DDI2 Is a Ubiquitin-Directed Endoprotease Responsible for Cleavage of Transcription Factor NRF1

Molecular Cell
A Barbara Dirac-SvejstrupJesper Q Svejstrup

Abstract

The Ddi1/DDI2 proteins are ubiquitin shuttling factors, implicated in a variety of cellular functions. In addition to ubiquitin-binding and ubiquitin-like domains, they contain a conserved region with similarity to retroviral proteases, but whether and how DDI2 functions as a protease has remained unknown. Here, we show that DDI2 knockout cells are sensitive to proteasome inhibition and accumulate high-molecular weight, ubiquitylated proteins that are poorly degraded by the proteasome. These proteins are targets for the protease activity of purified DDI2. No evidence for DDI2 acting as a de-ubiquitylating enzyme was uncovered, which could suggest that it cleaves the ubiquitylated protein itself. In support of this idea, cleavage of transcription factor NRF1 is known to require DDI2 activity in vivo. We show that DDI2 is indeed capable of cleaving NRF1 in vitro but only when NRF1 protein is highly poly-ubiquitylated. Together, these data suggest that DDI2 is a ubiquitin-directed endoprotease.

Citations

Jan 6, 2021·Communications Biology·Annamaria Ruggiano, Kristijan Ramadan
Jan 8, 2021·Frontiers in Cell and Developmental Biology·Manideep C PachvaRegina Groisman
Feb 23, 2021·Trends in Cell Biology·Ann Schirin MirsanayeNiels Mailand
Mar 30, 2021·EMBO Reports·Kevin G Mark, Michael Rape
Apr 5, 2021·Current Opinion in Chemical Biology·Kirandeep K Deol, Eric R Strieter
Aug 3, 2021·The Journal of Biological Chemistry·Kazuhiko IgarashiMitsuyo Matsumoto
Sep 17, 2021·Molecular Cell·Syed Arif Abdul RehmanYogesh Kulathu
Dec 28, 2021·IUBMB Life·Marianna KapetanouEfstathios S Gonos

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Datasets Mentioned

BETA
PXD018215
PXD019152

Methods Mentioned

BETA
electrophoresis
PCR
transfections
FACS
gel filtration
affinity purifications

Software Mentioned

Maxquant
Addgene
ImageJ
TIDE
Andromeda
UbiSite

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