A genome-wide CRISPR screen identifies host proteins required for depletion of surface MHCII by Salmonella

Abstract

Systemic infections caused by Salmonella enterica are largely controlled by activation of CD4 T cells. Dendritic cells phagocytose bacteria in the small intestine and present antigens to CD4 T cells via MHCII. Salmonella enterica serovar Typhimurium impairs MHCII presentation by infected dendritic cells. We recently identified SteD, a bacterial virulence protein that is translocated into host cells by the SPI-2 type 3 secretion system, as required and sufficient for this activity (Bayer-Santos et al., 2016). Although SteD interacts with MHCII, its mechanism of action was unclear. Using a genome-wide CRISPR Knock-Out screen of Mel Juso cells expressing SteD, we identified two host proteins involved in SteD-dependent depletion of mature MHCII (mMHCII) from the cell surface. One is WWP2, an E3 ligase belonging to the Nedd4 family. The second is TMEM127, a transmembrane protein, which interacts with both WWP2 and SteD. We propose that SteD recruits WWP2 via TMEM127, resulting in ubiquitination of mMHCII. Ubiquitination of mMHCII by this mechanism involves mostly K63-linked chains and leads to its lysosomal degradation. Remarkably, we found that SteD is itself ubiquitinated by the same mechanism and this modification is important for SteD function. This study reveals how Salmonella enterica promotes immune escape by redirecting the activity of host proteins.