Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213

Abstract

The evolutionary arms race between pathogens and hosts has resulted in pathogens acquiring diverse adaptive countermeasures that antagonize host immunity. Ubiquitylation of lipopolysaccharide (LPS) on cytosol-invading bacteria by the E3 ligase RNF213 creates eat-me signals for antibacterial autophagy but whether and how cytosol-adapted bacteria avoid LPS ubiquitylation remains poorly understood. Here we show that Shigella flexneri, a professional cytosol-dwelling enterobacterium, actively antagonizes LPS ubiquitylation through IpaH1.4, a secreted effector protein with ubiquitin E3 ligase activity. IpaH1.4 binds to the LPS E3 ubiquitin ligase RNF213, ubiquitylates it, and targets it for degradation by the proteasome, thus preventing LPS ubiquitylation. To understand how IpaH1.4 recognizes RNF213, we determined the structure of their complex using cryogenic electron microscopy. The specificity of the interaction is achieved via the leucine rich repeat of IpaH1.4, which binds the RING domain of RNF213 by hijacking the conserved RING interface required for binding of ubiquitin-charged E2 enzymes. Interestingly, IpaH1.4 also targets the E3 ligase LUBAC - required for the synthesis of M1-linked ubiquitin chains on cytosol-invading bacteria downstream of RNF213 - as well as multiple other E3 ligases involved in inflammation and immunity - through binding to the E2-interacting face of their RING domains. We conclude that IpaH1.4 has evolved to antagonize multiple anti-bacterial and pro-inflammatory host E3 ligases.