The N-terminal extension region of BamE coordinates interaction between the β-barrel domain of BamA and BamD for efficient assembly

In the Gram-negative bacteria, the assembly of {beta}-barrel proteins into the outer membrane is mediated by the {beta}-barrel Assembly Machinery (BAM) complex. BamA is a central component of the BAM complex. The molecular mechanisms of BamA when the substrate protein is assembled has been well elucidated and further the inhibitors targeting key mechanisms of BamA have been isolated. Although the BAM complex is a multi-subunit machine and its coordination is necessary for full function, the molecular mechanism remains unclear. Here we report on a fine-tuning system with a subunit called BamE, which is required for the cooperation of two essential subunits BamA and BamD. BamE is a lipoprotein with an N-terminal extension region between the lipid-modifying cysteine on the N-terminus and the periplasmic folding domain. Our interaction mapping revealed that the N-terminal extension region of BamE interacts with the {beta}-barrel domain of BamA, which contains a catalytic site for assembly termed lateral gate. The mutational analysis demonstrated that the N-terminal extension region of BamE fine-tunes the assembly stage dependent BamA-BamD interaction, responsible for the crucial role for assembly and integrity of the outer membrane. We suggest that this fine-tuning system plays an important role in the substrate relay system from the receptor BamD to the insertase BamA. Furthermore, structure prediction-based analysis suspects that the C-terminal region of BamD acts as the replacement of BamE in BamE-less bacteria.