Protein-Injection Machines in Bacteria

Abstract

Many bacteria have evolved specialized nanomachines with the remarkable ability to inject multiple bacterially encoded effector proteins into eukaryotic or prokaryotic cells. Known as type III, type IV, and type VI secretion systems, these machines play a central role in the pathogenic or symbiotic interactions between multiple bacteria and their eukaryotic hosts, or in the establishment of bacterial communities in a diversity of environments. Here we focus on recent progress elucidating the structure and assembly pathways of these machines. As many of the interactions shaped by these machines are of medical importance, they provide an opportunity to develop novel therapeutic approaches to combat important human diseases.

Figure 1. Type III secretion systems

(A) Phenotypes associated with T3SSs in pathogenic or symbiotic bacteria. (B) Structure of the T3SS needle complex. Surface views of the 3D reconstruction of the cryo EM map of the S. Typhimurium needle complex and the docking of the atomic structures of the different needle complex components onto the 3D cryo-EM map are shown. The different substructures are noted. OR1: outer ring 1; OR2: outer ring 2; IR1: inner ring 1; IR2: inner ring 2. (C and D) in situ cryo-ET structure (C) and molecular model (D) of the entire T3SS injectisome [adapted from (Hu et al., 2017a)]. A central section of a global average cryo ET structure of the intact T3SS injectisome is shown (C) as well as the molecular model with the fitting of the available atomic structure of the different components (D). (E) Model for the assembly of the type III secretion needle complex and associated structures (adapted from (Galán et al., 2014). The export apparatus inner membrane protein components are sequentially assembled into a complex that nucleates the assembly of the inner membrane rings of the NC. The outer ring of the NC assembles independently and docks to the inner rings through its long periplasmic neck. The sorting platform components are then recruited leading to the assembly of a functional T3SS that is only competent for the secretion of inner rod and needle filament proteins. Once assembly is finished, the machine becomes competent for the secretion of translocases and effector proteins [components are designated according to a universal nomenclature (Hueck, 1998)]. OM: outer membrane; PG: peptidoglycan; IM: inner membrane.

Figure 2. Type IV secretion systems

(A) T4SSs are involved in conjugation, DNA release and uptake, and in pathogenicity of eukaryotic hosts (Adapted from Grohmann et al. (2017)). (B) EM structure of the T4SS. A side view of the structure of a conjugative T4SS is shown featuring the outer membrane core complex (Core/OMC), the stalk, and the inner membrane complex (IMC) (top left, adapted from Low et al. 2014). The corresponding schematic diagram of the same structure with the location of the various VirB proteins is shown (top right). A cryo-electron tomogram of the structure of the Legionella Icm/Dot T4SS is also shown (bottom left) with the schematic diagram of the system (bottom right) (reproduced with permission from Ghosal et al., 2017). (C) Secretion mechanism of the relaxase-ssDNA complex by conjugative T4SSs as exemplified by the F plasmid. The T4SS is shown as in panel B with the addition of the VirD4 coupling protein. The relaxosome is composed of a relaxase molecule and several accessory components. Secretion starts with the formation of a pre-initiation T4SS-Relaxosome complex (step I), which lies dormant until stimulated by the contact of the pilus with a recipient cell. Upon stimulation (shown with a lightning bolt), the T4SS ATPases are activated, which in turn activate the relaxosome resulting in the formation of a single-strand DNA bubble (step II). A second relaxase molecule can then load onto the ssDNA bubble through its helicase domains (step III). Concomitantly, the first relaxase molecule cleaves OriT at nic and attaches covalently to the resulting 5′ phosphate of the T-strand (step IV). Finally, the ssDNA-bound relaxase is transported, while the second relaxase molecule unwinds the DNA and pumps the resulting ssDNA through the system (presumably also in coordination with T4SS ATPases). While the T-strand is being transferred to the recipient cell, the complementary strand remaining in the donor cell undergoes replication via PolIII. The relaxase must be present in the recipient cell to catalyze the end-joining recircularization of the DNA once a copy of the entire plasmid has been transferred.

Figure 3. Type VI secretion systems

(A) T6SSs are involved in pathogenicity during host infection (left) and in killing of competitor bacteria (right). Upon puncturing of the eukaryotic host membrane, V. cholera VgrG1 reaches the host cytosol and mediates actin crosslinking via its C-terminal ACD domain, thereby inhibiting actin polymerisation (left). P. aeruginosa delivers the effector proteins Tse1 and Tse3 in a T6SS-dependent manner into the periplasm of target cells (right). The amidase Tse1 and the muramidase Tse3 degrade the cell wall of target cells, causing cell lysis. Specific immunity proteins (Tsi1/3) prevent self-killing. Panels are adapted from Kapitein and Mogk (20130. (B) Structures of the T6SS extended and contracted sheath/tube complexes. The top left panel shows the extended sheath wrapping around a modeled Hcp tube (grey), the crystal structure of the VgrG (green), the PAAR complex (orange), and the EM structure of the membrane-embedded core complex (pale yellow). The baseplate is shown as a semi-transparent cone surrounding VgrG/PAAR. The top right panel shows the structure of the contracted sheath. The top panels were created by Marek Basler and coworkers. The bottom panels show the cryo-electron tomographic structure of the extended and contracted states of the T6SS from Amoebophilus Asiaticus [used with permission from (Böck et al., 2017)]. (C) Secretion by contractile nanomachines [adapted from (Brackmann et al., 2017)]. The two left panels show a schematic diagram of the extended (upper left panel) and contracted (lower left panel) state of the contractile structure by T6SS delivering protein effectors (left), phage T4 delivering DNA (middle) and R-type pyocins generating holes in the cell envelope (right). In the right panel, a schematic diagram shows the organization of the base plate: TssK attaches the baseplate to the membrane complex, TssF and TssG form a wedge and a core bundle of the baseplate, and TssE is a sheath initiator. VgrG and PAAR-repeat-proteins form the spike and spike tip complex and Hcp forms the tube. ClpV disassembles the contracted T6SS-sheath. Respective phage gene products (gp) are in brackets.