptides that are oppositely regulated by temperature and osmolarity (f), i.e. change significantly with decrease (left) or increase (right) as a function of challenge to Ψπ. (g) Kinase motif prediction analysis. All detected phosphopeptide sequences were queried for matches to known phosphorylation consensus motifs for a panel of kinases (based on the PHOSIDA database); proportion of phosphopeptides matching motifs for the six selected kinases is presented, comparing overall levels (grey bar) to the subset of phosphopeptides putatively regulated by Ψπ (proportion z-test: all differences are significant with adjusted p-value < 0.0001 for CK1, CK2, and GSK3, not significant for CDK1, CDK2, ERK/MAPK). Note that Ψπ-responsive phosphosites are enriched for motifs recognized by promiscuous kinases with established preference for IDRs (casein kinase 1, casein kinase 2, glycogen synthase kinase 3, see also refs. 97,98).
