From Chaperones to the Membrane with a BAM!

Abstract

Outer membrane proteins (OMPs) play a central role in the integrity of the outer membrane of Gram-negative bacteria. Unfolded OMPs (uOMPs) transit across the periplasm, and subsequent folding and assembly are crucial for biogenesis. Chaperones and the essential β-barrel assembly machinery (BAM) complex facilitate these processes. In vitro studies suggest that some chaperones sequester uOMPs in internal cavities during their periplasmic transit to prevent deleterious aggregation. Upon reaching the outer membrane, the BAM complex acts catalytically to accelerate uOMP folding. Complementary in vivo experiments have revealed the localization and activity of the BAM complex in living cells. Completing an understanding of OMP biogenesis will require a holistic view of the interplay among the individual components discussed here.

Keywords: BAM complex; chaperones; outer membrane proteins.

Figure 1, Key Figure. Depiction of Outer Membrane Protein biogenesis components in E. coli shown to scale

Unfolded OMPs enter the periplasm via the SecYEG translocase (teal, PDB: 2CFQ), which is located in the bacterial inner membrane. Once in the periplasm, unfolded OMPs interact with several chaperones, including: DegP (cyan, PDB: 3CSO), FkpA (yellow, PDB: 1Q6U), SurA (magenta, PDB: 1M5Y), and Skp (pale green, PDB: 1U2M). The outer-membrane localized BAM complex (BamABCDE shown in blue/green/magenta/pink/yellow respectively, PDB: 5D0O) facilitates uOMP folding into the OM (e.g. OmpLA; red, PDB: 1QD5). The multi-protein Acr complex (tan, PDBs: 1EK9, 2F1M, 2DHH) was used to position the inner and outer membranes. The structures of these membranes were derived from MD simulations of smaller patches that were concatenated to make this image [63]; phosphate atoms of lipid head groups are shown in orange spheres. Arrows indicate known interactions, although the exact sequence and mechanisms of these interactions are unknown. Note the peptidoglycan is excluded from this figure. This image was created in Pymol [76].

Figure 2. OmpLA forms extensive interactions with the outer membrane of E. coli [63]

This membrane is asymmetric, as the inner and outer leaflets (e.g. blue and purple sphere lipids, respectively) are composed of phospholipids and LPS, respectively. Phosphate atoms of lipid head groups are shown in orange spheres. All-atom MD simulations of an OMP embedded in an E. coli outer membrane have revealed that divalent ion-mediated interactions create electrostatic networks that impart rigidity and limited mobility in the LPS leaflet of the bilayer. This image was prepared in VMD [77].

Figure 3. Structural model showing uOMP encapsulated by Skp

The uOMP protrudes from the internal binding cavity of Skp. This model was constructed from SANS experiments of Skp bound to unfolded OmpW [18]. Skp is depicted as green cartoon, while uOMP is shown as grey surface. This figure was created in VMD [77].

Figure 4. Molecular Dynamics Simulation Snapshot of N. gonorhoea BamA barrel in membranes

(A) BamA β-barrel (blue) in dimyristoyl-glycero-3-phosphatidylethanolamine gel-phase lipids reveals that the β-barrel seam (strands 1 and 16, shown in green) of BamA is distorted [40]. The phosphorus atoms of the phospholipids are shown as orange spheres. (B) β-strands 1 and 16 form a non-canonical barrel seam, as these strands only form two hydrogen bonds in this particular barrel conformation. (C) The hydrophobic thickness on the two sides of the BamA barrel, indicated by two arrows, are different in this conformation. This image was created in VMD [77]. Trajectory file kindly provided by Prof. JC Gumbart.

Figure 5. A crystallographic structure of the BAM complex

(A) The structure of the BAM complex (PDB: 5D0O) suggests how the BAM lipoproteins bind to the BamA POTRA motifs [43]. BamD forms extensive contacts with BamA. BamABCDE are shown in blue, green, magenta, pink, and yellow respectively. (B) The BamA POTRA motifs encircle periplasmic face of the β-barrel; the BAM lipoproteins are excluded from this view. POTRA motifs are colored red, orange, tan, green, and light blue (P1–5). This image was created in VMD [77].