Cryoelectron-microscopy structure of the enteropathogenic Escherichia coli type III secretion system EspA filament

Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic Escherichia coli (EHEC) utilize a macromolecular type III secretion system (T3SS) to inject effector proteins into eukaryotic cells. This apparatus spans the inner and outer bacterial membranes and includes a helical needle protruding into the extracellular space. Thus far observed only in EPEC and EHEC and not found in other pathogenic Gram-negative bacteria that have a T3SS is an additional helical filament made by the EspA protein that forms a long extension to the needle, mediating both attachment to eukaryotic cells and transport of effector proteins through the intestinal mucus layer. Here, we present the structure of the EspA filament from EPEC at 3.4 Å resolution. The structure reveals that the EspA filament is a right-handed 1-start helical assembly with a conserved lumen architecture with respect to the needle to ensure the seamless transport of unfolded cargos en route to the target cell. This functional conservation is despite the fact that there is little apparent overall conservation at the level of sequence or structure with the needle. We also unveil the molecular details of the immunodominant EspA epitope that can now be exploited for the rational design of epitope display systems.

Enteropathogenic Escherichia coli (EPEC) is a major cause of infantile diarrhea, morbidity, and mortality in low- and middle-income countries (1), while enterohemorrhagic E. coli (EHEC) is a major cause of food poisoning in industrial countries (2). The ability of EPEC and EHEC to colonize the intestinal epithelium is encoded on a pathogenicity island named the locus of enterocyte effacement, which encodes gene regulators, the outer membrane adhesin intimin, structural components of a type III secretion system (T3SS), translocon components, chaperones, effectors, and an ATPase, which energizes protein translocation (3).T3SS is a common virulence factor among Gram-negative pathogens of humans, animals, and plants, including Salmonella enterica serovars, Shigella, Chlamydia, and Yersinia spp., Pseudomonas aeruginosa, and Pseudomonas syringae (4). The overall architecture of the multisubunit T3SS injectisome, which spans the entire cell envelope, is highly conserved among the different pathogens. It comprises several substructures, including a cytosolic C-ring and an ATPase complex (EscN in EPEC), a basal body consisting of a series of ring structures embedded in the bacterial inner and outer membranes (including a Secretin, EscC) and a periplasmic rod (EscI) which connects the inner membrane rings with a hollow extracellular needle projection (EscF). In EPEC, the EscF needle is 8–9 nm in diameter and 23 nm in length (5–7). In most pathogenic bacteria having a T3SS, the function of the needle is to connect the basal body to a translocation pore in the plasma membrane of the eukaryotic cell (3, 4).Electron microscopic observations of EPEC and EHEC have shown an ∼12-nm-diameter helical tube, made of the secreted translocator protein EspA (8–10), which serves as an extension to the needle, enclosing a central channel of ∼25 Å diameter (11, 12). Around 12 EspA filaments are elaborated on individual EPEC bacteria (8); when grown in vitro, EspA can vary in length and can reach 600 nm (7). Our current understanding is that the EPEC and EHEC EspA filaments evolved as an adaptation to their environment, where the needle alone would not be long enough to traverse the intestinal mucus layer. EspA filaments, like the needle, share similar helical symmetry parameters with flagellar structures and are elongated by addition of EspA subunits to the tip of the growing filament, the same mode of elongation that occurs in flagella filaments (13). Functionally, the filaments form a long flexible helical conduit which connects the tip of the needle with the translocation pore (made in EPEC by EspB and EspD), thus mediating effector translocation (3). Indeed, EspA has been shown to interact with both EspB and EspD (14, 15). In addition to their protein translocation activity, EspA filaments are important adhesins, mediating binding to both epithelial cells and edible leaves (16, 17). In the absence of EspA filaments, effectors can be secreted but not translocated; accordingly, the virulence of an espA deletion is highly attenuated in animal models (18). Moreover, EspA filaments are major antigens in vivo; antibodies against EspA were found in both human colostrum of mothers in Brazil and in serum from culture-positive patients infected with EHEC (19, 20). In animal models, IgG antibodies against EspA play a major role in clearing the pathogen (21).EspA alone is sufficient to form filamentous structures (22). Similarly to flagellar biosynthesis (23), EspA coiled-coil interactions between N- and C-terminal α-helical segments are required for assembly of the filament (24, 25). Monomeric EspA subunits are maintained in the cytosol via interactions with the chaperone CesAB (26), which has also been called CesA (22). CesAB is essential for stability of EspA within the bacterial cell prior to secretion. A cesAB deletion cannot secrete EspA or assemble EspA filaments (26). Crystallographic analysis of the CesAB–EspA complex at 2.8 Å resolution (22) showed that the EspA α-helices are also involved in extensive coiled-coil interactions with CesAB (22). Due to disorder in the parts of EspA not directly interacting with CesAB, only 72 of the 192 EspA residues were visualized in this complex. Importantly, the ATPase EscN selectively interacts with the CesAB–EspA complex; abrogation of this interaction attenuates EspA secretion and infection (27).Like flagella, EspA filaments show antigenic polymorphism, as EspA from different EPEC and EHEC clones show no immunological cross-reactivity (10). We have previously identified a surface-exposed hypervariable domain that contains the immunodominant EspA epitope (28). By exchanging the hypervariable domains of EspA(EPEC) and EspA(EHEC) we swapped the antigenic specificity of the EspA filaments (26). As with the Salmonella flagellin D3 domain (29), which is known to tolerate insertions of natural and artificial amino acid sequences (30), we were able to insert short peptides into the surface-exposed, hypervariable region of EspA (28).While EspA was first identified in 1996 (31), and the EspA filaments were first described in 1998 (8), low-resolution structures (at ∼15–25 Å resolution) were reported about 15 y ago (11, 12). The aim of this study was to obtain a high-resolution cryoelectron microscopy (cryo-EM) structure of the EPEC EspA filament.