A new paradigm for outer membrane protein biogenesis in the Bacteroidota

In Gram-negative bacteria, the outer membrane is the first line of defence against antimicrobial agents and immunological attacks1. A key part of outer membrane biogenesis is the insertion of outer membrane proteins by the β-barrel-assembly machinery (BAM)2–4. Here we report the cryo-electron microscopy structure of a BAM complex isolated from Flavobacterium johnsoniae, a member of the Bacteroidota, a phylum that includes key human commensals and major anaerobic pathogens. This BAM complex is extensively modified from the canonical Escherichia coli system and includes an extracellular canopy that overhangs the substrate folding site and a subunit that inserts into the BAM pore. The novel BamG and BamH subunits that are involved in forming the extracellular canopy are required for BAM function and are conserved across the Bacteroidota, suggesting that they form an essential extension to the canonical BAM core in this phylum. For BamH, isolation of a suppressor mutation enables the separation of its essential and non-essential functions. The need for a highly remodelled and enhanced BAM complex reflects the unusually complex membrane proteins found in the outer membrane of the Bacteroidota. Structural and biochemical studies of the β-barrel-assembly machinery from Flavobacterium johnsoniae reveal a subunit composition and assembly that are distinct from those of the canonical Escherichia coli complex.