A Photoaffinity Probe for S‑Guanylation Posttranslational Modification to Identify Its Interacting Proteins

S-guanylation is an endogenous posttranslational modification that has been implicated as a specific autophagic signal, yet its interacting proteins and underlying molecular mechanism remain largely unknown. Here, we developed the first diazirine-based S-guanylation photoaffinity probe (SGPP) to capture and identify its interacting proteins in living cells. The SGPP efficiently labeled target proteins in a time-, concentration-, and UV-crosslinking-dependent manner, as demonstrated by in-gel fluorescence scanning. Using a chemoproteomic workflow combining SGPP-mediated photocrosslinking, affinity enrichment, and mass spectrometry, we identified nine candidate binding proteins in HeLa cells, including ACAP2, APOD, DLGAP5, FAM83A, GNB4, LCN1, LSM4, OR5AC2, and RNASEH2A. Orthogonal anti‑GFP pull‑down validation confirmed GNB4 as a bona fide binding partner. Notably, the association of several candidates with guanine nucleotide binding activity validates the reliability of our chemoproteomic identification. To validate the degradation activity of the S-guanylation warhead and to establish a functionally relevant orthogonal model for validating candidate binding proteins, we established a tetracycline (TetON) inducible expression system, which overcame the limitations of strong constitutive promoters and demonstrated efficient S-guanylation-induced degradation of the target protein. Collectively, this study provides the first chemical tool for studying S-guanylation and identifies GNB4 as a validated binding partner, establishing a foundation for future screening of small molecule drugs that target selective autophagy.