Lipid transfer proteins and PI4KIIα generate a phosphoinositide-linked proteome.
Phosphoinositide (PIPn) lipid second messengers in membranes regulate numerous cellular processes. In the cytosol, the phosphatidylinositol (PI) 3-kinase (PI3K)/Akt pathway is scaffolded on IQGAP1 to facilitate the activation of Akt by the synthesis of PI3,4,5P3. In the nucleus, PIPn signaling occurs in compartments separate from membranes by stably linking PIPns to nuclear proteins. While several of these proteins have been identified, understanding the extent and impact of protein-linked PIPn signaling warrants further investigation. The tumor suppressor p53, was shown in the companion paper to be regulated by PI transfer proteins (PITPs) and a PI 4-kinase (PI4KIIα), which are required to form p53-PIPn complexes that assemble a nuclear PI3K/Akt pathway. Here we report that class I PITPs (PITPα/β) and PI4KIIα initiate PIPn linkages to many different proteins. PITPα/β and PI4KIIα accumulate in the nucleoplasm in response to stress and are necessary to synthesize nuclear PIPns linked to proteins. These PITPα/β-dependent protein-PIPn complexes are detected by metabolically labeling cells with the PIPn precursor [3H]-myo-inositol and resist denaturation and SDS-PAGE, indicating that these protein-PIPn complexes represent a putative posttranslational modification. Proteomic and gene set enrichment analysis of proteins that are linked to PI4,5P2 reveals an emerging PIPn-linked proteome (PIPylome) regulated by PITPα/β and enriched in proteins that play key functional roles in metabolism, cell motility/division, and the DNA damage response. The PIPn-linked proteome represents a third messenger signaling paradigm distinct from the canonical membrane-localized pathway whereby linked PIPn messengers regulate protein function.