Ca2+/calmodulin-dependent protein kinase II β decodes ER Ca2+ transients to trigger autophagosome formation

In multicellular organisms, very little is known about how Ca²⁺ transients on the ER outer surface elicited by autophagy stimuli are sustained and decoded to trigger autophagosome formation. Here, we show that Ca²⁺/calmodulin-dependent protein kinase II β (CaMKIIβ) integrates ER Ca²⁺ transients to trigger liquid-liquid phase separation (LLPS) of the autophagosome-initiating FIP200 complex. In response to ER Ca²⁺ transients, CaMKIIβ is recruited from actin filaments and forms condensates, which serve as sites for the emergence of or interaction with FIP200 puncta. CaMKIIβ phosphorylates FIP200 at Thr269, Thr1127, and Ser1484 to modulate LLPS and properties of the FIP200 complex, thereby controlling its function in autophagosome formation. CaMKIIβ also controls the amplitude, duration, and propagation of ER Ca²⁺ transients during autophagy induction. CaMKIIβ mutations identified in the neurodevelopmental disorder MRD54 affect the function of CaMKIIβ in autophagy. Our study reveals that CaMKIIβ is essential for sustaining and decoding ER Ca²⁺ transients to specify autophagosome formation in mammalian cells.