In Vivo Structures of the Helicobacter pylori cag Type IV Secretion System

Abstract

The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal the molecular architecture of the Helicobacter pylori cag T4SS. Although most components are unique to H. pylori, the cag T4SS exhibits remarkable architectural similarity to other T4SSs. Our images revealed that, when H. pylori encounters host cells, the bacterium elaborates membranous tubes perforated by lateral ports. Sub-tomogram averaging of the cag T4SS machinery revealed periplasmic densities associated with the outer membrane, a central stalk, and peripheral wing-like densities. Additionally, we resolved pilus-like rod structures extending from the cag T4SS into the inner membrane, as well as densities within the cytoplasmic apparatus corresponding to a short central barrel surrounded by four longer barrels. Collectively, these studies reveal the structure of a dynamic molecular machine that evolved to function in the human gastric niche.

Keywords: CagA; Helicobacter pylori; bacterial molecular machines; cryo-ET; electron cryotomography; gastric cancer; host-pathogen interaction; subtomogram averaging; type IV secretion system.

Figure 1. H. pylori Assembles Membranous Tubes When Proximal to Gastric Epithelial Cells

(A) Low-magnification view of a gastric epithelial cell grown on an electron microscopy grid and infected with H. pylori. (B) Low-magnification view of H. pylori interacting with a gastric epithelial cell surface. In (A) and (B), blue dashed lines indicate examples of H. pylori that were imaged by ECT, and orange dashed lines demarcate the edges of individual gastric epithelial cells. (C) Tomographic slice through WT H. pylori co-cultured with gastric epithelial cells. Arrows indicate membrane tubes extending from the H. pylori cell envelope. (D) Enlarged view of the longer tube shown in (C). Inset: cross-section of a membrane tube. The two leaflets of the tube membrane bilayer are labeled by two red lines; LPS is indicated by a yellow bracket. (E) Periodic densities lining the inside of the tube (red brackets). (F) An individual tube displaying lateral ports (arrows). (G and H) Distal (G) and proximal (H) cross-sections of ports within the boxed region of the tube depicted in (F). (I) 3D segmentation of the boxed region in (F). (J) Lateral ports (arrows) appeared to induce a slight bending of the tube. The two leaflets of the tube and lipopolysaccharide densities decorating the surface are labeled as in (D). The locations of erased gold fiducials during tomogram reconstruction are labeled with “g.” Scale bars: 2 μm in (A), which applies to (A) and (B); 100 nm in (C); 50 nm in (D); 50 nm in (F), which applies to (E)–(H) and (J). OM, outer membrane; IM, inner membrane; OL, outer leaflet; IL, inner leaflet. See also Figure S1.

Figure 2. In Vivo Structure of the cag T4SS

(A and B) Distal (A) and proximal (B) tomographic slices of the same region of the bacterial envelope identifying a cag T4SS particle (white arrow) adjacent to a tube-like appendage (black arrow). Dashed arrows represent the position of the tube and cag T4SS particle in the other tomographic slice. (C) Top views of individual cag T4SS particles (arrows). (D) Top view of the sub-tomogram average of cag T4SS reveals 14-fold symmetry. Numbers indicate the clockwise count of individual subunits visible in the ring structure. (E) Central slice through the side view of the composite sub-tomogram average of the cag T4SS. Averages aligned on the periplasmic and cytoplasmic parts are stitched using the IM as the boundary. (F and G) Distal (F) and proximal (G) off-center tomographic slices of the cytoplasmic apparatus from the side view reveal four distinct rod-like densities. (H) A top view of the cytoplasmic apparatus at the level of the white arrow in (G) shows two central lines and four corner densities. (I and J) 3D representation (I) and cut-away view (J) of the cag T4SS periplasmic structure. (K and L) 3D representation (K) and cut-away view (L) of the predicted five-barrel structure of the cytoplasmic apparatus. The shorter central barrel is indicated in light pink. (M–P) Simulated tomograms of the five-barrel model of the cytoplasmic apparatus corresponding to tomographic slices E (M), F (N), G (O), and H (P). The position of each predicted tomographic slice is indicated in the views of the five-barrel model to the right. Scale bars: 50 nm in (A), which applies to (A)–(C); 10 nm in (D), which applies to (D)–(H). OM, outer membrane; IM, inner membrane. See also Figure S2.

Figure 3. Pilus-like Rods Emerging from the cag T4SS

(A) cag T4SS particle exhibiting a typical cytoplasmic structure (arrow). (B) cag T4SS particle with a pilus-like rod density surrounded by an IM invagination (white arrow). The gastric epithelial cell plasma membrane (black arrow) is visible directly above the bacterial outer membrane. (C) cag T4SS particle with an extended pilus-like rod density and IM sheath (arrow). (D) cag T4SS particle with a long pilus-like rod density that appears to have ruptured the IM (arrow). (E–H) Schematic interpretation of the cag T4SS apparatus conformation in (A) (shown in E), (B) (shown in F), (C) (shown in G), and (D) (shown in H). Scale bar: 50 nm in (A), which applies to (A)–(D). OM, outer membrane; IM, inner membrane.

Figure 4. Comparison of Diverse T4SS Machinery Structures

(A and B) Side (A) and top (B) views of the purified E. coli R388 conjugation system (Low et al., 2014). (C and D) Side (C) and top (D) views of immunopurified cag T4SS core complex particles (adapted and modified from Frick-Cheng et al. [2016]). (E) Side view of the L. pneumophila dot/icm T4SS in vivo (Ghosal et al., 2017). (F) Model of the L. pneumophila DotL coupling protein complex (Kwak et al., 2017), with the DotL structure outlined in magenta. (G and H) Side (G) and top (H) views of the cag T4SS structure in vivo (present study). In (G), two duplicated side views are shown for clearer labeling. Orange outline indicates comparison of the R388 core complex to the cag T4SS structure; blue outline indicates the position of the purified cag T4SS core complex within the in vivo structure; magenta outline indicates the predicted location of the coupling protein Cag5 based on the structure of the DotL homolog shown in (F); green outline indicates the L. pneumophila dot/icm T4SS structure superimposed on the cag T4SS structure. Scale bar: 10 nm in (C), which applies to all panels. See also Figures S3 and S4.