Key Points
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Pore-forming toxins (PFTs), which are expressed as virulence factors by many pathogenic bacteria, and pore-forming proteins (PFPs) have been found in all kingdoms of life
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PFTs and PFPs undergo a structural and functional metamorphosis from soluble, inactive monomers to active, complex multimeric transmembrane pores that insert into the membranes of target cells
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Based on their structure and mechanism of pore formation, six families of PFTs and PFPs have been described, each of which has a distinct structure and mechanism of pore formation. These families can be grouped into two larger classes, α-PFTs and β-PFTs (or PFPs), based on the secondary structures of their transmembrane pore domains
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Owing to substantial recent advances in the structural biology of PFTs, we are beginning to understand the pore architecture and the mechanism of pore formation for all six families
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The specificity of PFTs and PFPs is determined by their interactions with lipids, sugars and/or protein receptors present in, or on, the target cell membrane
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Structural modularity enables toxins with the same pore-forming mechanism to target different host cell types by binding to different receptors
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For PFTs that contribute to infection, examining their structures, dynamics and interactions with host cells at molecular resolution provides cues for the development of therapeutics that could be highly effective in fighting disease
Abstract
Pore-forming toxins (PFTs) are virulence factors produced by many pathogenic bacteria and have long fascinated structural biologists, microbiologists and immunologists. Interestingly, pore-forming proteins with remarkably similar structures to PFTs are found in vertebrates and constitute part of their immune system. Recently, structural studies of several PFTs have provided important mechanistic insights into the metamorphosis of PFTs from soluble inactive monomers to cytolytic transmembrane assemblies. In this Review, we discuss the diverse pore architectures and membrane insertion mechanisms that have been revealed by these studies, and we consider how these features contribute to binding specificity for different membrane targets. Finally, we explore the potential of these structural insights to enable the development of novel therapeutic strategies that would prevent both the establishment of bacterial resistance and an excessive immune response.
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Main
Pore-forming toxins (PFTs) are produced by many pathogenic bacteria and are important components of their virulence arsenal1. PFTs are the largest class of bacterial toxins and constitute a major class of pore-forming proteins (PFPs) — an ancient protein family also found in non-pathogenic bacteria and indeed in all kingdoms of life. Although PFTs were initially viewed as unsophisticated proteins that simply form pores in membranes, advances in the past decade have revealed, with great detail, the astonishing complexity of their architecture and dynamics2. During bacterial infection, through the disruption of epithelial barriers and interactions with the immune system, PFTs promote pathogen growth and dissemination, although their precise contribution to these processes is difficult to establish. As with other PFPs, PFTs alter the plasma membrane permeability of their targets cells, potentially leading to cell death, but may also lead to a more subtle manipulation of cellular functions1,2,3 (Box 1).
PFTs (and, more generally, PFPs) can be classified into two large groups — α-PFTs and β-PFTs — based on whether the secondary structure of their membrane- spanning elements is composed of α-helices or β-barrels, respectively4,5,6. All PFPs initially fold into a water-soluble, generally monomeric, structure (Fig. 1). In the past decade, many structures of PFTs and PFPs have been described, which have revealed an elaborate range of strategies used by these proteins to undergo the very unusual metamorphosis from a soluble protein to a transmembrane protein. Six families have now been identified: three families of α-PFTs and three families of β-PFTs (Table 1).
In all documented cases, PFPs recognize the target cell by binding to specific receptors, which can be sugars, lipids or proteins. Surface binding leads to a drastic increase in the local concentration of PFPs, largely owing to a reduction in the dimensions of protein diffusion from a three-dimensional space to a two-dimensional plane. This increase in concentration favours oligomerization, which is a step required for pore formation for all classes of PFPs. Oligomerization either precedes or is concomitant to the exposure of hydrophobic surfaces that leads to membrane insertion (Fig. 1). The primary focus of this Review is PFTs, which are mainly — but not exclusively — found in bacteria; however, it should be noted that PFPs with similar structures are increasingly being found in eukaryotes, in particular as components of the immune systems of animals7,8,9.
Detailed analyses have revealed that different PFTs form pores with distinctive properties, which in turn induce different phenotypes and responses in target cells2. Although perforation of the plasma membrane by PFTs always leads to an increase in membrane permeability, the molecules to which the membrane becomes permeable can vary. Depending on the toxin, the pore may only allow specific ions, such as potassium and/or calcium, to pass through; in other cases, it may be permeable to small molecules such as ATP, or larger molecules such as proteins (Box 1). Therefore, an in-depth characterization of pore architecture is required to fully understand the cellular response to a specific PFT. Furthermore, the PFT concentration differs according to body site during infection. The most extreme cellular response possible is cell death, by necrosis, programmed necrosis, pyroptosis or apoptosis2; however, even at sub-lytic concentrations, PFTs remain toxic as they can still modify cellular behaviour. Through these various effects, PFTs contribute to bacterial growth and colonization, in part by protecting the invading bacteria from the host immune response10,11.
In this Review, we discuss recent work that has revealed the pore architectures and mechanisms of pore formation for each family of PFTs. Furthermore, we show how modularity of receptor recognition enables different PFTs within the same family to target different cell types and we consider how elucidating the mechanism of pore formation at an atomic level (Box 2) may eventually lead to the development of new therapeutic strategies to fight infection by targeting virulence rather than bacterial survival.
α-PFTs
The colicin family. Pore-forming colicins are produced by Escherichia coli to kill related bacterial species by forming pores in the inner bacterial membrane12. They have a crucial role in shaping the microbial population, possibly by killing competitors or invading an occupied niche13.
Before the first structures of colicins were solved, bioinformatics analyses indicated that colicins were likely to contain hydrophobic α-helices, in common with many other transmembrane proteins. The first PFT structure to be solved was that of the pore-forming domain of colicin A, which revealed an 'inside-out membrane protein' fold (that is, a hydrophobic helical hairpin sheltered within a bundle of amphipathic α-helices) that was consistent with a protein that can switch between soluble and transmembrane conformations14 (Fig. 2a).
Pore formation by colicins minimally requires the insertion of the hydrophobic helical hairpin into the inner membrane, which produces a nonspecific voltage- gated channel15,16; this leads to membrane depolarization, ATP depletion and, ultimately, target cell death13. The exact structure and stoichiometry of these pores has remained a mystery, owing to their inability to form stable oligomeric complexes that are amenable to structural analysis5. It is generally accepted that, upon interaction with the target membrane, the amphipathic helices move away from the hydrophobic helical hairpin, enabling its insertion into the membrane16. This rearrangement leads to the formation of a structure known as the 'umbrella' structure, a model originally proposed for colicin A17,18 (Fig. 2a) but subsequently extended to colicin E1 and colicin Ia19,20,21,22, and more recently supported by electron paramagnetic resonance (EPR) measurements on spin- labelled colicin A23. However, the formation of this structure seems to be insufficient for channel formation; therefore, it is expected that other mechanisms operate in concert with umbrella formation. One possibility is that the electrostatic complementarity of colicins and negatively charged bacterial membranes promotes the insertion of some of the other amphipathic helices into the membrane12,24. Another possibility is that the insertion of the hydrophobic hairpin could trigger multimerization, as observed for colicin A25 (that is, dimers) and colicin Ia26 (that is, trimers of dimers) (Table 1).
Outside of the colicin family, the colicin fold has subsequently been found in the translocation domain of diphtheria toxin27, which translocates the catalytic subunit of the toxin across endosomal membranes. The pore-forming insecticidal Cry toxins produced by Bacillus thuringiensis28 also have a colicin fold, and a homologous fold of probable common ancestry with colicins is present in the membrane translocators that form the tip of bacterial type III secretion systems29. Quite remarkably, eukaryotic proteins of the BAX and BCL-2 homologous antagonist/killer (BAK) family — which are thought to originate from phages — also have a colicin-like fold30. These proteins are involved in the control of apoptosis and serve to permeabilize mitochondria — that is, symbiotic prokaryotes30,31, consistent with the ancestral role of colicins.
The ClyA family. The cytolysin A (ClyA) family of α-PFTs includes the following toxins: ClyA (also known as haemolysin E (HlyE)), which is produced by certain strains of E. coli and by Salmonella enterica and Shigella flexneri32; and the Bacillus cereus toxins non-haemolytic tripartite enterotoxin (Nhe; which, despite its name, is haemolytic)32 and the B component of haemolysin BL enterotoxin (Hbl)33 (Table 1). Although ClyA PFTs have been reported to be virulence factors, the organisms in which they have been found already produce several toxins and effectors, and thus the breadth of toxicity and identity of specific receptors of this family of PFTs is still an open field of investigation34.
ClyA is one of the few PFTs for which the structure has been solved both in the soluble35 and transmembrane36 form, revealing the unique pore-formation process of this family of PFTs, which involves remarkable conformational changes. In solution, ClyA is an elongated, entirely α-helical protein, except for a short hydrophobic β-hairpin known as the β-tongue (Fig. 2a). In the vicinity of cholesterol-containing membranes, the β-tongue detaches from the core of the protein and dips into the lipid bilayer. This event triggers a massive rearrangement of the distal amino-terminal amphipathic α-helix, which swings around to reach the membrane. The length of this N-terminal helix varies between the members of this PFT family, as is apparent from the recently solved structure of NheA, a component of the ripartite Nhe toxin, in which the helix is much shorter37. This variation in length might have major consequences on the pore formation process and it has been proposed that NheA could even form β-barrel pores by a mechanism that has not yet been determined37.
Subsequently, pore formation by ClyA requires circular oligomerization of the toxin by a sequential mechanism38, which shares some common features with the actinoporins family (see below). This, in turn, concentrates the amphipathic helices in the centre of the ring-like structure, forming a helical barrel that inserts into the membrane by a wedge-like mechanism (Fig. 2a).
An alternative, contrasting pore formation process has been proposed whereby ClyA would oligomerize into soluble pre-pores encapsulated within bacterial outer membrane vesicles (OMVs) of E. coli39. Pre-pore-containing OMVs would be protected from pore formation as the conformational changes leading to membrane insertion require cholesterol, which is generally not present in bacterial membranes. A similar OMV-mediated delivery mechanism of PFTs has recently been proposed for Vibrio cholerae cytolysin (VCC)40, which belongs to the Staphylococcus aureus haemolysin family (see below). However, if pre-pores are indeed encapsulated within OMVs, it is not known how these OMV-embedded pre-pores would be delivered to the target membrane.
The actinoporin family. Actinoporins are eukaryotic proteins that are produced by sea anemones41. They form part of the venom that these sedentary animals rely on to paralyse and digest their prey (which range from plankton to fish and crustaceans), as well as to defend themselves from predators. By forming pores in the plasma membrane of target cells, actinoporins are thought to cause cell lysis.
X-ray structures have been reported for the soluble form of the actinoporins equinatoxin II (EqtII; produced by Actinia equina)42,43, sticholysin II (StnII; produced by Stichodactyla helianthus)44 and fragaceatoxin C (FraC; produced by Actinia fragacea)45 (Table 1). All actinoporins are composed of a β-sandwich flanked by two α-helices (Fig. 2a), in which the N-terminal amphipathic helix detaches from the core of the protein and inserts into the membrane41. This membrane insertion step is lipid-dependent, with a preference for target membranes that are enriched in sphingomyelin and/or have phase-separated lipid membranes41,46. Interestingly, membrane insertion of actinoporins can subsequently induce lipid mixing, as has recently been shown for sticholysin using differential scanning calorimetry and atomic force microscopy (AFM)47.
Membrane insertion of the N-terminal helix is followed by oligomerization and pore formation, with no pre-pore intermediate state48. The stoichiometry of the pores formed by these toxins varies from tetramers, which have been proposed for EqtII49 and StnII44, to nonamers, which have been proposed for FraC45. Until recently, the arrangement of proteins and lipids in the formation of actinoporin pores was unclear41, but X-ray structures for FraC in its monomeric, dimeric and octameric states have illuminated not only the final pore conformation but also some novel details of the pore formation mechanism50. The FraC octameric pore is assembled in a 1:1 ratio with sphingomyelin, which not only acts as a receptor that recruits FraC to the membrane but is also an indispensable cofactor that is required to trigger and complete the assembly of the mature pore (Fig. 2a). Furthermore, the X-ray structure of a stable FraC dimer revealed conformational changes in the membrane-inserted N-terminal amphipathic helix towards the protomer state found in pores, which in turn suggested that actinoporin protomers might assemble sequentially into a pore in a mechanism that excludes the formation of the pre-pore intermediate states observed for many β-PFTs (see below).
β-PFTs
The haemolysin family. The opportunistic human pathogen S. aureus, a leading cause of pneumonia and sepsis51, produces an arsenal of virulence factors. These virulence factors are encoded on mobile genetic elements, which leads to diverse toxin expression combinations in different infectious strains. The arsenal of S. aureus virulence factors includes several PFTs, which are either composed of a single component, as in the case of α-haemolysin (Hla), or of two components, as in the case of γ-haemolysin AB (HlgAB), HlgCB, leukocidin ED (LukED), Panton–Valentine leukocidin (PVL) and leukocidin AB (LukAB; also known as LukGH)52 (Table 1). These PFTs are not functionally redundant and target different cell types, mostly in the immune system, by interacting with different cell surface proteins10,52. PFTs in the haemolysin family contribute to S. aureus pathogenesis in several ways: some will kill various cells of the immune system, as an immune evasion strategy, whereas others, such as Hla, also disrupt epithelial barriers, thus promoting bacterial dissemination.
All staphylococcal PFT components have a similar fold, which is also shared by the necrotic enteritis toxin B (NetB)53, the δ-toxins54 from Clostridium perfringens and VCC55. The single-component toxins of this family assemble into heptameric pores, whereas the bi-component toxins form octameric pores56, containing four alternating copies of each subunit57. The haemolysin family is one of the best characterized PFT families in terms of structure, as Hla58, Hlg57,59, HlgB60, VCC55,61 and NetB53 have all been crystallized in the soluble and/or the pore configuration (Fig. 2b). This abundance of structural data has enabled the production of consistent and reliable pore models based on homology, as is the case for the δ-toxin from C. perfringens62. In the soluble state, S. aureus haemolysins form a rather compact structure, rich in β-strands58, in which the pre-stem domain (which subsequently becomes the transmembrane domain; Fig. 2b) forms a three-stranded β-sheet that is packed against the core of the protein. Following oligomerization into a heptameric or octameric pre-pore ring-like structure, the pre-stem domain (which localizes to the internal cavity of the ring) detaches from the core of the protein, readjusts into an anti-parallel β-hairpin and, in combination with neighbouring hairpins, generates a 14-stranded or 16-stranded β-barrel (Fig. 2b). As the outside of this barrel is hydrophobic, it spontaneously inserts into the lipid bilayer. Membrane insertion and formation of the amphipathic β-barrel are likely to be concomitant events. Note that, although it is essential for pore formation, the pre-stem loop is not required for oligomerization63.
The aerolysin family. The aerolysin family is a broad family of PFPs. The first described member, aerolysin, is produced by Gram-negative Aeromonas spp.64, and other bacterial aerolysins include the α-toxin produced by the Gram-positive human pathogen Clostridium septicum65, monalysin produced by Pseudomonas entomophila66 and several parasporins produced by B. thuringiensis28. In pathogens such as Aeromonas hydrophila, aerolysins contribute to bacterial dissemination, possibly through disruption of epithelial barriers, which would in some cases lead to deep wound infection64.
Bioinformatics analysis has revealed that the core aerolysin motif, which is composed of pairs of two β-strands separated by the pre-stem domain, can be found in all kingdoms of life7. Eukaryotic aerolysins include: enterolobin from the seeds of the tree Enterolobium contortisiliquum5, which is typically found in Brazil; biomphalysin produced by the snail Biomphalaria glabrata8; and βγ-CAT produced by the frog Bombina maxima9. Several aerolysin family members produced by animals have been shown to have a role in the immune system8,9,67,68.
In contrast to S. aureus haemolysins, the soluble form of aerolysin is a highly elongated, multidomain protein69 (Fig. 2b). At the high protein concentrations used for crystallography, aerolysin is dimeric70; in this form, the pre-stem region forms a β-strand-containing loop in the middle region of the elongated domain71, as initially shown for C. septicum α-toxin72. An unusual feature of aerolysin is that it is synthesized as a pro-toxin73 with a carboxy-terminal extension that prevents premature oligomerization64,70. Following cleavage of the C-terminal peptide, the toxin oligomerizes into heptameric ring-like structures70,74.
Only recently, using a combination of X-ray crystallography, cryo-electron microscopy (cryo-EM), molecular dynamics and modelling (Box 2), a near-atomic-level understanding of the pore-formation process was obtained for the aerolysin family75 (Fig. 2b). Using aerolysin mutants arrested at different stages along the pathway leading to pore formation, the structure of the intermediate pre-pore state and the structure of the mature pore were solved75. Monomers first assemble into a heptameric pre-pore structure. This complex docks onto the membrane surface, with the pre-stem loops ready to slide through a pocket into the interior cavity of the pre-pore (Fig. 2b). Triggering the transition from pre-pore to pore, the pre-stem loops eventually refold into amphipathic β-hairpins forming the transmembrane β-barrel. This conformational change is accompanied by a concerted swirling mechanism that flattens the extracellular portion of the pore as the β-barrel forms and inserts into the membrane. Aerolysin pores thus have a large, flat, disc-like extracellular structure, which is somewhat elevated with respect to the membrane (Fig. 2b). Despite a different pore-formation process, a similar architecture of the final pore was recently found for the haemolytic lectin CEL-III produced by the sea cucumber Cucumaria echinata76.
As amphipathic β-barrels could potentially move within or extrude from the membrane, different mechanisms have evolved to stabilize the barrel positioning. In the case of Hla produced by S. aureus, the cytosolic tip of the transmembrane β-hairpin has charged residues that anchor the tip in the cytosol, whereas the tips of the aerolysin transmembrane β-hairpins are hydrophobic and adopt a rivet-like configuration that prevents motion and anchors the barrel within the bilayer core71. Furthermore, the lumen of aerolysin β-barrels is markedly different from the lumen of S. aureus Hla, with a very high concentration of charged residues75, which might favour the conduction of anionic moieties and increase pore flexibility.
The primary structure of proteins from the aerolysin family may show very little, if any, similarity to one another. Crystallographic studies, however, have revealed remarkable structural similarities in the fold of aerolysins with diverse primary sequences, such as C. perfringens ε-toxin77,78, C. perfringens enterotoxin (CPE)79,80,81, a haemolytic lectin (LSL) produced by the parasitic mushroom Laetiporus sulphureus82, the hydralysin toxins produced by Cnidaria83 and the lysenin toxin produced by the earthworm Eisenia fetida84 (Table 1). Further studies on these proteins will establish whether they have the same global architecture as aerolysin and whether they share its swirling mechanism for membrane insertion.
The cholesterol-dependent cytolysin family. The cholesterol-dependent cytolysin (CDC) family is a large family of toxins mostly produced by Gram-positive bacteria of the Bacillus, Clostridium, Streptococcus and Listeria genera85, and more recently shown to be produced by some Gram-negative bacteria86. Depending on the pathogen, these PFTs contribute to infection in different ways: listeriolysin O (LLO) mediates the release of Listeria spp. once the bacterium has entered the target cell through a phagocytic-like mechanism; perfringolysin O (PFO) has an important role in the development of gangrene, which is often associated with C. perfringens infections; and pneumolysin (Ply) is required for tissue invasion by Streptococcus pneumoniae, and also contributes to inflammation and activation of the complement cascade85.
Structural studies have revealed that CDCs share the same fold as membrane attack complex component/perforin (MACPF) domains, which have primarily been described in the mammalian immune system87,88,89. MACPF domain proteins in non-mammalian eukaryotes include pleurotolysin in fungi90, and perforin-like proteins in apicomplexan parasites such as Toxoplasma gondii and Plasmodium falciparum91,92, which are involved in parasite release from the parasitophorous vacuole following replication. Although mainly described in eukaryotes, the MACPF fold has also been found in bacteria (for example, in Plu-MACPF from Photorhabdus luminescens88, BT3439 from Bacteroides thetaiotaomicron93 and BSAP-1 from Bacteroides fragilis94; Table 1). The precise role of these bacterial MACPF proteins in infection remains to be fully elucidated.
Several CDCs have been crystallized in their soluble form: PFO95, suilysin (SLY) produced by Streptococcus suis96, intermedilysin (ILY) produced by Streptococcus intermedius97, LLO produced by Listeria monocytogenes98, lectinolysin (LLY) produced by Streptococcus mitis99, anthrolysin O (ALO) produced by Bacillus anthracis100 and streptolysin O (SLO) produced by Streptococcus pyogenes101 (Table 1). However, no CDC has been crystallized in the pore configuration, owing to the stoichiometry of the complexes, in which up to 50 monomers assemble into very large ring-like structures. However, these structures are amenable to analysis by electron microscopy (EM)102 and AFM103, providing information on the pore architecture.
PFO, the archetypical toxin of this family, is an elongated, β-sheet-rich, multidomain protein95 (Fig. 2b). As opposed to the single β-hairpin contributed by haemolysin- and aerolysin-like toxins, each CDC molecule contributes two amphipathic β-hairpins to the final β-barrel104,105. Remarkably, in the soluble form, these regions are organized as two pairs of short α-helices that flank a central β-sandwich. Upon oligomerization and membrane insertion, they undergo a prion-like α-helix-to-β-strand transition104,105, a conversion that is also observed for the sea cucumber haemolytic lectin CEL-III76. The two β-hairpins subsequently arrange into a slightly curved β-sheet that joins with the neighbouring β-sheets in the oligomer to form a giant β-barrel composed of 80–200 β-strands, depending on the pore stoichiometry. Oligomerization of CDCs seems to occur by the sequential addition of monomers or multimers106,107 (Fig. 2b); however, in some instances oligomerization fails to occur completely, leading to the formation of arc-like structures — partially formed, open pores of lower stoichiometry — that have been proposed to nevertheless be active pores108 (Fig. 1). This was recently confirmed for SLY using a combination of cryo-EM, AFM and modelling techniques, which revealed a sequential mechanism of oligomerization that produces not only pores but also arc-like structures that are kinetically trapped at the pre-pore state. Both closed rings and incomplete arcs seem to share the ability to form active pores by excluding lipids109.
Correct alignment of the β-strands is essential for pore assembly, especially for such a large complex. Using disulfide scanning, it was found that partially unfolded β-hairpins are highly dynamic in the pre-pore complex, whereas in the pore state the β-barrel conformation is locked, producing a ∼20° tilt in the orientation of the β-strands with respect to the membrane106. A recent study revealed that the energy required for the pre-pore-to-pore transition is provided by the formation of a salt bridge between adjacent monomers at the completion of oligomerization110. This leads to the coordinated disruption of a critical interface within each monomer. In the transition from pre-pore to pore, CDCs undergo an elongation at the membrane surface, as was first observed using AFM103. Combining all available data, including EM analysis of CDCs, a molecular modelling study111 led to the elucidation of a general mechanism for CDC pore formation, in which the observed collapse from the pre-pore to the pore state could be explained by the simple rotation of the core domain of the toxin (Fig. 2b), through a mechanism reminiscent of the swirling mechanism reported for aerolysin collapse75. A very similar pore architecture was found for mammalian perforins89.
PFTs are generally defined as toxins for which pore formation represents the primary toxic activity. However, many other toxins have a pore-forming domain or subunit, which is used as a translocon to deliver a catalytic subunit with toxic activity into a target cell. As opposed to the effectors of bacterial secretion systems, bacterial toxins with pore-forming domains are autonomous, as a secretion system apparatus is not required for target cell entry. Although we do not review translocation domains of toxins in this article, it is worth mentioning two recent examples of studies that have revealed translocation pore architectures at atomic resolution. First, the transmembrane conformation of the translocation subunit (also known as the protective antigen (PA)) of the anthrax toxin was shown to form heptameric or octameric pores112,113. The most unusual feature of the anthrax pore is the extremely long 105 Å β-barrel. The lumen of the pore, which translocates the catalytic subunit, contains a structure known as a Φ-clamp114 that ratchets the unfolded protein through the lumen112 while ensuring that the pore remains impermeable to most ions. Second, in P. luminescens, binding of the TcB and TcC subunits of the Tc toxin complex to the TcA subunit was shown to induce the opening of the translocation channel of the toxin. The channel itself has a hydrophobic and narrow gate region similar to the anthrax Φ-clamp, which probably requires protein unfolding before translocation115,116.
Specificity of PFTs
Each of the PFT families described in this Review is defined by a given fold and, presumably, a cognate membrane insertion mechanism. PFTs within a family, however, can have diverse target membranes, as they are produced by different organisms that target different cells for different purposes (Box 1). Diversification has thus occurred in the domains specifically recognizing the host target membrane and associated receptors, as well as, to a lesser extent, in the residues that line the transmembrane pore (Fig. 3).
The sweet tooth of PFPs and PFTs. Many PFPs — and, in particular, many bacterial PFTs — bind to sugar molecules (Fig. 3a). For PFTs that target eukaryotic plasma membranes, these are usually glycans that are covalently attached to membrane-associated proteins or sugars that are present in the glycosylphosphatidylinositol (GPI) moiety in proteins with a GPI anchor. For example, in addition to the cytolytic domain it shares with S. aureus haemolysin, VCC has C-terminal domains with β-trefoil and β-prism folds55. The β-prism domain has lectin-like activity, as it interacts with β1-galactosyl-terminated glycoconjugates with nanomolar affinity117. This domain has been shown to be crucial for targeting erythrocyte membranes, by facilitating oligomerization and pore formation117,118, although a specific receptor for VCC has not yet been identified. Similarly, Vibrio vulnificus haemolysin (VVH) has multiple binding preferences, including glycerol, N-acetyl-d-galactosamine and N-acetyl-d-lactosamine, which enables it to recognize various cell surfaces119.
Aerolysin binds to the target membrane through its first N-terminal domain, which protrudes from the elongated core of the protein (Fig. 2b). In an interesting dual-sugar binding mechanism, these domains bind to N-linked sugars64,120 and to the glycan anchor of GPI-anchored proteins70,121, collectively leading to a very-high-affinity interaction (Fig. 3a). In other toxins in this family, such as C. perfringens ε-toxin122, C. perfringens enterotoxin79, lysenin84, haemolytic lectin82 and parasporin123, these two domains are replaced by domains with entirely different folds that are expected to correspond to different cognate target receptors. Although only a small number of receptors have been identified for aerolysin-like toxins, it has been shown that C. perfringens ε-toxin binds to an extensively O-linked glycoprotein, hepatitis A virus cellular receptor 1 (HAVCR1)124; it is thought that the binding site for ε-toxin on HAVCR1 is one of the sugar components of this glycoprotein. Another possible binding site on a sugar component of HAVCR1 was identified for the low-hazard H149A mutant variant of ε-toxin. This second binding site corresponded to the location of a β-octyl-glucoside glycan moiety in co-crystal structures of ε-toxin and HAVCR1 (Ref. 125). CDCs were also recently found to bind to glycans, in addition to, or before, binding to cholesterol126.
PFTs that target bacteria have been shown to have affinity for sugars that are covalently attached to lipids in bacterial membranes. For example, colicin N (ColN), which is secreted by — and active against — E. coli, binds to bacterial outer membrane lipopolysaccharides (LPS) (Fig. 3a; Table 1) as high-affinity receptors before translocating through outer membrane porin proteins to the inner membrane127. Some eukaryotic PFPs also bind to sugars in bacterial membranes, such as bactericidal C-type lectins present in the human gut, which bind to peptidoglycan carbohydrates to form hexameric pores in Gram-positive bacteria128.
Affinity for lipids and lipid domains. Many PFTs have an affinity for specific lipids or lipid domains129 (Fig. 3b). A role for lipid rafts in the pore-formation process was initially proposed for aerolysin130, which has also been shown to bind to lipid-anchored proteins (although this interaction is mediated by N-linked glycan sugars)64. Another PFT from the aerolysin family, lysenin, which is produced by earthworms, specifically binds to sphingomyelin131, which is enriched in lipid rafts. CDCs, as their name indicates, require cholesterol — another lipid enriched in lipid rafts — and therefore tend to oligomerize in lipid raft-like domains132. For instance, PFO oligomerization is dependent on the concentration of cholesterol in the target membrane. The composition and, in particular, the leaflet asymmetry of the target membrane seem to be crucial both to maintain the required cholesterol concentration and to stabilize the intermediate states of the membrane-inserted toxin during CDC pore formation133. These observations are intriguing, as they hint at the possibility that pore formation can be modulated by controlling the lipid composition of the two membrane leaflets. Cholesterol interaction is mediated by the undecapeptide ECTGLAWEWWR134, which is one of the most conserved sequences among CDCs (Fig. 2b). As recently shown for PFO, this peptide also provides allosteric coupling, as cholesterol-mediated membrane binding promotes oligomerization135. The lytic activity of CDCs may be modulated by the interaction of the undecapeptide with neighbouring cholesterol-sensing domains, as recently found for SLO101. A second motif, composed of a threonine–leucine pair (T490–L491), also mediates the recognition of, and binding to, cholesterol by PFO; this motif is highly conserved in the CDC family136. The most striking example of lipid specificity is seen in the sea anemone toxin FraC. As mentioned previously, sphingomyelin is a constitutive cofactor for the assembly of the FraC pore (Fig. 2a); furthermore, four distinct lipid-binding sites in this toxin modulate membrane binding with different affinity and specificity50.
Lipid specificity has also been reported for lipids not directly associated with rafts. In the haemolysin family, S. aureus Hla has phosphocholine binding pockets, which are also found, in a modified form, in the NetB toxin produced by C. perfringens53. Finally, lipid specificity has been reported in PFTs that target bacterial membranes. For colicins, the presence of anionic lipid species, such as cardiolipin, in the bacterial inner membrane seems to promote the formation of the umbrella conformation and conductive pores23 (Fig. 3b; Table 1).
Affinity for protein receptors. In addition to sugars and lipids, some PFTs require interactions with host membrane proteins to target the host cell membrane (Fig. 3c); that is, these PFTs recognize the polypeptide chain itself, in addition to (or instead of) sugar moieties that are covalently attached to the protein. This additional specificity is particularly important for S. aureus, which specifically targets subsets of cells in the host immune system through the expression of PFTs that bind to receptors that are expressed only on specific cell types10,52. The bi-component LukED targets macrophages, dendritic cells and T cells by binding to CC-chemokine receptor type 5 (CCR5)137 (Table 1) or neutrophils and monocytes by binding to CXC-chemokine receptor type 1 (CXCR1) and CXCR2 (Ref. 138), whereas PVL binds to C5a receptors (C5aRs) to target neutrophils and, to a lesser extent, to target monocytes and macrophages139. The γ-bi-component haemolysins AB and CB (HlgAB, HlgCB) bind to the chemokine receptors CXCR1, CXCR2 and CCR2, and to the complement receptors C5aR and C5L2, respectively, to target neutrophils and monocytes140. Finally, Hla targets epithelial cells by binding to disintegrin and metalloproteinase domain-containing protein 10 (ADAM10)141,142, in addition to phosphocholine head groups (Table 1).
Some CDCs, such as ILY, bind to the protein receptor CD59 (Refs 135,143), which is a potent inhibitor of the complement cascade, although cholesterol is still required for pore formation144 (Table 1). ILY has recently been crystallized in its soluble monomeric form in complex with human CD59, revealing that the toxin binds to CD59 on two distinct interfaces, thus producing an optimal alignment to interact with the cholesterol-rich membrane and adjacent protomers for pre-pore formation97. These structural data enabled the design of ILY-derived peptides that were able to disrupt the interaction with CD59; structure-guided design of receptor-binding peptides thus holds promise for therapeutic development.
Therapeutic development
The growing characterization of the structure and function of PFTs and PFPs has enabled the development of biotechnological applications that target and engineer these proteins, including antimicrobial drug development, cancer gene therapy145 and DNA sequencing146,147.
The knowledge of conformational rearrangements and protomer interfaces established upon pore formation in PFTs can be applied to a traditional structure-based drug discovery approach, in which high-affinity small compounds are identified that target structural features to block pore formation and impair bacterial virulence (Fig. 4a). For example, it was shown that natural compounds, such as oroxylin A, oroxin A and oroxin B, inhibit the haemolytic activity of Hla, probably by blocking loop transition upon pore formation148,149. This inhibitory mechanism could aid in the design and development of anti-virulence agents to treat infections with multidrug-resistant strains of S. aureus. Similarly, DNA aptamers have been designed that specifically target the cytotoxic activity of Hla to inhibit S. aureus infections150. The identification of conformational rearrangements and protomer interfaces that are crucial for oligomerization and pore formation in other PFTs151 may enable the structure-based design of drugs that prevent pore formation for a given toxin.
A structure-based strategy could also be used to prevent the binding of PFTs to their specific receptors (Fig. 4a). For PFTs in the aerolysin family, synthetic GPI molecules and GPI analogues have been proposed as inhibitors of pore assembly by preventing the correct attachment of the PFT to the plasma membrane152. Equally of note is the potential of therapeutic antibodies to impair pore formation by a similar mechanism. It has recently been shown that some individuals possess high-affinity neutralizing antibodies against S. aureus Hla that target the cap and rim domains; this is expected to impede receptor binding and membrane recognition153. Although the mechanism underlying the protective action of these antibodies requires further investigation, these results open the way to the development of interesting, novel therapeutics for bacterial infections that target PFTs.
As a reverse strategy, the receptor — rather than the cognate PFT — could be targeted, as in the case of ADAM10 for Hla154 or CCR5 for LukED toxins. For CCR5, antagonists such as maraviroc were shown to block LukED-dependent cell death, and CCR5-deficient mice were resistant to infection with a strain of S. aureus that was lethal in wild-type mice, highlighting the therapeutic potential of targeting CCR5 (Ref. 137). However, it should be noted that broadly targeting leukocidin receptors could have harmful repercussions on the activation of the immune system, and so the value of this approach as a therapeutic strategy is unclear.
Another antimicrobial strategy that targets PFTs is the use of PFTs with reduced toxicity as recombinant toxoid vaccines that trigger an immune response (Fig. 4b). Knowledge of toxin structure and pore architecture can be beneficial in this scenario, enabling the rational design of site-directed mutations that reduce host membrane binding and cytotoxic efficiency while introducing minimal antigenic modifications, as recently shown for variants of NetB155 and ε-toxin156. Ply, a CDC that is produced by S. pneumoniae, has long been studied for toxoid vaccine development, recently resulting in promising pneumolysoid candidates, including the Ply mutant known as Δ6PLY157 and proteins produced by genetic fusion with other pneumococcal proteins, such as pneumococcal surface adhesin A (PsaA)158 and choline-binding protein A (CbpA)159.
Possibly more promising is the use of nanoparticles coated with red blood cell membranes that act as sinks for PFTs, which enables the non-toxic use of wild-type PFTs and thus preserves antigen presentation (Fig. 4b). The resulting complex, known as a nanotoxoid, can thus be used in vivo to trigger an effective immune response, as recently shown for nanoparticles with S. aureus Hla pores160,161. Given the ubiquitous presence of PFTs in the most pathogenic bacteria, the development of nanotoxoid vaccines may have the potential to soon address the urgent need for new treatments that are effective against antibiotic-resistant infections.
From a different clinical perspective, the induction of cell death following pore formation can be exploited to promote suicide in malignant cancer cells (Fig. 4c); this has been shown by transfecting the gene encoding SLO into several cancer cell lines145, which demonstrated the potential of this PFT for application in suicide gene therapy. Similarly, suicide gene therapy has successfully been used to target tumours overexpressing claudin 3, claudin 4 (Ref. 162) and claudin 6 (Ref. 163), which are receptors for CPE164.
Summary and conclusions
PFTs are sophisticated and widely spread virulence factors produced by pathogenic bacteria. They disrupt epithelial barriers and modulate or kill cells of the host immune system, thereby contributing to bacterial dissemination and growth, and trigger complex cellular responses that remain incompletely characterized (Box 1). All PFTs undergo a functional metamorphosis that leads inactive, soluble and monomeric proteins to assemble into conductive transmembrane pores at the target cell membrane (Fig. 1). However, as advances in the past decade have shown, each of the six PFT families has a distinct structural fold, pore architecture and mechanism of membrane insertion (Fig. 2; Table 1). Furthermore, the identification of lipids, sugars and protein receptors that bind to PFTs has furthered our understanding of the determinants of host cell specificity (Fig. 3). Collectively, these molecular insights have enabled the design of therapeutics that interfere with pore formation and could thus be used to treat infections, potentially as a component of combination treatments.
Structural studies have revealed that, to combat microbial infections, the immune systems of various animals make use of PFPs that have similar structures to the PFTs used by microorganisms to attack hosts. The most recent example is the identification of aerolysin family members in the frog species B. maxima, which has an immune system very similar to that of mammals67. βγ-CAT, which contains an aerolysin-like protein domain68, protects B. maxima against microbial infections9 in the bacteria-rich mud pools in which the frog lives. Similarly, immune cells in the snail B. glabrata produce biomphalysin to kill Schistosoma mansoni sporocysts8. It is likely that the structural characterization of future PFPs that are identified in animals will highlight interesting variations in mechanisms used to achieve target specificity.
Some PFTs remain unclassified orphans, such as the PFT subfamily of the repeats-in-toxin (RTX) family of proteins, which have numerous glycine–aspartate-rich repeats involved in calcium binding165. PFTs in this RTX subfamily include HlyA, which is produced by various E. coli species; the bifunctional haemolysin–adenylyl cyclase (CyaA) toxin produced by Bordetella pertussis165; and the multifunctional autoprocessing repeats-in-toxin (MARTX) family of toxins produced by A. hydrophila and several other pathogens166. Very little is known about the structure and mechanism of RTX toxins, as they need to be purified using high concentrations of chaotropic agents and, as a result, they have been unamenable to crystallographic analysis. The only structural hint derives from the prediction of nine amphipathic α-helices, thought to be responsible for pore formation, in the N-terminal domain of HlyA167.
The structural characterization of PFTs has recently revealed new conformations in the pore formation pathway. Therefore, for most PFT families, we now have a fairly clear view of the pore architecture at different stages of pore formation. The main challenges ahead are to comprehensively characterize the kinetics of this process and to design therapeutics — antibodies, drugs, peptides or nanotoxoids — that may inhibit its effects (Fig. 4). Finally, understanding how cells sense the changes in cytoplasmic ion composition that result from pore formation and how they respond to these changes at a molecular level will undoubtedly reveal novel mechanisms of membrane repair and danger sensing. As such, PFTs exemplify the value of studying bacterial virulence as a tool to elucidate the mechanisms underlying basic cellular functions.
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Acknowledgements
Work in the authors' laboratories is supported by the Swiss National Science Foundation (SNSF). The authors apologize to colleagues whose work could not be duly discussed owing to space limitations. The authors thank M. Dunstone for providing the coordinates of perfringolysin O oligomers used in the figures.
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Glossary
- Lipid droplets
-
Cellular organelles that store metabolic energy in the form of neutral lipids, such as triglycerides. These neutral lipids form the core of the droplet, which is surrounded by a phospholipid monolayer.
- Exosomes
-
Vesicles that are released into the extracellular space from the lumen of multivesicular bodies.
- Caveolae
-
Surface invaginations that may pinch off to allow cellular uptake of extracellular material.
- Multivesicular bodies
-
Late endocytic organelles that contain intraluminal vesicles that are formed by inward invagination of the limiting membrane.
- Programmed necrosis
-
A form of necrosis that is mediated by regulated pathways.
- Pyroptosis
-
A caspase 1-dependent form of programmed cell death that occurs as an antimicrobial response.
- Electron paramagnetic resonance
-
(EPR). A spectroscopy technique used to study paramagnetic molecules (that is, molecules with unpaired electrons). In biology, paramagnetic spin labels are covalently added to protein complexes to extract low-resolution information about their structure and dynamics.
- Outer membrane vesicles
-
(OMVs). Vesicles that are derived from the outer membrane of Gram-negative bacteria.
- Sphingomyelin
-
A sphingolipid found in animal cells that generally has a phosphocholine headgroup.
- Phase-separated lipid membranes
-
Membranes within which lipids are separated into different domains.
- Differential scanning calorimetry
-
A technique used to characterize the energetics associated with conformational changes of biomolecules, such as protein folding or phase transitions in lipid and lipid–protein mixtures upon temperature variation.
- Atomic force microscopy
-
(AFM). A technique that uses the deflection of a sharp-tipped probe to measure the local conformation and mechanical properties of a sample (for example, proteins embedded in a membrane) with up to nanometre resolution.
- Lectin
-
One of a family of proteins that bind to sugar moieties in glycoproteins.
- Parasitophorous vacuole
-
The endosome-like organelle in which parasites reside upon engulfment by the target cell.
- Disulfide scanning
-
An approach in which each amino acid in a sequence of interest is sequentially mutated to cysteine using a single point mutation. The reactivity of the introduced cysteine is analysed, for example, using a functional assay, to assess the dynamic location of the amino acid in the protein structure.
- Translocon
-
A protein channel that enables the translocation of client proteins across a membrane.
- GPI anchor
-
A glycosylphosphatidylinositol (GPI) lipid that is covalently linked to the carboxy terminus of a peripheral protein. The anchor attaches the protein to the outer leaflet of the plasma membrane.
- Lipid rafts
-
Microscale or nanoscale domains of biological membranes that are rich in cholesterol and sphingolipids.
- DNA aptamers
-
Short oligonucleotides engineered and selected to specifically bind to target molecules with high affinity. As with antibodies (their protein counterparts), DNA aptamers have broad applications both in biotechnology and therapeutics.
- Toxoids
-
Bacterial toxins engineered to decrease virulence. Toxoids are used as vaccines for microbial infections as they contribute to the development of an immune response against the native toxin.
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Peraro, M., van der Goot, F. Pore-forming toxins: ancient, but never really out of fashion. Nat Rev Microbiol 14, 77–92 (2016). https://doi.org/10.1038/nrmicro.2015.3
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DOI: https://doi.org/10.1038/nrmicro.2015.3