Regulation of phosphoribosyl-linked serine ubiquitination by deubiquitinases DupA and DupB, Shin et al

The family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacterium causing Legionnaires’ disease. Here we describe identification of two bacterial effectors (LaiE and LaiF) that actively reverse PR-ubiquitination during infection and are thus named DeUbiquitinases for PR-ubiquitination (DUPs; DupA/LaiE and DupB/LaiF). 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 dictates its catalytic activity allowing DupA to predominantly 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 next exploited a catalytically inactive DupA mutant to trap and subsequently 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 uncovered by DupA-mediated trapping strategy provides critical insights into host-pathogen interactions during Legionella infection.