Mycobacterial cell envelopes are rich in unusual lipids and glycans that play key roles during infection and vaccination. The most abundant envelope glycolipid is trehalose dimycolate (TDM). TDM compromises the host response to mycobacterial species via multiple mechanisms, including inhibition of phagosome maturation. The molecular mechanism by which TDM inhibits phagosome maturation has been elusive. We find that a clickable, photoaffinity TDM probe phenocopies native TDM in macrophage host cells and binds several host SNARE proteins, including VTI1B, STX8, and VAMP2. VTI1B and STX8 normally promote endosome fusion by forming a complex with VAMP8. However in the presence of native TDM or Mycobacterium tuberculosis , VTI1B and STX8 can complex with VAMP2, which in turn inhibits VAMP8 binding. VAMP2 inhibits phagosome maturation and promotes intracellular M. tuberculosis replication. Thus one mechanism by which TDM constrains the innate immune response to M. tuberculosis is via non-canonical SNARE complexation.
Significance statement: Glycolipids from the Mycobacterium tuberculosis cell envelope, particularly trehalose dimycolate (TDM), play key roles in subverting the immune response to this intracellular pathogen. How subversion occurs is often unclear because glycans and lipids are technically challenging to study in cells. We discovered that a TDM-mimicking chemical probe interacts with three host SNARE proteins, including two that regulate endosome fusion and one that does not. The presence of TDM or M. tuberculosis triggers abnormal binding of these SNAREs, which in turn inhibits the fusion of M. tuberculosis -containing phagosomes with lysosomes and promotes M. tuberculosis replication. Our work provides an unusual example of a bacterial pathogen restricting the immune response via glycolipid-SNARE interactions.