Nuclear phosphatidylinositol 3,4,5-trisphosphate interactome uncovers an enrichment in nucleolar proteins

Abstract

Polyphosphoinositides (PPIn) play essential functions as lipid signalling molecules and many of their functions have been elucidated in the cytoplasm. However, PPIn are also intranuclear where they contribute to chromatin remodelling, transcription and mRNA splicing. The PPIn, phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) has been mapped to the nucleus and nucleoli but its role remains unclear in this subcellular compartment. To gain further insights into the nuclear functions of PtdIns(3,4,5)P3, we applied a previously developed quantitative mass spectrometry-based approach to identify the targets of PtdIns(3,4,5)P3 from isolated nuclei. We identified 179 potential PtdIns(3,4,5)P3-interacting proteins and gene ontology analysis for the biological functions of this dataset revealed an enrichment in RNA processing/splicing, cytokinesis, protein folding and DNA repair. Interestingly, about half of these interactors were common to nucleolar protein datasets, some of which had dual functions in rRNA transcription and DNA repair, including Poly(ADP-Ribose) Polymerase 1 (PARP1/ARTD1). PARP1 was found to interact directly with PtdIns(3,4,5)P3 as well as PtdIns(3,4)P2 and to co-localise with PtdIns(3,4,5)P3 in the nucleolus and with PtdIns(3,4)P2 in nucleoplasmic foci. In conclusion, the PtdIns(3,4,5)P3 interactome reported here identified several nucleolar proteins and further pointed to roles for this lipid in these processes.

When PIP2 Meets p53: Nuclear Phosphoinositide Signaling in the DNA Damage Response

“…This approach led to the identification of 168 nuclear proteins harboring lysine/ arginine-rich patches or phosphoinositide-binding domains. Similar studies were performed recently using PI(3,4,5)P 3coated beads (Mazloumi Gavgani et al, 2021). This led to an identification of a small set of DNA damage repair proteins; including proteins from various repair pathways.…”

“…This implies that PI(4,5)P 2 might play a role in regulating the PARylation of p53, which is required for its rapid recruitment to DNA damage sites and hence repair pathway selection. Furthermore, a recent interactome study validates PARP1 as a PI(4,5)P 2 -binding protein (Mazloumi Gavgani et al, 2021). The interactions between PARP1, PI(4,5)P 2 /PI(3,4,5)P 3 and p53 form a new signaling axis and how nuclear PI(4,5)P 2 affects DNA repair pathway selection warrants further investigation.…”

“…A recent study from the same author(s) characterized the nuclear PI(3,4,5)P 3 interactome that was composed of 179 proteins and identified new interaction partners associated with the nucleolus. A few DNA damage repair proteins including PARP1 were also identified (Mazloumi Gavgani et al, 2021). In an independent study, synthetic probes featuring PI(3,4,5)P 3 headgroups with photoaffinity tags were used for covalently labeling PI(3,4,5) P 3 -binding proteins.…”

“…Additionally, the binding of PI(4,5)P 2 prevents p53 from interacting with MDM2, which is another mechanism to stabilize p53. The binding of PI(4,5)P 2 to p53 is mapped to the C-terminal polybasic stretch of p53, which indicates electrostatic interactions play a major role when interacting with phosphoinositide lipids in nucleus (Mazloumi Gavgani et al, 2021). Surprisingly, the PI(4,5)P 2 -p53 interaction was very stable and was resistant to denaturation during SDS-polyacrylamide gel electrophoresis (SDS-PAGE) (Choi et al, 2019).…”