Discovery of polyphosphate-interacting human lysine-rich proteins and their functional implications

Inorganic polyphosphate (polyP), a conserved phosphate polymer, modulates protein function across diverse biological systems, yet its human protein interactome remains poorly defined. While prior studies identified denaturation-resistant polyP modifications on lysine-rich sequences in yeast and bacteria, such targets in human proteins were previously unknown. Here, we performed a systematic screen of 57 lysine-rich human proteins, selected via mass spectrometry and bioinformatics, identifying 41 proteins that exhibit denaturation-resistant polyP modifications. This marks the first identification of lysine-rich motifs as polyP targets in human proteins. Through mutagenesis and binding assays, we establish these lysine-rich motifs, rather than traditional PASK domains, are critical for polyP binding, with consecutive lysine residues and intrinsic disorder as key determinants. Functional assays demonstrate that polyP binding inhibits phase separation of the transcriptional regulator NKAP, suppresses K-RAS GTPase activation, and reduces DDX55 helicase activity, revealing direct regulatory mechanisms. This work not only marks the first identification of denaturation-resistant polyP modifications in human proteins but also provides a comprehensive resource for investigating polyP's roles in human cellular homeostasis and disease.