Prolipoprotein:phosphatidylglycerol diacylglyceryl transferase (Lgt) performs the first and committed step in the bacterial lipoprotein modification pathway by catalyzing the transfer of a diacylglyceryl moiety from diacylglycerol phospholipid onto pre-prolipoproteins. This enzyme is unique in bacteria and functionally and structurally highly conserved among species. Lgt is essential for bacterial viability and virulence, making it a promising target for antibacterial development. Previous reports identified specific inhibitors of E. coli Lgt, including peptide G2824, a 12-residue cyclic peptide containing non-natural amino acids (NNAA). Here, we aimed to elucidate the mode of action underlying Lgt inhibition by G2824 that, as its linear and scrambled analogues, inhibits Lgt activity in vitro and growth and viability of E. coli. The inhibitory activity of NNAA peptides is abolished when NNAA are replaced by L-phenylalanine. Furthermore, the defect on cell growth and morphology caused by G2824 could not be compensated by elevated levels of Lgt. Our structural and biophysical analyses demonstrate that the NNAA peptides directly act on the phospholipid membrane, causing loss of membrane potential leading to membrane permeabilization and cell lysis. Taken together, our data show that inhibition of Lgt by G2824 and related NNAA peptides does not result from direct enzyme targeting but rather from preferential perturbation of phosphatidylglycerol containing membranes, thereby preventing acyl donor availability and indirectly abolishing Lgt catalytic activity.

The adenylate cyclase toxin (CyaA) from Bordetella pertussis intoxicates host cells by directly translocating its N-terminal catalytic domain across the plasma membrane; however, the forces driving this unique process remain poorly defined. Here, we dissect the membrane translocation mechanisms of two peptide segments derived from CyaA: P233 and P454 from the catalytic domain and the translocation region, respectively. Both P454 and P233 are calmodulin-binding segments that are sequentially involved in the translocation and activation of the catalytic domain. Using a newly developed Droplet Interface Bilayer (DIB) approach, called DIB-Pipette, which enables direct visualization of peptide transport under controlled membrane potentials, we show that P454 translocates across membranes independently of membrane potential, whereas P233 translocation requires a negative electric membrane potential. Strikingly, covalent coupling of P233 and P454 enables efficient translocation of the resulting peptide even in the absence of a membrane potential. Together, these results suggest that two distinct membrane-active segments within CyaA act cooperatively to promote translocation at the peptide level, revealing an intrinsic mechanism that may contribute to membrane potential-dependent translocation. These findings provide new mechanistic insights into the CyaA cell intoxication process and reveal a multifunctional strategy for protein delivery across membranes.

Abstract Streptococcus gallolyticus subsp. gallolyticus (SGG) is a gut pathobiont associated with colorectal cancer. Like many Firmicutes, SGG utilizes a specialized Type VII Secretion System (T7SSb) to export WXG100 and LXG proteins, the latter involved in bacterial competition. We previously identified TelE, an LXG protein whose C-terminus mediates membrane pore formation in Escherichia coli . In SGG UCN34, TelE (Gallo_0562) is co-expressed with six proteins (Gallo_0559 to Gallo_0565), including its immunity protein TipE (Gallo_0565). Here we show that the absence of those co-expressed proteins affects TelE stability and secretion. These proteins associate with TelE to form a soluble and stable seven-protein complex. Gallo_0559 and Gallo_0560 interact with the N-terminal LXG domain of TelE, Gallo_0561 binds to its central region, while the six-transmembrane protein Gallo_0563, together with Gallo_0564 and TipE associates with its C-terminal domain. These findings describe a new modular complex that stabilizes TelE while reducing its toxicity and optimizing its T7SSb-mediated delivery.

Carrier proteins are chemically linked to poorly immunogenic antigens to generate conjugate vaccines, significantly improving immunogenicity. CRM197, a genetically detoxified diphtheria toxin (DT) mutant carrying the G52E mutation, is a widely used carrier protein as it retains lysine residues for antigen conjugation. In the past, CRM197 has been expressed in Corynebacterium diphtheriae, but low yields and high costs have prompted the exploration of alternative expression systems. Although high-yield expression and native refolding of CRM197 in E. coli are challenging due to its reducing cytoplasm, recent advances have enabled the production of soluble and well-folded recombinant CRM197 proteins, namely EcoCRM® and EcoCRM®(-Met). In this study, we use Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) to compare the structural dynamics of EcoCRM and EcoCRM(-Met) with DT wild-type. Our HDX-MS data show that the presence or the absence of the N-terminal methionine does not affect the structural dynamics of the two recombinant EcoCRM proteins. Furthermore, our results elucidate the molecular mechanism underlying the lack of toxicity of CRM197 compared to DT wild-type: the G52E mutation in the CRM197 proteins exclusively alters the stability of the NAD-binding pocket and induces allosteric effects within the receptor-binding domain. Altogether, these insights support the substitution of CRM197 produced by C. diphtheriae with the recombinant EcoCRM and EcoCRM(-Met) proteins produced in E. coli, offering a cost-effective solution for use in conjugate vaccines. Data are available via ProteomeXchange with identifier PXD057388.

SprA1 and SprA2 are small hydrophobic peptides that belong to the type I toxin-antitoxin systems expressed by Staphylococcus aureus. Both peptides induce S. aureus death when overexpressed. Although they share 71% of amino acids sequence similarity, SprA2 exhibits stronger hemolytic activity than SprA1. In this study, we investigated the mode of action of these toxins on both prokaryotic-like and eukaryotic-like membranes. We first confirmed that SprA2, like SprA1, is an alpha-helical peptide located at the S. aureus membrane. By overexpressing each toxin, we demonstrated that SprA1 forms stable pores in the S. aureus membrane, evidenced by concomitant membrane depolarization, permeabilization and ATP release leading to growth arrest, whereas SprA2 forms transient pores, causing concomitant membrane depolarization, ATP release, and growth arrest. We showed that the unique cysteine residue present in SprA1 and SprA2 is required for toxicity through disulfide bond formation. Next, we found that both synthetic peptides induce slight leakage in anionic DOPC-DOPG lipid vesicles mimicking prokaryotic membranes, concomitant with lipid vesicles aggregation and/or fusion. Moreover, we observed that SprA1 permeabilizes S. aureus protoplasts, via its ability to form stable pores, whereas SprA2 permeabilizes and lyses them. However, no permeabilization of intact bacteria was detected after the addition of SprA1 and SprA2 in the extracellular medium. Finally, we confirmed that SprA2 has strong activity on zwitterionic DOPC lipid vesicles mimicking eukaryotic membranes, without inducing aggregation. This work highlights the strong selectivity of SprA2 for eukaryotic membranes, suggesting that this toxin may play a role in S. aureus virulence.

Post-translational modifications critically shape protein conformation and function, yet how they regulate bacterial toxins remains elusive. The adenylate cyclase (CyaA) toxin is a major virulence factor of Bordetella pertussis , the causative agent of whooping cough. CyaA is produced as an inactive precursor, proCyaA, which is activated by acylation of two lysine residues within the bacterium. Once acylated and secreted, CyaA invades innate immune cells and disrupts their phagocytic functions. High-resolution structural characterization of CyaA has remained elusive due to its size, multi-domain organization, flexibility, and aggregation propensity. Here, we overcome these challenges and generate the first structural ensembles of both non-acylated and acylated CyaA in solution by combining experimental data with integrative modeling. Coarse-grained molecular dynamics simulations reveal that acylation is critical to stabilize the native fold and to favorably orient CyaA on the target membrane. Overall, our findings reveal how post-translational acylation triggers native folding and provide mechanistic insights into the early steps of host cell intoxication. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, 21-CE11-0014-01-3DTransCyaA, ANR-11-EQPX-0008 Institut Pasteur, SPAIS/PTR 166-19, SPAIS/PTR 502-22, DARRI-Emergence S-PI15006-12B CNRS Inserm

A unified excluded volume model based upon the effective hard particle approximation is developed and used to quantitatively model previously published experimental measurements of the effect of adding high concentrations of an "inert" polymer, Ficoll 70, on conformational transitions of the toxin protein RCL that are induced by addition of calcium at constant temperature or by increasing temperature in the absence and presence of high calcium concentrations. The best-fit of this model, which accounts quantitatively for all of the published data to within experimental precision, yields an estimate of the volume of solution excluded to Ficoll by each of four identified conformational states of RCL: H - the most compact conformation adopted in the limits of high calcium concentration and low temperature, H* - the conformation adopted in the limits of high calcium concentration and high temperature, A - the conformation adopted in the limits of low (or no) calcium at low temperature, and A* - the conformation adopted in the limits of low calcium and high temperature. Ficoll exclusion volumes increase in the order H < H* < A < A*. These results are discussed in the context of the physiological functions of the RTX proteins, which are involved in the secretion process and the calcium-induced folding of bacterial virulence factors.

OPINION article Front. Mol. Biosci., 22 March 2024Sec. Molecular Biophysics Volume 11 - 2024 | https://doi.org/10.3389/fmolb.2024.1359408

Equine influenza virus (EIV) remains a threat to horses, despite the availability of vaccines. Strategies to monitor the virus and prevent potential vaccine failure revolve around serological assays, RT-qPCR amplification, and sequencing the viral hemagglutinin (HA) and neuraminidase (NA) genes. These approaches overlook the contribution of other viral proteins in driving virulence. This study assesses the potential of long-read nanopore sequencing for fast and precise sequencing of circulating equine influenza viruses. Therefore, two French Florida Clade 1 strains, including the one circulating in winter 2018–2019 exhibiting more pronounced pathogenicity than usual, as well as the two currently OIE-recommended vaccine strains, were sequenced. Our results demonstrated the reliability of this sequencing method in generating accurate sequences. Sequence analysis of HA revealed a subtle antigenic drift in the French EIV strains, with specific substitutions, such as T163I in A/equine/Paris/1/2018 and the N188T mutation in post-2015 strains; both substitutions were in antigenic site B. Antigenic site E exhibited modifications in post-2018 strains, with the N63D substitution. Segment 2 sequencing also revealed that the A/equine/Paris/1/2018 strain encodes a longer variant of the PB1-F2 protein when compared to other Florida clade 1 strains (90 amino acids long versus 81 amino acids long). Further biological and biochemistry assays demonstrated that this PB1-F2 variant has enhanced abilities to abolish the mitochondrial membrane potential ΔΨm and permeabilize synthetic membranes. Altogether, our results highlight the interest in rapidly characterizing the complete genome of circulating strains with next-generation sequencing technologies to adapt vaccines and identify specific virulence markers of EIV.

The CyaA toxin, a 1706-residue long protein, is one of the major virulence factors produced by Bordetella pertussis. The secretion of CyaA is initiated by its C-terminal extremity through a dedicated Type 1 secretion system (T1SS). We are interested to decipher how CyaA is recognized, uptake and secreted by the T1SS. We have identified a C-terminal membrane-interacting region (MIR), which exhibits high affinity for membranes composed of lipids mimicking the inner leaflet of Bordetella pertussis (ilbp)inner membrane. We show by a combination of approaches that MIR undergoes conformational changes upon interactions with ilbp membranes. We further characterized the parameters tuning MIR/membrane interactions such as pH, ionic strength, and lipid composition. Moreover, key residues of MIR involved in membrane partitioning have been identified. These results allow us to propose a model of MIR/membrane interactions, which may help to recruit CyaA at the surface of the inner membrane, at proximity of the entry gate of the T1SS. These data pave the way to characterize the interaction of the full length CyaA toxin with the inner membrane of Bordetella pertussis prior its secretion from the bacterium.

Bordetella pertussis, the causative agent of whooping cough, secretes an adenylate cyclase toxin (CyaA, 1706 residues) that plays an essential role in the early stages of respiratory tract colonization of humans. After its secretion, CyaA intoxicates human cells via a direct translocation of its catalytic domain (ACD, 1-364) across the plasma membrane. Once in the cytosol, ACD binds to calmodulin and catalyses high amounts of cAMP, leading to cell death. Our results illustrate how the structural flexibility of CyaA is essential for its secretion, its folding, its translocation across plasma membrane and its enzymatic activity leading to cell intoxication. All of these steps involve disorder-to-order structural transitions that are finely tuned to the environmental conditions that CyaA successively experiences along its journey from the bacterium to the eukaryotic cell cytoplasm. Here, we focus on our recent results on ACD translocation across target cell membranes. The CyaA translocation region (TR, 365-520) contains a segment, P454 (residues 454-484), which exhibits membrane-active properties related to antimicrobial peptides. We show that P454 can translocate across membranes and interact with endogenous calmodulin. Structural and biophysical analyses reveal the key residues of P454 involved in membrane destabilization and calmodulin binding. Mutational analysis demonstrates that these residues play a crucial role in ACD translocation into target cells. We propose that after CyaA binding to target cells, the P454 segment destabilizes the plasma membrane, translocates across the lipid bilayer and binds calmodulin. Trapping of CyaA by the CaM:P454 interaction in the cytosol may assist the entry of ACD by converting the stochastic motion of the polypeptide chain through the membrane into an efficient vectorial chain translocation into host cells. These data open new avenues for biotechnological applications using CyaA as antigen delivery vehicle.

Streptococcus gallolyticus subsp. gallolyticus (SGG) is an opportunistic gut pathogen associated with colorectal cancer. We previously showed that colonization of the murine colon by SGG in tumoral conditions was strongly enhanced by the production of gallocin A, a two-peptide bacteriocin. Here, we aimed to characterize the mechanisms of its action and resistance. Using a genetic approach, we demonstrated that gallocin A is composed of two peptides, GllA1 and GllA2, which are inactive alone and act together to kill "target" bacteria. We showed that gallocin A can kill phylogenetically close relatives of the pathogen. Importantly, we demonstrated that gallocin A peptides can insert themselves into membranes and permeabilize lipid bilayer vesicles. Next, we showed that the third gene of the gallocin A operon, gip, is necessary and sufficient to confer immunity to gallocin A. Structural modeling of GllA1 and GllA2 mature peptides suggested that both peptides form alpha-helical hairpins stabilized by intramolecular disulfide bridges. The presence of a disulfide bond in GllA1 and GllA2 was confirmed experimentally. Addition of disulfide-reducing agents abrogated gallocin A activity. Likewise, deletion of a gene encoding a surface protein with a thioredoxin-like domain impaired the ability of gallocin A to kill Enterococcus faecalis. Structural modeling of GIP revealed a hairpin-like structure strongly resembling those of the GllA1 and GllA2 mature peptides, suggesting a mechanism of immunity by competition with GllA1/2. Finally, identification of other class IIb bacteriocins exhibiting a similar alpha-helical hairpin fold stabilized with an intramolecular disulfide bridge suggests the existence of a new subclass of class IIb bacteriocins. IMPORTANCE Streptococcus gallolyticus subsp. gallolyticus (SGG), previously named Streptococcus bovis biotype I, is an opportunistic pathogen responsible for invasive infections (septicemia, endocarditis) in elderly people and is often associated with colon tumors. SGG is one of the first bacteria to be associated with the occurrence of colorectal cancer in humans. Previously, we showed that tumor-associated conditions in the colon provide SGG with an ideal environment to proliferate at the expense of phylogenetically and metabolically closely related commensal bacteria such as enterococci (1). SGG takes advantage of CRC-associated conditions to outcompete and substitute commensal members of the gut microbiota using a specific bacteriocin named gallocin, recently renamed gallocin A following the discovery of gallocin D in a peculiar SGG isolate. Here, we showed that gallocin A is a two-peptide bacteriocin and that both GllA1 and GllA2 peptides are required for antimicrobial activity. Gallocin A was shown to permeabilize bacterial membranes and kill phylogenetically closely related bacteria such as most streptococci, lactococci, and enterococci, probably through membrane pore formation. GllA1 and GllA2 secreted peptides are unusually long (42 and 60 amino acids long) and have very few charged amino acids compared to well-known class IIb bacteriocins. In silico modeling revealed that both GllA1 and GllA2 exhibit a similar hairpin-like conformation stabilized by an intramolecular disulfide bond. We also showed that the GIP immunity peptide forms a hairpin-like structure similar to GllA1/GllA2. Thus, we hypothesize that GIP blocks the formation of the GllA1/GllA2 complex by interacting with GllA1 or GllA2. Gallocin A may constitute the first class IIb bacteriocin which displays disulfide bridges important for its structure and activity and might be the founding member of a subtype of class IIb bacteriocins.

Amphitropic proteins and peptides reversibly partition from solution to membrane, a key process that regulates their functions. Experimental approaches classically used to measure protein partitioning into lipid bilayers, such as fluorescence and circular dichroism, are hardly usable when the peptides or proteins do not exhibit significant polarity and/or conformational changes upon membrane binding. Here, we describe binding to lipid vesicles (B2LiVe), a simple, robust, and widely applicable nuclear magnetic resonance (NMR) method to determine the solution-to-membrane partitioning of unlabeled proteins or peptides. B2LiVe relies on previously described proton 1D-NMR fast-pulsing techniques. Membrane partitioning induces a large line broadening, leading to a loss of protein signals; therefore, the decrease of the NMR signal directly measures the fraction of membrane-bound protein. The method uses low polypeptide concentrations and has been validated on several membrane-interacting polypeptides, ranging from 3 to 54 kDa, with membrane vesicles of different sizes and various lipid compositions.

The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells are still a matter of intense research. Bordetella pertussis, the causative agent of whooping cough, produces an adenylate cyclase (CyaA) toxin that plays an essential role in the early stages of respiratory tract colonization. CyaA displays a unique intoxication pathway of human cells via a direct translocation of its catalytic domain (AC) across the plasma membrane. Once in the cytosol, AC impairs the physiology of immune cells, leading to cell death.

Calmodulin (CaM) is an evolutionarily conserved eukaryotic multifunctional protein that functions as the major sensor of intracellular calcium signaling. Its calcium-modulated function regulates the activity of numerous effector proteins involved in a variety of physiological processes in diverse organs, from proliferation and apoptosis, to memory and immune responses. Due to the pleiotropic roles of CaM in normal and pathological cell functions, CaM antagonists are needed for fundamental studies as well as for potential therapeutic applications. Calmidazolium (CDZ) is a potent small molecule antagonist of CaM and one the most widely used inhibitors of CaM in cell biology. Yet, CDZ, as all other CaM antagonists described thus far, also affects additional cellular targets and its lack of selectivity hinders its application for dissecting calcium/CaM signaling. A better understanding of CaM:CDZ interaction is key to design analogs with improved selectivity. Here, we report a molecular characterization of CaM:CDZ complexes using an integrative structural biology approach combining SEC-SAXS, X-ray crystallography, HDX-MS, and NMR. We provide evidence that binding of a single molecule of CDZ induces an open-to-closed conformational reorientation of the two domains of CaM and results in a strong stabilization of its structural elements associated with a reduction of protein dynamics over a large time range. These CDZ-triggered CaM changes mimic those induced by CaM-binding peptides derived from physiological protein targets, despite their distinct chemical natures. CaM residues in close contact with CDZ and involved in the stabilization of the CaM:CDZ complex have been identified. Our results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists. Calmidazolium is a potent and widely used inhibitor of calmodulin, a major mediator of calcium-signaling in eukaryotic cells. Structural characterization of calmidazolium-binding to calmodulin reveals that it triggers open-to-closed conformational changes similar to those induced by calmodulin-binding peptides derived from enzyme targets. These results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists.

Various bacterial pathogens are producing toxins that target the cyclic Nucleotide Monophosphate (cNMPs) signaling pathways in order to facilitate host colonization. Among them, several are exhibiting potent nucleotidyl cyclase activities that are activated by eukaryotic factors, such as the adenylate cyclase (AC) toxin, CyaA, from Bordetella pertussis or the edema factor, EF, from Bacillus anthracis. The characterization of these toxins frequently requires accurate measurements of their enzymatic activity in vitro, in particular for deciphering their structure-to-function relationships by protein engineering and site-directed mutagenesis. Here we describe a simple and robust in vitro assay for AC activity based on the spectrophotometric detection of cyclic AMP (cAMP) after chromatographic separation on aluminum oxide. This assay can accurately detect down to fmol amounts of B. pertussis CyaA and can even be used in complex media, such as cell extracts. The relative advantages and disadvantages of this assay in comparison with other currently available methods are briefly discussed.

The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells have thus far remained elusive. The adenylate cyclase (CyaA) toxin from Bordetella pertussis displays a unique intoxication pathway in which its catalytic domain is directly translocated across target cell membranes. We have previously identified a translocation region in CyaA that contains a segment, P454 (residues 454–484), exhibiting membrane-active properties related to antimicrobial peptides. Herein, we show that this peptide is able to translocate across membranes and interact with calmodulin. Structural and biophysical analyses have revealed the key residues of P454 involved in membrane destabilization and calmodulin binding. Mutational analysis demonstrated that these residues play a crucial role in CyaA translocation into target cells. We have also shown that calmidazolium, a calmodulin inhibitor, efficiently blocks CyaA internalization. We propose that after CyaA binding to target cells, the P454 segment destabilizes the plasma membrane, translocates across the lipid bilayer and binds calmodulin. Trapping of the CyaA polypeptide chain by the CaM:P454 interaction in the cytosol may assist the entry of the N-terminal catalytic domain by converting the stochastic process of protein translocation into an efficient vectorial chain transfer into host cells.