Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB.

Donghyuk Shin,Yan Liu,Volker Dötsch,Rukmini Mukherjee,Gerhard Hummer,Marcel Heinz,Vladimir V Rogov,Yaobin Liu,Florian Bonn,Ivan Dikic,Alexandra Stolz,Zhao-Qing Luo,Sagar Bhogaraju,Alexis Gonzalez

doi:10.1016/j.molcel.2019.10.019

Abstract

SummaryThe family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila. Here, we describe identification of two bacterial effectors that reverse PR ubiquitination and are thus named deubiquitinases for PR ubiquitination (DUPs; DupA and DupB). Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain. However, unlike SidE ubiquitin ligases, DupA displays increased affinity to PR-ubiquitinated substrates, which allows DupA to cleave PR ubiquitin from substrates. Interfering with DupA-ubiquitin binding switches its activity toward SidE-type ligase. Given the high affinity of DupA to PR-ubiquitinated substrates, we exploited a catalytically inactive DupA mutant to trap and identify more than 180 PR-ubiquitinated host proteins in Legionella-infected cells. Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets. The global map of PR-ubiquitinated substrates provides critical insights into host-pathogen interactions during Legionella infection.

Highlights

Ubiquitination is one of the most versatile post-translational modifications, controlling a wide variety of cellular processes (Hochstrasser, 2009)
Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain
Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets

Summary

Introduction

Ubiquitination is one of the most versatile post-translational modifications, controlling a wide variety of cellular processes (Hochstrasser, 2009). Subsequent additions of further Ub moieties create polymers of Ub, which have diverse structures and functions (Yau and Rape, 2016). These Ub structures can be recognized by specific receptors that contain Ub-binding domains (UBDs) that can result in the delivery of ubiquitinated substrate to the proteasome for degradation or to selective autophagy pathways to changes in protein function and/or cellular localization (Dikic, 2017). The mechanism underlying the ubiquitination process is well established. It involves a cascade of three enzymes: E1-Ub activating enzyme, E2-Ub conjugating enzyme, and E3-Ub ligase. Specific enzymes called deubiquitinases (DUBs) cleave off Ub from substrates and regulate the abundance of ubiquitinated proteins (Clague et al, 2019)

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