Molecular basis of SIFI activity in the integrated stress response

Zhi Yang, Diane L. Haakonsen, Michael Heider, Samuel R. Witus, Alex Zelter, Tobias Beschauner, Michael J. MacCoss and Michael Rapé ()
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Zhi Yang: University of California at Berkeley
Diane L. Haakonsen: University of California at Berkeley
Michael Heider: University of California at Berkeley
Samuel R. Witus: University of California at Berkeley
Alex Zelter: University of Washington
Tobias Beschauner: University of California at Berkeley
Michael J. MacCoss: University of Washington
Michael Rapé: University of California at Berkeley

Nature, 2025, vol. 643, issue 8073, 1117-1126

Abstract: Abstract Chronic stress response activation impairs cell survival and causes devastating degenerative diseases1–3. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase silencing factor of the integrated stress response (SIFI), to terminate stress response signalling and ensure cellular homeostasis4. How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here we combine cryo-electron microscopy analysis of endogenous SIFI with AlphaFold modelling and biochemical studies to report the structural and mechanistic basis of the silencing of the integrated stress response. SIFI detects both stress indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and therefore allows a single enzyme to monitor and, if needed, modulate a complex cellular state.

Date: 2025
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DOI: 10.1038/s41586-025-09074-z

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