Molecular recognition of lipopolysaccharide by the lantibiotic nisin

Nisin Inhibition of Gram-Negative Bacteria

Aims: This study investigates the activity of the broad-spectrum bacteriocin nisin against a large panel of Gram-negative bacterial isolates, including relevant plant, animal, and human pathogens. The aim is to generate supportive evidence towards the use/inclusion of bacteriocin-based therapeutics and open avenues for their continued development. Methods and Results: Nisin inhibitory activity was screened against a panel of 575 strains of Gram-negative bacteria, encompassing 17 genera. Nisin inhibition was observed in 309 out of 575 strains, challenging the prevailing belief that nisin lacks effectiveness against Gram-negative bacteria. The genera Acinetobacter, Helicobacter, Erwinia, and Xanthomonas exhibited particularly high nisin sensitivity. Conclusions: The findings of this study highlight the promising potential of nisin as a therapeutic agent for several key Gram-negative plant, animal, and human pathogens. These results challenge the prevailing notion that nisin is less effective or ineffective against Gram-negative pathogens when compared to Gram-positive pathogens and support future pursuits of nisin as a complementary therapy to existing antibiotics. Significance and Impact of Study: This research supports further exploration of nisin as a promising therapeutic agent for numerous human, animal, and plant health applications, offering a complementary tool for infection control in the face of multidrug-resistant bacteria.

Simple, sensitive, colorimetric detection of pyrophosphate via the analyte-triggered decomposition of metal-organic frameworks regulating their adaptive multi-color Tyndall effect

This paper describes initially the application of the Tyndall effect (TE) of metal-organic framework (MOF) materials as a colorimetric signaling strategy for the sensitive detection of pyrophosphate ion (PPi). The used MOF NH2-MIL-101(Fe) was prepared with Fe3+ ions and fluorescent ligands of 2-amino terephthalic acid (NH2-BDC). The fluorescence of NH2-BDC in MOF is quenched due to the ligand-to-metal charge transfer effect, while the NH2-MIL-101(Fe) suspension shows a strong TE. In the presence of PPi analyte, the MOFs will undergo decomposition because of the competitive binding of Fe3+ by PPi over NH2-BDC, resulting in a significant decrease in the TE signal and fluorescence restoration from the released ligands. The results demonstrate that the new method only requires a laser pointer pen (for TE creation) and a smartphone (for portable quantitative readout) to detect PPi in a linear concentration range of 1.25-800 μM, with a detection limit of ~210 nM (3σ) which is ~38 times lower than that obtained from traditional fluorescence with a spectrophotometer (linear concentration range, 50-800 µM; detection limit, 8.15 µM). Moreover, the acceptable recovery of PPi in several real samples (i.e., pond water, black tea, and human serum and urine) ranges from 97.66 to 119.15%.

Identification of a two-component regulatory system involved in antimicrobial peptide resistance in Streptococcus pneumoniae

Two-component regulatory systems (TCS) are among the most widespread mechanisms that bacteria use to sense and respond to environmental changes. In the human pathogen Streptococcus pneumoniae, a total of 13 TCS have been identified and many of them have been linked to pathogenicity. Notably, TCS01 strongly contributes to pneumococcal virulence in several infection models. However, it remains one of the least studied TCS in pneumococci and its functional role is still unclear. In this study, we demonstrate that TCS01 cooperates with a BceAB-type ABC transporter to sense and induce resistance to structurally-unrelated antimicrobial peptides of bacterial origin that all target undecaprenyl-pyrophosphate or lipid II, which are essential precursors of cell wall biosynthesis. Even though tcs01 and bceAB genes do not locate in the same gene cluster, disruption of either of them equally sensitized the bacterium to the same set of antimicrobial peptides. We show that the key function of TCS01 is to upregulate the expression of the transporter, while the latter appears the main actor in resistance. Electrophoretic mobility shift assays further demonstrated that the response regulator of TCS01 binds to the promoter region of the bceAB genes, implying a direct control of these genes. The BceAB transporter was overexpressed and purified from E. coli. After reconstitution in liposomes, it displayed substantial ATPase and GTPase activities that were stimulated by antimicrobial peptides to which it confers resistance to, revealing new functional features of a BceAB-type transporter. Altogether, this inducible defense mechanism likely contributes to the survival of the opportunistic microorganism in the human host, in which competition among commensal microorganisms is a key determinant for effective host colonization and invasive path.

Molecular and Cellular Mechanisms Influenced by Postbiotics

In recent years, commensal bacteria colonizing the human body have been recognized as important determinants of health and multiple pathologic conditions. Among the most extensively studied commensal bacteria are the gut microbiota, which perform a plethora of functions, including the synthesis of bioactive products, metabolism of dietary compounds, and immunomodulation, both through attenuation and immunostimulation. An imbalance in the microbiota population, i.e., dysbiosis, has been linked to many human pathologies, including various cancer types and neurodegenerative diseases. Targeting gut microbiota and microbiome-host interactions resulting from probiotics, prebiotics, and postbiotics is a growing opportunity for the effective treatment of various diseases. As more research is being conducted, the microbiome field is shifting from simple descriptive analysis of commensal compositions to more molecular, cellular, and functional studies. Insight into these mechanisms is of paramount importance for understanding and modulating the effects that microbiota, probiotics, and their derivatives exert on host health.

Interactions of polymyxin B with lipopolysaccharide-containing membranes

Bacterial resistance to antibiotics constantly remodels the battlefront between infections and antibiotic therapy. Polymyxin B, a cationic peptide with an anti-Gram-negative spectrum of activity is re-entering use as a last resort measure and as an adjuvant. We use fluorescence dequenching to investigate the role of the rough chemotype bacterial lipopolysaccharide from E. coli BL21 as a molecular facilitator of membrane disruption by LPS. The minimal polymyxin B/lipid ratio required for leakage onset increased from 5.9 × 10⁻⁴ to 1.9 × 10⁻⁷ in the presence of rLPS. We confirm polymyxin B activity against E. coli BL21 by the agar diffusion method and determined a MIC of 291 μg ml⁻¹. Changes in lipid membrane stability and dynamics in response to polymyxin and the role of LPS are investigated by ³¹P NMR and high resolution ³¹P MAS NMR relaxation is used to monitor selective molecular interactions between polymyxin B and rLPS within bilayer lipid membranes. We observe a strong facilitating effect from rLPS on the membrane lytic properties of polymyxin B and a specific, pyrophosphate-mediated process of molecular recognition of LPS by polymyxin B.

Polymyxin B uses bacterial LPS as docking receptor to cross the outer membrane.

Solid state NMR of membrane proteins: methods and applications

Membranes of cells are active barriers, in which membrane proteins perform essential remodelling, transport and recognition functions that are vital to cells. Membrane proteins are key regulatory components of cells and represent essential targets for the modulation of cell function and pharmacological intervention. However, novel folds, low molarity and the need for lipid membrane support present serious challenges to the characterisation of their structure and interactions. We describe the use of solid state NMR as a versatile and informative approach for membrane and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement in high resolution NMR spectra through DNP is discussed as a tool for whole cell and interaction studies.

Modifications of polysaccharide-based biomaterials under structure-property relationship for biomedical applications

Polysaccharides are well accepted biomaterials that have attracted considerable attention. Compared with other materials under research, polysaccharides show unique advantages: they are available in nature and are normally easily acquired, those acquired from nature show favorable immunogenicity, and are biodegradable and bioavailable. The bioactivity and possible applications are based on their chemical structure; however, naturally acquired polysaccharides sometimes have unwanted flaws that limit further applications. For this reason, carefully summarizing the possible modifications of polysaccharides to improve them is crucial. Structural modifications can not only provide polysaccharides with additional functional groups but also change their physicochemical properties. This review based on the structure-property relation summarizes the common chemical modifications of polysaccharides, the related bioactivity changes, possible functionalization methods, and major possible biomedical applications based on modified polysaccharides.

In-cell Solid-State NMR Studies of Antimicrobial Peptides

Antimicrobial peptides (AMPs) have attracted attention as alternatives to classic antibiotics due to their expected limited pressure on bacterial resistance mechanisms. Yet, their modes of action, in particular in vivo, remain to be elucidated. In situ atomistic-scale details of complex biomolecular assemblies is a challenging requirement for deciphering the complex modes of action of AMPs. The large diversity of molecules that modulate complex interactions limits the resolution achievable using imaging methodology. Herein, the latest advances in in-cell solid-state NMR (ssNMR) are discussed, which demonstrate the power of this non-invasive technique to provide atomic details of molecular structure and dynamics. Practical requirements for investigations of intact bacteria are discussed. An overview of recent in situ NMR investigations of the architecture and metabolism of bacteria and the effect of AMPs on various bacterial structures is presented. In-cell ssNMR revealed that the studied AMPs have a disruptive action on the molecular packing of bacterial membranes and DNA. Despite the limited number of studies, in-cell ssNMR is emerging as a powerful technique to monitor in situ the interplay between bacteria and AMPs.

EcDBS1R4, an Antimicrobial Peptide Effective against Escherichia coli with In Vitro Fusogenic Ability

Discovering antibiotic molecules able to hold the growing spread of antimicrobial resistance is one of the most urgent endeavors that public health must tackle. The case of Gram-negative bacterial pathogens is of special concern, as they are intrinsically resistant to many antibiotics, due to an outer membrane that constitutes an effective permeability barrier. Antimicrobial peptides (AMPs) have been pointed out as potential alternatives to conventional antibiotics, as their main mechanism of action is membrane disruption, arguably less prone to elicit resistance in pathogens. Here, we investigate the in vitro activity and selectivity of EcDBS1R4, a bioinspired AMP. To this purpose, we have used bacterial cells and model membrane systems mimicking both the inner and the outer membranes of Escherichia coli, and a variety of optical spectroscopic methodologies. EcDBS1R4 is effective against the Gram-negative E. coli, ineffective against the Gram-positive Staphylococcus aureus and noncytotoxic for human cells. EcDBS1R4 does not form stable pores in E. coli, as the peptide does not dissipate its membrane potential, suggesting an unusual mechanism of action. Interestingly, EcDBS1R4 promotes a hemi-fusion of vesicles mimicking the inner membrane of E. coli. This fusogenic ability of EcDBS1R4 requires the presence of phospholipids with a negative curvature and a negative charge. This finding suggests that EcDBS1R4 promotes a large lipid spatial reorganization able to reshape membrane curvature, with interesting biological implications herein discussed.

Membrane Stability in the Presence of Methacrylate Esters

Bioproduction of poly(methyl methacrylate) is a fast growing global industry that is limited by cellular toxicity of monomeric methacrylate intermediates to the producer strains. Maintaining high methacrylate concentrations during biofermentation, required by economically viable technologies, challenges bacterial membrane stability and cellular viability. Studying the stability of model lipid membranes in the presence of methacrylates offers unique molecular insights into the mechanisms of methacrylate toxicity, as well as into the fundamental structural bases of membrane assembly. We investigate the structure and stability of model membranes in the presence of high levels of methacrylate esters using solid-state nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS). Wide-line ³¹P NMR spectroscopy shows that butyl methacrylate (BMA) can be incorporated into the lipid bilayer at concentrations as high as 75 mol % without significantly disrupting membrane integrity and that lipid acyl chain composition can influence membrane tolerance and ability to accommodate BMA. Using high resolution ¹³C magic angle spinning (MAS) NMR, we show that the presence of 75 mol % BMA lowers the lipid main transition temperature by over 12 degrees, which suggests that BMA intercalates between the lipid chains, causing uncoupling of collective lipid motions that are typically dominated by chain trans-gauche isomerization. Potential uncoupling of the bilayer leaflets to accommodate a separate BMA subphase was not supported by the SAXS experiments, which showed that membrane thickness remained unchanged even at 80% BMA. Reduced X-ray scattering contrast at the polar/apolar interface suggests BMA localization in that region between the lipid molecules.

Effect of Sonication on the Properties of Flaxseed Gum Films Incorporated with Carvacrol

Carvacrol is a natural compound known to be a highly effective antibacterial; however, it is a hydrophobic molecule, which is a limitation to its use within food packaging. Flaxseed gum (FG) films containing different contents of carvacrol (C) were produced by a film-casting method with sonication. The effects of sonication power and time on the properties of the FG-C films were investigated by measuring the film thickness, mechanical properties, contact angle, opacity, water vapor permeability (WVP), water sorption isotherm, Fourier transform infrared spectroscopy(FTIR), differential scanning calorimetry (DSC), antibacterial and antioxidant activities, and microstructure. The results showed that sonication power and time had significant effects on mechanical and barrier properties, film opacity, and degradability (p < 0.05). The tensile strength (TS) and elongation at break (EB) values exhibited an obvious improvement after sonication, and FG-0.5C-6030 had the lowest TS (33.40 MPa) and EB (4.46%) values. FG-C films formed a denser structure and the contact angle was improved as a result of sonication, which improved the integration of carvacrol into the FG matrix. In terms of microstructure, sonication resulted in a homogeneous and continuous crosssection of FG-C films, and regular surface and cross-sectional images were obtained through the highest acoustic intensity and longest time treatment. The FG films incorporated with carvacrol displayed antibacterial properties against Staphylococcus aureus, Vibrio parahaemolyticus, Shewanella putrefaciens, and Pseudomonas fluorescens, as well as increased antioxidant properties, and sonication was proven to enhance both of them.

GTP Preference of d-Glycero-α-d-manno-Heptose-1-Phosphate Guanylyltransferase from Yersinia pseudotuberculosis

d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC) is the fourth enzyme synthesizing a building component of lipopolysaccharide (LPS) of Gram-negative bacteria. Since HddC is a potential new target to develop antibiotics, the analysis of the structural and functional relationship of the complex structure will lead to a better idea to design inhibitory compounds. X-ray crystallography and biochemical experiments to elucidate the guanine preference were performed based on the multiple sequence alignment. The crystal structure of HddC from Yersinia pseudotuberculosis (YPT) complexed with guanosine 5′-(β-amino)-diphosphate (GMPPN) has been determined at 1.55 Å resolution. Meanwhile, the mutants revealed their reduced guanine affinity, instead of acquiring noticeable pyrimidine affinity. The complex crystal structure revealed that GMPPN is docked in the catalytic site with the aid of Glu80 positioning on the conserved motif EXXPLGTGGA. In the HddC family, this motif is expected to recruit nucleotides through interacting with bases. The crystal structure shows that oxygen atoms of Glu80 forming two hydrogen bonds play a critical role in interaction with two nitrogen atoms of the guanine base of GMPPN. Interestingly, the binding of GMPPN induced the formation of an oxyanion hole-like conformation on the L(S/A/G)X(S/G) motif and consequently influenced on inducing a conformational shift of the region around Ser55.

Interactions between Mutant Bacterial Lipopolysaccharide (LPS-Ra) Surface Layers: Surface Vesicles, Membrane Fusion, and Effect of Ca2+and Temperature

Lipopolysaccharides (LPS) are a major component of the protective outer membrane of Gram-negative bacteria. Understanding how the solution conditions may affect LPS-containing membranes is important to optimizing the design of antibacterial agents (ABAs) which exploit electrostatic and hydrophobic interactions to disrupt the bacteria membrane. Here, interactions between surface layers of LPS (Ra mutants) in aqueous media have been studied using a surface force apparatus (SFA), exploring the effects of temperature and divalent Ca²⁺ cations. Complementary dynamic light scattering (DLS) characterization suggests that vesicle-like aggregates of diameter ∼28-80 nm are formed by LPS-Ra in aqueous media. SFA results show that LPS-Ra vesicles adsorb weakly onto mica in pure water at room temperature (RT) and the surface layers are readily squeezed out as the two surfaces approach each other. However, upon addition of calcium (Ca²⁺) cations at near physiological concentration (2.5 mM) at RT, LPS multilayers or deformed LPS liposomes on mica are observed, presumably due to bridging between LPS phosphate groups and between LPS phosphates and negatively charged mica mediated by Ca²⁺, with a hard wall repulsion at surface separation D₀ ∼ 30-40 nm. At 40 °C, which is above the LPS-Ra β-α acyl chain melting temperature (T_m = 36 °C), fusion events between the surface layers under compression could be observed, evident from δD ∼ 8-10 nm steps in the force-distance profiles attributed to LPS-bilayers being squeezed out due to enhanced fluidity of the LPS acyl-chain, with a final hard wall surface separation D₀ ∼ 8-10 nm corresponding to the thickness of a single bilayer confined between the surfaces. These unprecedented SFA results reveal intricate structural responses of LPS surface layers to temperature and Ca²⁺, with implications to our fundamental understanding of the structures and interactions of bacterial membranes.