Cyclin dependent kinase 16 (CDK16), also known as PCTAIRE-1 or PCTK1, is an atypical member of the Cyclin-dependent kinase (CDK) family that forms a ternary complex with Cyclin Y (CCNY) and 14-3-3 proteins. Cyclin Y acts as an activator for CDK16, forming an active kinase complex that serves as a regulator involved in diverse cellular processes, including autophagy regulation, translation control, and stress response dynamics. This thesis explores CDK16’s substrates and interactions through advanced proteomic techniques, focusing on its functional relevance in autophagy and cellular stress management. Our initial investigations used BioID mass spectrometry to identify Cyclin Y/CDK16 interactors and phosphorylation targets, revealing multiple proteins involved in autophagy, including BAG3 and ULK1. Specifically, phosphorylation at S289 on BAG3 and validation of ULK1 as a substrate underline CDK16’s regulatory role in autophagic processes, coordinated through AMPK signaling. GO term analysis further supports CDK16's role within autophagy mechanisms. Beyond autophagy, we identified ASPSCR1/TUG and LARP6 as novel CDK16 phosphorylation substrates, with TUG specifically facilitating VCP/p97 disassembly in endoplasmic reticulum-associated degradation (ERAD), thus underlining its contribution to protein quality control and ER stress modulation. Phosphorylation analysis of LARP6 also highlighted its involvement in cytoskeletal organization, further linking CDK16 to cellular structural integrity. A key finding was the role of CDK16 in stress granule (SG) dynamics through interactions with SERBP1, a prominent RNA-binding protein. We demonstrated that SERBP1 is phosphorylated by Cyclin Y/CDK16 at S234, impacting SG formation and stability. Notably, siRNA-mediated knockdown of both CDK16 and SERBP1 resulted in an additive increase in SG formation, suggesting independent yet convergent pathways in stress response regulation. This disruption of SG dynamics was found to affect protein synthesis under stress, as both CDK16 and SERBP1 depletion reduced nascent protein production by over 30%. In sum, this work highlights Cyclin Y/CDK16 as an important kinase coordinating cellular homeostasis through its involvement in autophagy, stress granule regulation, and translation control. The regulatory mechanisms described not only deepen our understanding of CDK16’s cellular roles but also present new possibilities for treatment in diseases related to problems with autophagy and stress granule issues.
Jan Amelang (Wed,) studied this question.