Peptidoglycan and Teichoic Acid Levels and Alterations in Staphylococcus aureus by Cell-Wall and Whole-Cell Nuclear Magnetic Resonance

High-Sensitivity Analysis of Native Bacterial Biofilms Using Dynamic Nuclear Polarization-Enhanced Solid-State NMR

Bacterial biofilms cause persistent infections that are difficult to treat and contribute greatly to antimicrobial resistance. However, high-resolution structural information on native bacterial biofilms remain very limited. This limitation is primarily due to methodological constraints associated with analyzing complex native samples. Although solid-state NMR (ssNMR) is a promising method in this regard, its conventional applications typically suffer from sensitivity limitations, particularly for unlabeled native samples. Through the use of Dynamic Nuclear Polarization (DNP), we applied sensitivity enhanced ssNMR to characterize native Pseudomonas fluorescens colony biofilms. The increased ssNMR sensitivity by DNP enabled ultrafast structural characterization of the biofilm samples without isotope-labelling, and chemical or physical modification. We collected 1D 13 C and 15 N, and 2D 1 H- 13 C, 1 H- 15 N and 13 C- 13 C ssNMR spectra within seconds/minutes or hours, respectively which enabled us to identify biofilm components as polysaccharides, proteins, and eDNA effectively. This study represents the first application of ultrasensitive DNP ssNMR to characterize a native bacterial biofilm and expands the technical scope of ssNMR towards obtaining insights into the composition and structure of a wide array of in vitro and ex vivo biofilm applications. Such versatility should greatly boost efforts to develop structure-guided approaches for combating infections caused by biofilm-forming microbes.

High-resolution 2D solid-state NMR provides insights into nontuberculous mycobacteria

We present a high-resolution magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize nontuberculous mycobacteria (NTM). We studied two different NTM strains, Mycobacterium smegmatis, a model, non-pathogenic strain, and Mycobacterium abscessus, an emerging and important human pathogen. Hydrated NTM samples were studied at natural abundance without isotope-labelling, as whole-cells versus cell envelope isolates, and native versus fixed sample preparations. We utilized 1D13C and 2D 1H-13C ssNMR spectra and peak deconvolution to identify NTM cell-wall chemical sites. More than ∼100 distinct 13C signals were identified in the ssNMR spectra. We provide tentative assignments for ∼30 polysaccharides by using well resolved 1H/13C chemical shifts from the 2D INEPT-based 1H-13C ssNMR spectrum. The signals originating from both the flexible and rigid fractions of the whole-cell bacteria samples were selectively analyzed by utilizing either CP or INEPT based 13C ssNMR spectra. CP buildup curves provide insights into the dynamical similarity of the cell-wall components for NTM strains. Signals from peptidoglycan, arabinogalactan and mycolic acid were identified. The majority of the 13C signals were not affected by fixation of the whole cell samples. The isolated cell envelope NMR spectrum overlap with the whole-cell spectrum to a large extent, where the latter has more signals. As an orthogonal way of characterizing these bacteria, electron microscopy (EM) was used to provide spatial information. ssNMR and EM data suggest that the M. abscessus cell-wall is composed of a smaller peptidoglycan layer which is more flexible compared to M. smegmatis, which may be related to its higher pathogenicity. Here in this work, we used high-resolution 2D ssNMR first time to characterize NTM strains and identify chemical sites. These results will aid the development of structure-based approaches to combat NTM infections.

MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments

Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13C13C and heteronuclear 1H15N, 1H13C and 15N13C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples.

Insight into the structure, biosynthesis, isolation method and biological function of teichoic acid in different gram-positive microorganisms: A review

Teichoic acid (TA) is a weakly anionic polymer present in the cell walls of Gram-positive bacteria. It can be classified into wall teichoic acid (WTA) and lipoteichoic acid (LTA) based on its localization in the cell wall. The structure and biosynthetic pathway of TAs are strain-specific and have a significant role in maintaining cell wall stability. TAs have various beneficial functions, such as immunomodulatory, anticancer and antioxidant activities. However, the purity and yield of TAs are generally not high, and different isolation methods may even affect their structural integrity, which limits the research progress on the probiotic functions of TA. This paper reviews an overview of the structure and biosynthetic pathway of TAs in different strains, as well as the research progress of the isolation and purification methods of TAs. Furthermore, this review also highlights the current research status on the biological functions of TAs. Through a comprehensive understanding of this review, it is expected to pave the way for advancements in isolating and purifying high-quality TAs and, in turn, lay a foundation for contributing to the development of targeted probiotic therapies.

Tapping into the native Pseudomonas bacterial biofilm structure by high-resolution multidimensional solid-state NMR

We present a multidimensional magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize native Pseudomonas fluorescens colony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D 1H-13C ssNMR spectrum and thorough peak deconvolution at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT 13C ssNMR spectra to differentiate signals originating from the mobile and rigid fractions of the biofilm, and qualitatively determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC protein signals as a template, a biofilm forming functional amyloid from Pseudomonas. We identified several biofilm polysaccharide species such as glucose, mannan, galactose, heptose, rhamnan, fucose and N-acylated mannuronic acid by using 1H and 13C chemical shifts obtained from the 2D spectrum. To our knowledge, this study marks the first high-resolution multidimensional ssNMR characterization of a native bacterial biofilm. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.

CPMAS NMR platform for direct compositional analysis of mycobacterial cell-wall complexes and whole cells

Tuberculosis and non-tuberculosis mycobacterial infections are rising each year and often result in chronic incurable disease. Important antibiotics target cell-wall biosynthesis, yet some mycobacteria are alarmingly resistant or tolerant to currently available antibiotics. This resistance is often attributed to assumed differences in composition of the complex cell wall of different mycobacterial strains and species. However, due to the highly crosslinked and insoluble nature of mycobacterial cell walls, direct comparative determinations of cell-wall composition pose a challenge to analysis through conventional biochemical analyses. We introduce an approach to directly observe the chemical composition of mycobacterial cell walls using solid-state NMR spectroscopy. 13C CPMAS spectra are provided of individual components (peptidoglycan, arabinogalactan, and mycolic acids) and of in situ cell-wall complexes. We assigned the spectroscopic contributions of each component in the cell-wall spectrum. We uncovered a higher arabinogalactan-to-peptidoglycan ratio in the cell wall of M. abscessus, an organism noted for its antibiotic resistance, relative to M. smegmatis. Furthermore, differentiating influences of different types of cell-wall targeting antibiotics were observed in spectra of antibiotic-treated whole cells. This platform will be of value in evaluating cell-wall composition and antibiotic activity among different mycobacteria and in considering the most effective combination treatment regimens.

Tapping into the native Pseudomonas Bacterial Biofilm Structure by High-Resolution 1D and 2D MAS solid-state NMR

We present a high-resolution 1D and 2D magic-angle spinning (MAS) solid-state NMR (ssNMR) study to characterize native Pseudomonas fluorescens colony biofilms at natural abundance without isotope-labelling. By using a high-resolution INEPT-based 2D 1 H- 13 C ssNMR spectrum and thorough peak deconvolution approach at the 1D ssNMR spectra, approximately 80/134 (in 1D/2D) distinct biofilm chemical sites were identified. We compared CP and INEPT 13 C ssNMR spectra to different signals originating from the mobile and rigid fractions of the biofilm, and qualitative determined dynamical changes by comparing CP buildup behaviors. Protein and polysaccharide signals were differentiated and identified by utilizing FapC signals as a template, a biofilm forming functional amyloid from Pseudomonas . We also attempted to identify biofilm polysaccharide species by using 1 H/ 13 C chemical shifts obtained from the 2D spectrum. This study marks the first demonstration of high-resolution 2D ssNMR spectroscopy for characterizing native bacterial biofilms and expands the scope of ssNMR in studying biofilms. Our experimental pipeline can be readily applied to other in vitro biofilm model systems and natural biofilms and holds the promise of making a substantial impact on biofilm research, fostering new ideas and breakthroughs to aid in the development of strategic approaches to combat infections caused by biofilm-forming bacteria.

Detection of intact vancomycin-arginine as the active antibacterial conjugate in E. coli by whole-cell solid-state NMR

The introduction of new and improved antibacterial agents based on facile synthetic modifications of existing antibiotics represents a promising strategy to deliver urgently needed antibacterial candidates to treat multi-drug resistant bacterial infections. Using this strategy, vancomycin was transformed into a highly active agent against antibiotic-resistant Gram-negative organisms in vitro and in vivo through the addition of a single arginine to yield vancomycin-arginine (V-R). Here, we report detection of the accumulation of V-R in E. coli by whole-cell solid-state NMR using 15N-labeled V-R. 15N CPMAS NMR revealed that the conjugate remained fully amidated without loss of arginine, demonstrating that intact V-R represents the active antibacterial agent. Furthermore, C{N}REDOR NMR in whole cells with all carbons at natural abundance 13C levels exhibited the sensitivity and selectivity to detect the directly bonded 13C-15N pairs of V-R within E. coli cells. Thus, we also present an effective methodology to directly detect and evaluate active drug agents and their accumulation within bacteria without the need for potentially perturbative cell lysis and analysis protocols.

Pseudomonas aeruginosa and Staphylococcus aureus Display Differential Proteomic Responses to the Silver(I) Compound, SBC3

The urgent need to combat antibiotic resistance and develop novel antimicrobial therapies has triggered studies on novel metal-based formulations. N-heterocyclic carbene (NHC) complexes coordinate transition metals to generate a broad range of anticancer and/or antimicrobial agents, with ongoing efforts being made to enhance the lipophilicity and drug stability. The lead silver(I) acetate complex, 1,3-dibenzyl-4,5-diphenylimidazol-2-ylidene (NHC*) (SBC3), has previously demonstrated promising growth and biofilm-inhibiting properties. In this work, the responses of two structurally different bacteria to SBC3 using label-free quantitative proteomics were characterised. Multidrug-resistant Pseudomonas aeruginosa (Gram-negative) and Staphylococcus aureus (Gram-positive) are associated with cystic fibrosis lung colonisation and chronic wound infections, respectively. SBC3 increased the abundance of alginate biosynthesis, the secretion system and drug detoxification proteins in P. aeruginosa, whilst a variety of pathways, including anaerobic respiration, twitching motility and ABC transport, were decreased in abundance. This contrasted the affected pathways in S. aureus, where increased DNA replication/repair and cell redox homeostasis and decreased protein synthesis, lipoylation and glucose metabolism were observed. Increased abundance of cell wall/membrane proteins was indicative of the structural damage induced by SBC3 in both bacteria. These findings show the potential broad applications of SBC3 in treating Gram-positive and Gram-negative bacteria.

Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1 H-Detected Solid-State NMR Spectroscopy

Solid-state NMR (ssNMR) spectroscopy facilitates the non-destructive characterization of structurally heterogeneous biomolecules in their native setting, for example, comprising proteins, lipids and polysaccharides. Here we demonstrate the utility of high and ultra-high field ¹ H-detected fast MAS ssNMR spectroscopy, which exhibits increased sensitivity and spectral resolution, to further elucidate the atomic-level composition and structural arrangement of the cell wall of Schizophyllum commune, a mushroom-forming fungus from the Basidiomycota phylum. These advancements allowed us to reveal that Cu(II) ions and the antifungal peptide Cathelicidin-2 mainly bind to cell wall proteins at low concentrations while glucans are targeted at high metal ion concentrations. In addition, our data suggest the presence of polysaccharides containing N-acetyl galactosamine (GalNAc) and proteins, including the hydrophobin proteins SC3, shedding more light on the molecular make-up of cells wall as well as the positioning of the polypeptide layer. Obtaining such information may be of critical relevance for future research into fungi in material science and biomedical contexts.

Influence of Sodium Bicarbonate on Wall Teichoic Acid Synthesis and β-Lactam Sensitization in NaHCO3-Responsive and Nonresponsive Methicillin-Resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) strains pose major treatment challenges due to their innate resistance to most β-lactams under standard in vitro antimicrobial susceptibility testing conditions. A novel phenotype among MRSA, termed "NaHCO3 responsiveness," where certain strains display increased susceptibility to β-lactams in the presence of NaHCO3, has been identified among a relatively large proportion of MRSA isolates. One underlying mechanism of NaHCO3 responsiveness appears to be related to decreased expression and altered functionality of several genes and proteins involved in cell wall synthesis and maturation. Here, we studied the impact of NaHCO3 on wall teichoic acid (WTA) synthesis, a process intimately linked to peptidoglycan (PG) synthesis and functionality, in NaHCO3-responsive versus -nonresponsive MRSA isolates. NaHCO3 sensitized responsive MRSA strains to cefuroxime, a specific penicillin-binding protein 2 (PBP2)-inhibitory β-lactam known to synergize with early WTA synthesis inhibitors (e.g., ticlopidine). Combining cefuroxime with ticlopidine with or without NaHCO3 suggested that these latter two agents target the same step in WTA synthesis. Further, NaHCO3 decreased the abundance and molecular weight of WTA only in responsive strains. Additionally, NaHCO3 stimulated increased autolysis and aberrant cell division in responsive strains, two phenotypes associated with disruption of WTA synthesis. Of note, studies of key genes involved in the WTA biosynthetic pathway (e.g., tarO, tarG, dltA, and fmtA) indicated that the inhibitory impact of NaHCO3 on WTA biosynthesis in responsive strains likely occurred posttranslationally. IMPORTANCE MRSA is generally viewed as resistant to standard β-lactam antibiotics. However, a NaHCO3-responsive phenotype is observed in a substantial proportion of clinical MRSA strains in vitro, i.e., isolates which demonstrate enhanced susceptibility to standard β-lactam antibiotics (e.g., oxacillin) in the presence of NaHCO3. This phenotype correlates with increased MRSA clearance in vivo by standard β-lactam antibiotics, suggesting that patients with infections caused by such MRSA strains might be amenable to treatment with β-lactams. The mechanism(s) behind this phenotype is not fully understood but appears to involve mecA-PBP2a production and maturation axes. Our study adds significantly to this body of knowledge in terms of additional mechanistic targets of NaHCO3 in selected MRSA strains. This investigation demonstrates that NaHCO3 has direct impacts on S. aureus wall teichoic acid biosynthesis in NaHCO3-responsive MRSA. These findings provide an additional target for new agents being designed to synergistically kill MRSA using β-lactam antibiotics.

Direct Bactericidal Comparison of Metal Nanoparticles and Their Salts against S. aureus Culture by TEM and FT-IR Spectroscopy

We report the bactericidal effect of Ag and Cu NPs with different concentrations on methicillin-resistant S. aureus strain in comparison to the effect of AgNO₃ and CuCl₂ solutions, characterized by microbiological tests, TEM and Fourier-transform infrared spectroscopy. NPs were produced by nanosecond laser ablation in distilled water and characterized by scanning electron microscopy, UV-vis, energy dispersive X-ray, FT-IR spectroscopy, as well as X-ray diffraction, dynamic light scattering size and zeta-potential measurements. Microbiological tests showed antibacterial activity of NPs and metal ion-containing salts. Comparative FT-IR spectroscopy of bacteria, treated with metal NPs and salts, showed the broadening of amide I and II bands, a CH₂-related peak and its frequency decrease, indicating the increase of membrane fluidity. The main mechanisms of the antibacterial effect were proposed: Ag and Cu NPs release ions and ROS, which result in lipid peroxidation; AgNO₃ forms precipitates on the cell surface, which lead to the mechanical rupture of the membrane and subsequent possible penetration of the precipitates in the emerged damaged spots, complete destruction of the membrane and bacterial death; Cu ions from the CuCl₂ solution cause damage to phosphorus- and sulfur-containing biomolecules, which leads to disruption of intracellular biochemical processes. The theories were confirmed by FT-IR spectroscopy and TEM.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Electrostatic Interaction with the Bacterial Cell Envelope Tunes the Lytic Activity of Two Novel Peptidoglycan Hydrolases

Peptidoglycan (PG) hydrolases, due to their crucial role in the metabolism of the bacterial cell wall (CW), are increasingly being considered suitable targets for therapies, and a potent alternative to conventional antibiotics. In the light of contradictory data reported, detailed mechanism of regulation of enzymes activity based on electrostatic interactions between hydrolase molecule and bacterial CW surface remains unknown. Here, we report a comprehensive study on this phenomenon using as a model two novel PG hydrolases, SpM23_A, and SpM23_B, which although share the same bacterial host, similarities in sequence conservation, domain architecture, and structure, display surprisingly distinct net charges (in 2D electrophoresis, pI 6.8, and pI 9.7, respectively). We demonstrate a strong correlation between hydrolases surface net charge and the enzymes activity by modulating the charge of both, enzyme molecule and bacterial cell surface. Teichoic acids, anionic polymers present in the bacterial CW, are shown to be involved in the mechanism of enzymes activity regulation by the electrostatics-based interplay between charged bacterial envelope and PG hydrolases. These data serve as a hint for the future development of chimeric PG hydrolases of desired antimicrobial specificity. IMPORTANCE This study shows direct relationship between the surface charge of two recently described enzymes, SpM23_A and SpM23_B, and bacterial cell walls. We demonstrate that by (i) surface charge probing of bacterial strains collection, (ii) reduction of the net charge of the positively charged enzyme, and (iii) altering the net charge of the bacterial surface by modifying the content and composition of teichoic acids. In all cases, we observed that lytic activity and binding strength of SpM23 enzymes, are regulated by electrostatic interactions with the bacterial cell envelope and that this interaction contributes to the determination of the spectrum of susceptible bacterial species. Moreover, we revealed the regulatory role of charged cell wall components, namely, teichoic and lipoteichoic acids, over the SpM23 enzymes. We believe that our findings make an important contribution to understand the means of hydrolases activity regulation in the complex environment of the bacterial cell wall.

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.

Deuterium Solid State NMR Studies of Intact Bacteria Treated With Antimicrobial Peptides

Solid state NMR has been tremendously useful in characterizing the structure and dynamics of model membranes composed of simple lipid mixtures. Model lipid studies employing solid state NMR have included important work revealing how membrane bilayer structure and dynamics are affected by molecules such as antimicrobial peptides (AMPs). However, solid state NMR need not be applied only to model membranes, but can also be used with living, intact cells. NMR of whole cells holds promise for helping resolve some unsolved mysteries about how bacteria interact with AMPs. This mini-review will focus on recent studies using ²H NMR to study how treatment with AMPs affect membranes in intact bacteria.

Imitate to illuminate: labeling of bacterial peptidoglycan with fluorescent and bio-orthogonal stem peptide-mimicking probes

Because of its high involvement in antibiotic therapy and the emergence of drug-resistance, the chemical structure and biosynthesis of bacterial peptidoglycan (PGN) have been some of the key topics in bacteriology for several decades. Recent advances in the development of fluorescent or bio-orthogonal stem peptide-mimicking probes for PGN-labeling have rekindled the interest of chemical biologists and microbiologists in this area. The structural designs, bio-orthogonal features and flexible uses of these peptide-based probes allow directly assessing, not only the presence of PGN in different biological systems, but also specific steps in PGN biosynthesis. In this review, we summarize the design rationales, functioning mechanisms, and microbial processes/questions involved in these PGN-targeting probes. Our perspectives on the limitations and future development of these tools are also presented.

By imitating the structures of stem peptide, many fluorescent and bio-orthogonal labeling probes have been designed and used in illuminating the peptidoglycan biosynthesis processes.

Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants

Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.

Exploring the possible targeting strategies of liposomes against methicillin-resistant Staphylococcus aureus (MRSA)

Multi antibiotic-resistant bacterial infections are on the rise due to the overuse of antibiotics. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the pathogens listed under the category of serious threats where vancomycin remains the mainstay treatment despite the availability of various antibacterial agents. Recently, decreased susceptibility to vancomycin from clinical isolates of MRSA has been reported and has drawn worldwide attention as it is often difficult to overcome and leads to increased medical costs, mortality, and longer hospital stays. Development of antibiotic delivery systems is often necessary to improve bioavailability and biodistribution, in order to reduce antibiotic resistance and increase the lifespan of antibiotics. Liposome entrapment has been used as a method to allow higher drug dosing apart from reducing toxicity associated with drugs. The surface of the liposomes can also be designed and enhanced with drug-release properties, active targeting, and stealth effects to prevent recognition by the mononuclear phagocyte system, thus enhancing its circulation time. The present review aimed to highlight the possible targeting strategies of liposomes against MRSA bacteremia systemically while investigating the magnitude of this effect on the minimum inhibitory concentration level.

β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium

The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.

Tailoring NMR experiments for structural characterization of amorphous biological solids: A practical guide

Many interesting solid-state targets for biological research do not form crystalline structures; these materials include intrinsically disordered proteins, plant biopolymer composites, cell-wall polysaccharides, and soil organic matter. The absence of aligned repeating structural elements and atomic-level rigidity presents hurdles to achieving structural elucidation and obtaining functional insights. We describe strategies for adapting several solid-state NMR methods to determine the molecular structures and compositions of these amorphous biosolids. The main spectroscopic problems in studying amorphous structures by NMR are over/under-sampling of the spin signals and spectral complexity. These problems arise in part because amorphous biosolids typically contain a mix of rigid and mobile domains, making it difficult to select a single experiment or set of acquisition conditions that fairly represents all nuclear spins in a carbon-based organic sample. These issues can be addressed by running hybrid experiments, such as using direct excitation alongside cross polarization-based methods, to develop a more holistic picture of the macromolecular system. In situations of spectral crowding or overlap, the structural elucidation strategy can be further assisted by coupling 13C spins to nuclei such as 15N, filtering out portions of the spectrum, highlighting individual moieties of interest, and adding a second or third spectral dimension to an NMR experiment in order to spread out the resonances and link them pairwise through space or through bonds. We discuss practical aspects and illustrations from the recent literature for 1D experiments that use cross or direct polarization and both homo- and heteronuclear 2D and 3D solid-state NMR experiments.

Novel probiotic lactic acid bacteria isolated from indigenous fermented foods from West Sumatera, Indonesia

Background and Aim:

Probiotics play an important role in maintaining a healthy gut and consequently promote good health. This study aimed to find novel probiotic lactic acid bacteria (LAB) from indigenous fermented foods of West Sumatera, Indonesia.

Materials and Methods:

This study utilized 10 LAB previously isolated from fermented buffalo milk (dadih), fermented fish (budu), and fermented cassava (tape) which have the ability to produce gamma-aminobutyric acid. The study commenced with the screening of LAB for certain properties, such as resistance to acid and bile salts, adhesion to mucosal surface, and antagonism against enteric pathogens (Escherichia coli, Salmonella Enteritidis, and Staphylococcus aureus). The promising isolates were identified through biochemical and gram staining methods.

Results:

All isolates in this study were potential novel probiotics. They survived at a pH level of 2.5 for 3 h (55.27-98.18%) and 6 h (50.98-84.91%). Survival in bile at a concentration of 0.3% was 39.90-58.61% and the survival rate was 28.38-52.11% at a concentration of 0.5%. The inhibitory diameter ranged from 8.75 to 11.54 mm for E. coli, 7.02 to 13.42 mm for S. aureus, and 12.49 to 19.00 mm for S. Enteritidis. All the isolates (84.5-92%) exhibited the ability to adhere to mucosal surfaces. This study revealed that all the isolates were potential probiotics but N16 proved to be superior because it was viable at a pH level of 2 (84.91%) and it had a good survival rate in bile salts assay (55.07%). This isolate was identified as Lactobacillus spp., Gram-positive bacilli bacteria, and tested negative in both the catalase and oxidase tests.

Conclusion:

All the isolates in this study may be used as probiotics, with isolate N16 (Lactobacillus spp.) as the most promising novel probiotic for poultry applications based on its ability to inhibit pathogenic bacteria.

Variation in the ratio of curli and phosphoethanolamine cellulose associated with biofilm architecture and properties

Bacterial biofilms are communities of bacteria entangled in a self-produced extracellular matrix (ECM). Escherichia coli direct the assembly of two insoluble biopolymers, curli amyloid fibers, and phosphoethanolamine (pEtN) cellulose, to build remarkable biofilm architectures. Intense curiosity surrounds how bacteria harness these amyloid-polysaccharide composites to build biofilms, and how these biopolymers function to benefit bacterial communities. Defining ECM composition involving insoluble polymeric assemblies poses unique challenges to analysis and, thus, to comparing strains with quantitative ECM molecular correlates. In this work, we present results from a sum-of-the-parts ¹³ C solid-state nuclear magnetic resonance (NMR) analysis to define the curli-to-pEtN cellulose ratio in the isolated ECM of the E. coli laboratory K12 strain, AR3110. We compare and contrast the compositional analysis and comprehensive biofilm phenotypes for AR3110 and a well-studied clinical isolate, UTI89. The ECM isolated from AR3110 contains approximately twice the amount of pEtN cellulose relative to curli content as UTI89, revealing plasticity in matrix assembly principles among strains. The two parent strains and a panel of relevant gene mutants were investigated in three biofilm models, examining: (a) macrocolonies on agar, (b) pellicles at the liquid-air interface, and (c) biomass accumulation on plastic. We describe the influence of curli, cellulose, and the pEtN modification on biofilm phenotypes with power in the direct comparison of these strains. The results suggest that curli more strongly influence adhesion, while pEtN cellulose drives cohesion. Their individual and combined influence depends on both the biofilm modality (agar, pellicle, or plastic-associated) and the strain itself.

Chemical Biology Tools for Examining the Bacterial Cell Wall

Bacteria surround themselves with cell walls to maintain cell rigidity and protect against environmental insults. Here we review chemical and biochemical techniques employed to study bacterial cell wall biogenesis. Recent advances including the ability to isolate critical intermediates, metabolic approaches for probe incorporation, and isotopic labeling techniques have provided critical insight into the biochemistry of cell walls. Fundamental manuscripts that have used these techniques to discover cell wall-interacting proteins, flippases, and cell wall stoichiometry are discussed in detail. The review highlights that these powerful methods and techniques have exciting potential to identify and characterize new targets for antibiotic development.

Pulsed Third-Spin-Assisted Recoupling NMR for Obtaining Long-Range 13C-13C and 15N-13C Distance Restraints

We present a class of pulsed third-spin-assisted recoupling (P-TSAR) magic-angle-spinning solid-state NMR techniques that achieve efficient polarization transfer over long distances to provide important restraints for structure determination. These experiments utilize second-order cross terms between strong 1H-13C and 1H-15N dipolar couplings to achieve 13C-13C and 15N-13C polarization transfer, similar to the principle of continuous-wave (CW) TSAR experiments. However, in contrast to the CW-TSAR experiments, these P-TSAR experiments require much less radiofrequency (rf) energy and allow a much simpler routine for optimizing the rf field strength. We call the technique PULSAR (pulsed proton-assisted recoupling) for homonuclear spin pairs. For heteronuclear spin pairs, we improve the recently introduced PERSPIRATIONCP (proton-enhanced rotor-echo short pulse irradiation cross-polarization) experiment by shifting the pulse positions and removing the z-filters, which significantly broaden the bandwidth and increase the efficiency of polarization transfer. We demonstrate the PULSAR and PERSPIRATIONCP techniques on the model protein GB1 and found cross peaks for distances as long as 10 and 8 Å for 13C-13C and 15N-13C spin pairs, respectively. We then apply these methods to the amyloid fibrils formed by the peptide hormone glucagon and show that long-range correlation peaks are readily observed to constrain intermolecular packing in this cross-β fibril. We provide an analytical model for the PULSAR and PERSPIRATIONCP experiments to explain the measured and simulated chemical shift dependence and pulse flip angle dependence of polarization transfer. These two techniques are useful for measuring long-range distance restraints to determine the three-dimensional structures of proteins and other biological macromolecules.

Wall teichoic acids govern cationic gold nanoparticle interaction with Gram-positive bacterial cell walls

Molecular-level understanding of nanomaterial interactions with bacterial cell surfaces can facilitate design of antimicrobial and antifouling surfaces and inform assessment of potential consequences of nanomaterial release into the environment. Here, we investigate the interaction of cationic nanoparticles with the main surface components of Gram-positive bacteria: peptidoglycan and teichoic acids. We employed intact cells and isolated cell walls from wild type Bacillus subtilis and two mutant strains differing in wall teichoic acid composition to investigate interaction with gold nanoparticles functionalized with cationic, branched polyethylenimine. We quantified nanoparticle association with intact cells by flow cytometry and determined sites of interaction by solid-state 31P- and 13C-NMR spectroscopy. We find that wall teichoic acid structure and composition were important determinants for the extent of interaction with cationic gold nanoparticles. The nanoparticles interacted more with wall teichoic acids from the wild type and mutant lacking glucose in its wall teichoic acids than those from the mutant having wall teichoic acids lacking alanine and exhibiting more restricted molecular motion. Our experimental evidence supports the interpretation that electrostatic forces contributed to nanoparticle-cell interactions and that the accessibility of negatively charged moieties in teichoic acid chains influences the degree of interaction. The approaches employed in this study can be applied to engineered nanomaterials differing in core composition, shape, or surface functional groups as well as to other types of bacteria to elucidate the influence of nanoparticle and cell surface properties on interactions with Gram-positive bacteria.

Phosphoglycerol-type wall and lipoteichoic acids are enantiomeric polymers differentiated by the stereospecific glycerophosphodiesterase GlpQ

The cell envelope of Gram-positive bacteria generally comprises two types of polyanionic polymers linked to either peptidoglycan (wall teichoic acids; WTA) or to membrane glycolipids (lipoteichoic acids; LTA). In some bacteria, including Bacillus subtilis strain 168, both WTA and LTA are glycerolphosphate polymers yet are synthesized through different pathways and have distinct but incompletely understood morphogenetic functions during cell elongation and division. We show here that the exolytic sn-glycerol-3-phosphodiesterase GlpQ can discriminate between B. subtilis WTA and LTA. GlpQ completely degraded unsubstituted WTA, which lacks substituents at the glycerol residues, by sequentially removing glycerolphosphates from the free end of the polymer up to the peptidoglycan linker. In contrast, GlpQ could not degrade unsubstituted LTA unless it was partially precleaved, allowing access of GlpQ to the other end of the polymer, which, in the intact molecule, is protected by a connection to the lipid anchor. Differences in stereochemistry between WTA and LTA have been suggested previously on the basis of differences in their biosynthetic precursors and chemical degradation products. The differential cleavage of WTA and LTA by GlpQ reported here represents the first direct evidence that they are enantiomeric polymers: WTA is made of sn-glycerol-3-phosphate, and LTA is made of sn-glycerol-1-phosphate. Their distinct stereochemistries reflect the dissimilar physiological and immunogenic properties of WTA and LTA. It also enables differential degradation of the two polymers within the same envelope compartment in vivo, particularly under phosphate-limiting conditions, when B. subtilis specifically degrades WTA and replaces it with phosphate-free teichuronic acids.

Constructing and deconstructing the bacterial cell wall

The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.

Carbon compositional analysis of hydrogel contact lenses by solid-state NMR spectroscopy

Contact lenses are worn by over 140 million people each year and tremendous research and development efforts contribute to the identification and selection of hydrogel components and production protocols to yield lenses optimized for chemical and physiological properties, eye health and comfort. The final molecular composition and extent of incorporation of different components in contact lenses is routinely estimated after lens production through the analysis of the soluble components that were not included in the lens, i.e. remaining starting materials. Examination of composition in the actual intact materials is always valued and can reveal details that are missed by only examining the non-incorporated components, for example identifying chemical changes to components in lenses during the production process. Solid-state nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for the direct compositional analysis of insoluble and heterogeneous materials and is also uniquely suited to determining parameters of architecture in contact lenses. We utilized ¹³C cross-polarization magic angle spinning (CPMAS) NMR to examine and compare the carbon composition of soft contact lenses. ¹³C NMR spectra of individual polymer components enabled the determination of the approximate molecular carbon contributions of major lens components. Comparisons of the conventional etafilcon A hydrogel (1 Day Acuvue MOIST) lenses and silicone hydrogel lenses (Acuvue Oasys, Dailies Total 1, Clariti 1 Day, Biofinity, and Pure Vision) revealed major spectral differences, with considerable variation even among different silicone hydrogel lenses. The solid-state NMR approach provides a direct spectral reporting of carbon types in the hydrogel lens itself. This approach represents a valuable complementary analysis to benefit contact lens research and development and could be extended to isotopically labeled hydrogel lenses to map proximities and architecture between hydrogel components.

A Dual-Function Antibiotic-Transporter Conjugate Exhibits Superior Activity in Sterilizing MRSA Biofilms and Killing Persister Cells

New strategies are urgently needed to target MRSA, a major global health problem and the leading cause of mortality from antibiotic-resistant infections in many countries. Here, we report a general approach to this problem exemplified by the design and synthesis of a vancomycin-d-octaarginine conjugate (V-r8) and investigation of its efficacy in addressing antibiotic-insensitive bacterial populations. V-r8 eradicated MRSA biofilm and persister cells in vitro, outperforming vancomycin by orders of magnitude. It also eliminated 97% of biofilm-associated MRSA in a murine wound infection model and displayed no acute dermal toxicity. This new dual-function conjugate displays enhanced cellular accumulation and membrane perturbation as compared to vancomycin. Based on its rapid and potent activity against biofilm and persister cells, V-r8 is a promising agent against clinical MRSA infections.