In the arms race between pathogens and hosts, Shigella flexneri uses the bacteria-encoded effector protein IpaH1.4 to ubiquitylate the host-encoded E3 ligases RNF213, thus preventing the bacteria from being marked for autophagy via LPS ubiquitylation
Unlike Salmonella, which is ubiquitylated by the host E3 ligase RNF213, Shigella evades this defence by deploying the effector protein IpaH1.4 to ubiquitylate RNF213, marking it for proteasomal degradation. This prevents the host from tagging Shigella for destruction.
Ubiquitylation is a common post-translational modification in which a ubiquitin protein is covalently conjugated to a substrate. It plays a crucial role in regulating substrate degradation, thereby maintaining cellular homeostasis by controlling the quality and quantity of intracellular materials. While it was once thought that only proteins underwent ubiquitylation, Felix Randow’s group in the LMB’s PNAC division recently discovered that Salmonella bacteria invading the host cytosol are attacked by the ubiquitin E3 ligase RNF213, which ubiquitylates lipopolysaccharide (LPS) molecules on the bacterial membrane, triggering autophagy. This finding has electrified the ubiquitin field, as the ubiquitylation of non-proteinaceous substrates suggests an even broader scope for ubiquitylation in regulating cell fate than previously anticipated. Felix’s group has since set out to answer some of the questions raised by their discovery of RNF213 as an LPS ubiquitin ligase. Would bacteria adapted to life in the host cytosol also be subject to LPS ubiquitylation? If not, why not? Their newly published research focuses on the cytosol-adapted bacterium Shigella flexneri, which they discovered does not become ubiquitin-coated in the cytosol, and for which they identified the mechanism by which it evades LPS ubiquitylation.
Investigating the apparent lack of LPS ubiquitylation, Claudio Pathe, a former PhD student now at AstraZeneca, and Keith Boyle, a postdoc in Felix’s group, examined the biology of the host-Shigella interaction, finding at its core a battle between two ubiquitin E3 ligases (Figure 1). The invading Shigella bacteria actively antagonise LPS ubiquitylation through IpaH1.4, a secreted bacterial effector protein with ubiquitin E3 ligase activity. Claudio and Keith discovered that IpaH1.4 binds to RNF213, ubiquitylates it, and targets it for degradation by the proteasome, suggesting absence of RNF213 in Shigella-infected cells prevents LPS ubiquitylation. To confirm the importance of IpaH1.4 to the bacteria’s defence, the group studied infection by mutant Shigella strains lacking this effector protein, in which they found the Shigella LPS was ubiquitylated by RNF213.
To better understand how IpaH1.4 recognises RNF213, Katerina Naydenova, a postdoc in the group, solved the complex’s structure using electron cryo-microscopy. Katerina’s work revealed that the leucine-rich repeat (LRR) domain of IpaH1.4 binds to the RING domain of RNF213 (Figure 2). RING domains are essential for the catalytic activity of many E3 ligases because they serve as the docking site for ubiquitin-charged E2 enzymes before ubiquitin is transferred to the target substance. In the case of Shigella, IpaH1.4 hijacks the conserved E2-binding interface of the RNF213 RING domain, thus enabling IpaH1.4 to ubiquitylate RNF213 and induce its proteasome-dependent degradation.
Interestingly, the group found that IpaH1.4 also targets several other E3 ligases involved in inflammation and immunity by binding to the E2-interacting surface of their respective RING domains. A prominent example is the E3 ligase LUBAC, which is essential for the synthesis of specialized ubiquitin chains on cytosol-invading bacteria downstream of RNF213. Taken together, the newly published research demonstrates how IpaH1.4 has evolved to antagonise multiple anti-bacterial and pro-inflammatory host E3 ligases, thereby gaining the bacterium an advantage in the ‘arms race’ with their host organisms. Katerina Naydenova says that “… we believe the future study of bacterial effector proteins will shine more light on uncharacterized immune phenomena.”
This work was funded by UKRI MRC, the Wellcome Trust, the German Research Foundation and the Swiss National Science Foundation.
Further references
Shigella flexneri evades LPS ubiquitylation through IpaH1.4-mediated degradation of RNF213. Naydenova, K., Boyle, K.B., Pathe, C., Pothukuchi, P., Crespillo-Casado, A., Scharte, F., Hammoudi, P-M., Otten, E.G., Randow, F. Nature Structural & Molecular Biology
Felix’s group page
Previous Insight on Research articles
A new way to mark bacterial invaders for destruction
New pathway for cells to detect bacterial infection