Mechanism of controlling autophagy by liquid-liquid phase separation revealed

Under JST’s Strategic Basic Research Programs, Noda Nobuo (Laboratory Head) and Fujioka Yuko (Senior Researcher) of the Institute of Microbial Chemistry, in collaboration with other researchers, discovered that a liquid-like condensate (liquid droplets(1)) in which the Atg protein is clustered through the liquid-liquid phase separation(2) is the structure responsible for the progression of autophagy.

Autophagy is one of the mechanisms through which cellular protein is degraded. Previously, it was known that Atg proteins assemble to form a structure called PAS(3). However, the mechanism through which Atg proteins assemble and the physicochemical property of the formed structures had been unclear.

The research team elucidated characteristics of PAS through observing the Atg protein using a fluorescence microscope and successfully reconstituted PAS in vitro. The team revealed, for the first time, that PAS is in the state of liquid droplets formed by liquid-liquid phase separation of Atg13 together with other Atg proteins and that this liquid droplet is responsible for autophagy.

The finding that liquid-liquid phase separation directly controls autophagy suggests its involvement in a wide range of intracellular life phenomena. Reconsideration of molecular mechanisms underlying various intracellular phenomena is expected to proceed. Moreover, development of autophagy-specific control agents that focus on the regulation of liquid-liquid phase separation in autophagy-related diseases is anticipated.

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(1) Liquid droplet

A condensate of macromolecules with fluidity created when protein and/or nucleic acids undergo liquid-liquid phase separation. The droplets are also known as “membraneless organelles” and perform various functions within the cell. A droplet spontaneously assumes a spherical form. It also has high internal fluidity, and it actively exchanges molecules with its surroundings.

(2) Liquid-liquid phase separation

This is the phenomenon of a uniform liquid phase separating into multiple liquid phases. It is observed in daily life as the separation of water and oil, and occurs within cells with proteins and nucleic acids.

(3) PAS (Pre-autophagosomal structure)

The collected structure that the Atg protein forms near the vacuole under nutrient starvation in yeast is called PAS. It is assumed that autophagosomes formation starts at PAS.