Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes

Highlights of the 14th International Bordetella Symposium

Pertussis, or whooping cough, is a highly contagious and acute respiratory illness caused primarily by the gram-negative coccobacillus Bordetella pertussis. Despite near-universal vaccination, pertussis remains one of the least-controlled vaccine-preventable infectious diseases. Since 2023, pertussis incidence has been rising, and widespread pertussis outbreaks have resurged in many countries. In response to these emerging challenges, almost 300 experts from institutions across 24 countries convened at the 14th International Bordetella Symposium in Prague, Czech Republic, from 24 to 28 June 2024 to discuss pertussis epidemiology and research and strategies to mitigate the global pertussis burden. We present here the highlights of the symposium, comprising epidemiological and clinical aspects of Bordetella infections, results of clinical trials of pertussis vaccination in pregnant women and effectiveness of maternal vaccination in protecting newborn infants in Africa and Europe, the controlled human infection model (CHIM), and the latest insights into the biology, immunology, and pathogenesis of B. pertussis infection.

Aeromonas hydrophila RTX adhesin has three ligand-binding domains that give the bacterium the potential to adhere to and aggregate a wide variety of cell types

Bacteria often make initial contact with their hosts through the ligand-binding domains of large adhesin proteins. Recent analyses of repeats-in-toxin (RTX) adhesins in Gram-negative bacteria suggest that ligand-binding domains can be identified by the way they emerge from "split" domains within the adhesin. Here, using this criterion and an AlphaFold3 model of a 5047-residue RTX adhesin from Aeromonas hydrophila, we identified three different ligand-binding domains in this fibrillar protein. The crystal structures of the two novel domains were solved to 1.4 and 1.95 Å resolution, respectively, and demonstrate excellent agreement with their modeled structures. The other domain was recognized as a carbohydrate-binding module based on its beta-strand topology and confirmed by its micromolar affinity for fucosylated glycans, including the Lewis B and Y antigens. This lectin-like module, which was recombinantly produced with its companion split domain and nearby extender domain, bound to a wide variety of cells including yeasts, diatoms, erythrocytes, and human endothelial cells. In each case, 50 mM free fucose prevented this binding and may offer some protection from infection. The carbohydrate-binding module with its neighboring domains also caused aggregation of yeast and erythrocytes, which was again blocked by the addition of free fucose. The second putative ligand-binding domain has a beta-roll structure supported by a parallel alpha-helix, and the third is a homolog of a von Willebrand Factor A domain. These two domains bind to a more limited range of cell types, and their ligands have yet to be identified.IMPORTANCECharacterizing the ligand-binding domains of fibrillar adhesins is important for understanding how bacteria can colonize host surfaces and how this colonization might be blocked. Here, we show that the opportunistic pathogen, Aeromonas hydrophila, uses a carbohydrate-binding module (CBM) to attach to several different cell types. The CBM is one of three ligand-binding domains at the distal tip of the adhesin. Identifying the glycans bound by the CBM as Lewis B and Y antigens has helped explain the range of cell types that the bacterium will bind and colonize, and it has suggested sugars that might interfere with these processes. Indeed, fucose, which is a constituent of the Lewis B and Y antigens, is effective at 50 mM concentrations in blocking the attachment of the CBM to host cells. This will lead to the design of more effective inhibitors against bacterial infections.

Intranasal application of a bifunctional pertactin-RTX fusion antigen elicits protection of mouse airway mucosa against Bordetella pertussis colonization

The adenylate cyclase toxin (ACT, AC-Hly, or CyaA) plays a key role in airway infections by Bordetella pertussis and ablates the oxidative burst and opsonophagocytic capacity of sentinel phagocytes. CyaA fragments eliciting toxin-neutralizing antibodies are considered prime antigen candidates for improved acellular pertussis (aP) vaccines but their contribution to aP-mediated protection against B. pertussis infection awaits demonstration. We explored whether hybrid antigens inducing simultaneously CyaA-neutralizing and anti-Prn opsonizing antibody responses can enhance aP-elicited protection of mouse airways from infection. Fusion to the N-terminus of an RTX908 antigen derived from CyaA enabled an accelerated folding of the pertactin passenger domain (rPrn) in function of calcium loading of the RTX908 moiety and conferred on the rPrn-RTX908 fusion antigen a superior capacity to induce functional anti-Prn IgG antibodies. The rPrn-RTX908 fusion antigen also elicited CyaA neutralizing anti-RTX antibodies that relieved the toxin-imposed inhibition of oxidative burst and opsonophagocytic uptake of B. pertussis bacteria by HL-60 cells exposed to physiological concentrations of the CyaA toxin. Intranasal immunization of mice with the rPrn-RTX908 antigen admixed into a PT and FHA-based aP vaccine elicited specific sIgA responses in mucosal secretions (saliva) and conferred a significantly enhanced protection of mouse lung and nose mucosa against B. pertussis infection, yielding a significantly accelerated clearance of bacteria from the infected lungs within a single day from infection. These results demonstrate the added value of anti-CyaA antibodies elicited by intranasal application of the rPrn-RTX908 fusion antigen in the protection of the airway against B. pertussis infection.

IMPORTANCE

Despite high vaccine coverage, unexpectedly massive whooping cough outbreaks are currently resurging in the most developed countries using the acellular pertussis (aP) vaccine. Accelerated development of improved aP vaccines, conferring a more complete and longer-lasting protection of the airway from Bordetella pertussis infection, is sorely needed. The highly immunosuppressive RTX adenylate cyclase toxin (CyaA) was proposed as a prime antigen candidate for inclusion into improved aP vaccines. We show here that a soluble RTX-derived antigen fused to the major opsonizing antibody target pertactin (rPrn-RTX908 hybrid) elicits opsonizing and toxin-neutralizing antibody responses that relieve the CyaA-imposed block of bactericidal opsonophagocytic uptake capacities of sentinel phagocytes. Intranasal immunization with the rPrn-RTX908 hybrid antigen then enables a significantly accelerated clearance of B. pertussis bacteria from mouse lungs and superior protection of mouse nasal mucosa from bacterial infection. These results unravel the added value of RTX antigen inclusion into the next generation of aP vaccines.

The Actinobacillus pleuropneumoniae apxIV operon encodes an antibacterial toxin-immunity pair

The ApxIVA protein belongs to a distinct class of a "clip and link" activity of Repeat-in-ToXin (RTX) exoproteins. Along with the three other pore-forming RTX toxins (ApxI, ApxII and ApxIII), ApxIVA serves as a major virulence factor of Actinobacillus pleuropneumoniae, the causative agent of porcine pneumonia. The gene encoding ApxIVA is located on a bicistronic operon downstream of the orf1 gene and is expressed exclusively under in vivo conditions. Both ApxIVA and ORF1 are essential for full virulence of A. pleuropneumoniae, but the molecular mechanisms by which they contribute to the pathogenicity are not yet understood. Here, we provide a comprehensive structural and functional analysis of ApxIVA and ORF1 proteins. Our findings reveal that the N-terminal segment of ApxIVA shares structural similarity with colicin M (ColM)-like bacteriocins and exhibits an antimicrobial activity. The ORF1 protein resembles the colicin M immunity protein (Cmi) and, like Cmi, is exported to the periplasm through its N-terminal signal peptide. Additionally, ORF1 can protect bacterial cells from the antimicrobial activity of ApxIVA, suggesting that ORF1 and ApxIVA function as an antibacterial toxin-immunity pair. Moreover, we demonstrate that fetal bovine serum could elicit ApxIVA and ORF1 production under in vitro conditions. These findings highlight the coordinated action of various RTX determinants, where the fine-tuned spatiotemporal production of ApxIVA may enhance the fitness of A. pleuropneumoniae, facilitating its invasion to a resident microbial community on the surface of airway mucosa.

Modification of the RTX domain cap by acyl chains of adapted length rules the formation of functional hemolysin pores

The acylated pore-forming Repeats in ToXin (RTX) cytolysins α-hemolysin (HlyA) and adenylate cyclase toxin (CyaA) preferentially bind to β2 integrins of myeloid leukocytes but can also promiscuously bind and permeabilize cells lacking the β2 integrins. We constructed a HlyA1-563/CyaA860-1706 chimera that was acylated either by the toxin-activating acyltransferase CyaC, using sixteen carbon-long (C16) acyls, or by the HlyC acyltransferase using fourteen carbon-long (C14) acyls. Cytolysin assays with the C16- or C14-acylated HlyA/CyaA chimeric toxin revealed that the RTX domain of CyaA can functionally replace the RTX domain of HlyA only if it is modified by C16-acyls on the Lys983 residue of CyaA. The C16-monoacylated HlyA/CyaA chimera was as pore-forming and cytolytic as native HlyA, whereas the C14-acylated chimera exhibited very low pore-forming activity. Hence, the capacity of the RTX domain of CyaA to support the insertion of the N-terminal pore-forming domain into the target cell membrane, and promote formation of toxin pores, strictly depends on the modification of the Lys983 residue by an acyl chain of adapted length.

Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach

Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.

The adenylate cyclase toxin RTX domain follows a series templated folding mechanism with implications for toxin activity

Folding of the Repeats-in-toxin (RTX) domain of the bacterial adenylate cyclase toxin-hemolysin (CyaA) is critical to its toxin activities and the virulence of the whooping cough agent Bordetella pertussis. The RTX domain (RD) contains five RTX blocks (RTX-i to RTX-v) and their folding is driven by the binding of calcium. However, the detailed molecular mechanism via which the folding signal transmits within the five RTX blocks remains unknown. By combining single molecule optical tweezers, protein engineering, and toxin activity assays, here we demonstrate that the folding of the RD follows a strict hierarchy, with the folding starting from its C-terminal block RTX-v and proceeding towards the N-terminal RTX-i block sequentially. Our results reveal a strict series, templated folding mechanism, where the folding signal is transmitted along the RD in a series fashion from its C terminus continuously to the N terminus. Due to the series nature of this folding signal transmission pathway, the folding of RD can be disrupted at any given RTX block, rendering the RTX blocks located N-terminally to the disruption site and the acylation region of CyaA unfolded and abolishing CyaA's toxin activities. Our results reveal key mechanistic insights into the secretion and folding process of CyaA and may open up new potential avenues towards designing new therapeutics to abolish toxin activity of CyaA and combat B. pertussis.

A conserved tryptophan in the acylated segment of RTX toxins controls their β2 integrin-independent cell penetration

The acylated Repeats in ToXins (RTX) leukotoxins, the adenylate cyclase toxin (CyaA) or α-hemolysin (HlyA), bind β2 integrins of leukocytes but also penetrate cells lacking these receptors. We show that the indoles of conserved tryptophans in the acylated segments, W876 of CyaA and W579 of HlyA, are crucial for β2 integrin-independent membrane penetration. Substitutions of W876 by aliphatic or aromatic residues did not affect acylation, folding, or the activities of CyaA W876L/F/Y variants on cells expressing high amounts of the β2 integrin CR3. However, toxin activity of CyaA W876L/F/Y on cells lacking CR3 was strongly impaired. Similarly, a W579L substitution selectively reduced HlyA W579L cytotoxicity towards cells lacking β2 integrins. Intriguingly, the W876L/F/Y substitutions increased the thermal stability (Tm) of CyaA by 4 to 8 °C but locally enhanced the accessibility to deuteration of the hydrophobic segment and of the interface of the two acylated loops. W876Q substitution (showing no increase in Tm), or combination of W876F with a cavity-filling V822M substitution (this combination decreasing the Tm closer to that of CyaA), yielded a milder defect of toxin activity on erythrocytes lacking CR3. Furthermore, the activity of CyaA on erythrocytes was also selectively impaired when the interaction of the pyrrolidine of P848 with the indole of W876 was ablated. Hence, the bulky indoles of residues W876 of CyaA, or W579 of HlyA, rule the local positioning of the acylated loops and enable a membrane-penetrating conformation in the absence of RTX toxin docking onto the cell membrane by β2 integrins.

Outsmarting Pathogens with Antibody Engineering

There is growing interest in identifying antibodies that protect against infectious diseases, especially for high-risk individuals and pathogens for which no vaccine is yet available. However, pathogens that manifest as opportunistic or latent infections express complex arrays of virulence-associated proteins and are adept at avoiding immune responses. Some pathogens have developed strategies to selectively destroy antibodies, whereas others create decoy epitopes that trick the host immune system into generating antibodies that are at best nonprotective and at worst enhance pathogenesis. Antibody engineering strategies can thwart these efforts by accessing conserved neutralizing epitopes, generating Fc domains that resist capture or degradation and even accessing pathogens hidden inside cells. Design of pathogen-resistant antibodies can enhance protection and guide development of vaccine immunogens against these complex pathogens. Here, we discuss general strategies for design of antibodies resistant to specific pathogen defense mechanisms.

Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin

Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β₂ integrins on phagocytes. The Bordetella adenylate cyclase toxin (ACT) uses the α_Mβ₂ integrin as a receptor, but the structural basis for integrin binding and neutralization by antibodies is poorly understood. Here, we use cryoelectron microscopy to determine a 2.7 Å resolution structure of an ACT fragment bound to α_Mβ₂. This structure reveals that ACT interacts with the headpiece and calf-2 of the α_M subunit in a non-canonical manner specific to bent, inactive α_Mβ₂. Neutralizing antibody epitopes map to ACT residues involved in α_M binding, providing the basis for antibody-mediated attachment inhibition. Furthermore, binding to α_Mβ₂ positions the essential ACT acylation sites, which are conserved among toxins exported by type I secretion systems, at the cell membrane. These findings reveal a structural mechanism for integrin-mediated attachment and explain antibody-mediated neutralization of ACT intoxication.

Blockade of the Adenylate Cyclase Toxin Synergizes with Opsonizing Antibodies to Protect Mice against Bordetella pertussis

Bordetella produces an array of virulence factors, including the adenylate cyclase toxin (ACT), which is essential, immunogenic in humans, and highly conserved. Despite mediating immune-evasive functions as a leukotoxin, ACT’s potential role as a protective antigen is unclear. To better understand the contributions of humoral anti-ACT immunity, we evaluated protection against Bordetella pertussis by antibodies binding structurally defined ACT epitopes in a mouse pneumonia model. An ACT-neutralizing antibody, but not a nonneutralizing antibody or an isotype control, significantly increased mouse survival after lethal challenge with B. pertussis. When modified to impair Fc effector functions, the neutralizing antibody retained protective capabilities, indicating that protection was mediated by the blockade of the interactions of ACT with its α_Mβ₂ integrin receptor. After infection with a lower bacterial dose, ACT neutralization synergistically reduced lung bacterial colonization levels when combined with an opsonic antibody binding the surface antigen pertactin. Notably, protection was significantly enhanced when antibodies were administered intranasally as opposed to systemically, indicating that local immune responses are key to antibody-mediated protection against ACT and pertactin. These data reconcile previous conflicting reports to indicate that neutralizing anti-ACT antibodies support the phagocytosis of opsonized B. pertussis and thereby contribute to pertussis protection in vivo.

Templated folding of the RTX domain of the bacterial toxin adenylate cyclase revealed by single molecule force spectroscopy

The RTX (repeats-in-toxin) domain of the bacterial toxin adenylate cyclase (CyaA) contains five RTX blocks (RTX-i to RTX-v) and its folding is essential for CyaA’s functions. It was shown that the C-terminal capping structure of RTX-v is critical for the whole RTX to fold. However, it is unknown how the folding signal transmits within the RTX domain. Here we use optical tweezers to investigate the interplay between the folding of RTX-iv and RTX-v. Our results show that RTX-iv alone is disordered, but folds into a Ca²⁺-loaded-β-roll structure in the presence of a folded RTX-v. Folding trajectories of RTX-iv-v reveal that the folding of RTX-iv is strictly conditional upon the folding of RTX-v, suggesting that the folding of RTX-iv is templated by RTX-v. This templating effect allows RTX-iv to fold rapidly, and provides significant mutual stabilization. Our study reveals a possible mechanism for transmitting the folding signal within the RTX domain.

The authors use optical tweezers to show that the folding of repeats-in-toxin (RTX) block-iv in adenylate cyclase is templated by the folded RTX block-v. The findings suggest a possible mechanism for transmitting the folding signal in the RTX domain.

Kingella kingae RtxA Cytotoxin in the Context of Other RTX Toxins

The Gram-negative bacterium Kingella kingae is part of the commensal oropharyngeal flora of young children. As detection methods have improved, K. kingae has been increasingly recognized as an emerging invasive pathogen that frequently causes skeletal system infections, bacteremia, and severe forms of infective endocarditis. K. kingae secretes an RtxA cytotoxin, which is involved in the development of clinical infection and belongs to an ever-growing family of cytolytic RTX (Repeats in ToXin) toxins secreted by Gram-negative pathogens. All RTX cytolysins share several characteristic structural features: (i) a hydrophobic pore-forming domain in the N-terminal part of the molecule; (ii) an acylated segment where the activation of the inactive protoxin to the toxin occurs by a co-expressed toxin-activating acyltransferase; (iii) a typical calcium-binding RTX domain in the C-terminal portion of the molecule with the characteristic glycine- and aspartate-rich nonapeptide repeats; and (iv) a C-proximal secretion signal recognized by the type I secretion system. RTX toxins, including RtxA from K. kingae, have been shown to act as highly efficient 'contact weapons' that penetrate and permeabilize host cell membranes and thus contribute to the pathogenesis of bacterial infections. RtxA was discovered relatively recently and the knowledge of its biological role remains limited. This review describes the structure and function of RtxA in the context of the most studied RTX toxins, the knowledge of which may contribute to a better understanding of the action of RtxA in the pathogenesis of K. kingae infections.

Antibodies binding diverse pertactin epitopes protect mice from B. pertussis infection

Infection by the bacterium Bordetella pertussis continues to cause considerable morbidity and mortality worldwide. Many current acellular pertussis vaccines include the antigen pertactin, which has presumptive adhesive and immunomodulatory activities, but is rapidly lost from clinical isolates after the introduction of these vaccines. To better understand the contributions of pertactin antibodies to protection and pertactin's role in pathogenesis, we isolated and characterized recombinant antibodies binding four distinct epitopes on pertactin. We demonstrate that four of these antibodies bind epitopes that are conserved across all three classical Bordetella strains, and competition assays further showed that antibodies binding these epitopes are also elicited by B. pertussis infection of baboons. Surprisingly, we found that representative antibodies binding each epitope protected mice against experimental B. pertussis infection. A cocktail of antibodies from each epitope group protected mice against a subsequent lethal dose of B. pertussis and greatly reduced lung colonization levels after sublethal challenge. Each antibody reduced B. pertussis lung colonization levels up to 100-fold when administered individually, which was significantly reduced when antibody effector functions were impaired, with no antibody mediating antibody-dependent complement-induced lysis. These data suggest that antibodies binding multiple pertactin epitopes protect primarily by the same bactericidal mechanism, which overshadows contributions from blockade of other pertactin functions. These antibodies expand the available tools to further dissect pertactin's role in infection and understand the impact of antipertactin antibodies on bacterial fitness.