SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains

The outer membrane (OM) in Gram-negative bacteria consists of an asymmetric phospholipid – lipopolysaccharide bilayer densely packed with beta-barrel proteins (OMPs) and lipoproteins. The architecture and composition of this bilayer is closely monitored and essential to cell integrity and survival. Here we find that SlyB, a lipoprotein in the PhoPQ stress regulon forms stable stress-induced complexes with the outer membrane proteome. SlyB consists of a 10 kDa periplasmic beta-sandwich domain and a glycine zipper domain that forms a transmembrane alpha-helical hairpin with a discrete phospholipid and LPS binding site. Loss in lipid asymmetry makes SlyB oligomerize into ring-shaped transmembrane complexes that encapsulate beta-barrel proteins into lipid nanodomains of variable size. We find SlyB nanodomain formation is essential during LPS destabilization by antimicrobial peptides or acute cation shortage, conditions that result in a loss of OMPs and compromised OM barrier function in absence of a functional SlyB. Our data reveal SlyB as a compartmentalizing transmembrane guard protein involved in cell envelope proteostasis and integrity, and suggest SlyB represents a larger family of broadly conserved (lipo)proteins with 2TM glycine zipper domains capable of forming lipid nanodomains.