Ubiquitin Chains Modified by the Bacterial Ligase SdeA Are Protected from Deubiquitinase Hydrolysis

Abstract

The SidE family of Legionella pneumophila effectors is a unique group of ubiquitin-modifying enzymes. Along with catalyzing NAD+-dependent ubiquitination of certain host proteins independent of the canonical E1/E2/E3 pathway, they have also been shown to produce phosphoribosylated free ubiquitin. This modified ubiquitin product is incompatible with conventional E1/E2/E3 ubiquitination processes, with the potential to lock down various cellular functions that are dependent on ubiquitin signaling. Here, we show that in addition to free ubiquitin, Lys63-, Lys48-, Lys11-, and Met1-linked diubiquitin chains are also modified by SdeA in a similar fashion. Both the proximal and distal ubiquitin moieties are targeted in the phosphoribosylation reaction. Furthermore, this renders the ubiquitin chains unable to be processed by a variety of deubiquitinating enzymes. These observations broaden the scope of SdeA’s modulatory functions during Legionella infection.

Post-translational regulation of ubiquitin signaling

“…ADPR-Ub and PR-Ub produced by SidEs potently interfere with ubiquitination catalyzed by the canonical mechanism (Bhogaraju et al, 2016). Furthermore, diubiquitins modified by ADPR are resistant to cleavage by various DUBs that use different mechanisms for isopeptide bond hydrolysis (Puvar et al, 2017). Although one can produce ADPR-Ub and PR-Ub in large quantities by biochemical reactions with mutants lacking PDE activity or with wild-type SdeA (Bhogaraju et al, 2016; Kotewicz et al, 2017), these forms of modified ubiquitin likely are scarce, even in cells infected with L. pneumophila.…”

ADP-Ribosylation of the Ubiquitin C-Terminus by Dtx3L/Parp9

“…Incubation of lysine 48-or methionine 1-linked ubiquitin tetramers with SdeC led to ADP-ribosylation of the incorporated ubiquitin [24]. Further investigation showed that ADP-ribosylation and phosphoribosylation of lysine 63-, lysine 48-, lysine 11-, or methionine 1-linked diubiquitin chains could be catalyzed by SdeA [52]. No preference for modification of either ubiquitin within the diubiquitin was observed.…”

“…No preference for modification of either ubiquitin within the diubiquitin was observed. In most cases, the ADP-ribosylated or phosphoribosylated diubiquitins were resistant to hydrolysis by deubiquitinases, suggesting SidE proteins could have broad effects in host cell by changing deubiquitinase susceptibility of polyubiquitin chains on various target substrates [52].…”

Ubiquitin, SUMO, and NEDD8: Key Targets of Bacterial Pathogens

“…Phosphoribosylation of UBI, for example, that is catalyzed by the Legionella SdeA effector, was reported to interfere with multiple steps in the ubiquitination cascade [47]. The presence of phosphoribosylated UBI in chains further confers resistance to various deubiquitinases [55]. SdeA, by both triggering E1 and E2-independent ubiquitination of specific host targets, and by inhibiting ubiquitination of others, thus efficiently controls the host ubiquitinome [47].…”