Dismantling the bacterial glycocalyx: Chemical tools to probe, perturb, and image bacterial glycans

Chemical biology tools to probe bacterial glycans

Bacterial cells are covered by a complex carbohydrate coat of armor that allows bacteria to thrive in a range of environments. As a testament to the importance of bacterial glycans, effective and heavily utilized antibiotics including penicillin and vancomycin target and disrupt the bacterial glycocalyx. Despite their importance, the study of bacterial glycans lags far behind their eukaryotic counterparts. Bacterial cells use a large palette of monosaccharides to craft glycans, leading to molecules that are significantly more complex than eukaryotic glycans and that are refractory to study. Fortunately, chemical tools designed to probe bacterial glycans have yielded insights into these molecules, their structures, their biosynthesis, and their functions.

Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology

With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.

Advances in glycoside and oligosaccharide synthesis

The structural complexity of glycans poses a serious challenge in the chemical synthesis of glycosides, oligosaccharides and glycoconjugates. Glycan complexity, determined by composition, connectivity, and configuration far exceeds what nature achieves with nucleic acids and proteins. Consequently, glycoside synthesis ranks among the most complex tasks in organic synthesis, despite involving only a simple type of bond-forming reaction. Here, we introduce the fundamental principles of glycoside bond formation and summarize recent advances in glycoside bond formation and oligosaccharide synthesis.

Thioglycosides Act as Metabolic Inhibitors of Bacterial Glycan Biosynthesis

Glycans that coat the surface of bacteria are compelling antibiotic targets because they contain distinct monosaccharides that are linked to pathogenesis and are absent in human cells. Disrupting glycan biosynthesis presents a path to inhibiting the ability of a bacterium to infect the host. We previously demonstrated that O-glycosides act as metabolic inhibitors and disrupt bacterial glycan biosynthesis. Inspired by a recent study which showed that thioglycosides (S-glycosides) are 10 times more effective than O-glycosides at inhibiting glycan biosynthesis in mammalian cells, we crafted a panel of S-glycosides based on rare bacterial monosaccharides. The novel thioglycosides altered glycan biosynthesis and fitness in pathogenic bacteria but had no notable effect on glycosylation or growth in beneficial bacteria or mammalian cells. In contrast to findings in mammalian cells, S-glycosides and O-glycosides exhibited comparable potency in bacteria. However, S-glycosides exhibited enhanced selectivity relative to O-glycosides. These novel metabolic inhibitors will allow selective perturbation of the bacterial glycocalyx for functional studies and set the stage to expand our antibiotic arsenal.

Chemoenzymatic Preparation of a Campylobacter jejuni Lipid-Linked Heptasaccharide on an Azide-Linked Polyisoprenoid

Complex poly- and oligosaccharides on the surface of bacteria provide a unique fingerprint to different strains of pathogenic and symbiotic microbes that could be exploited for therapeutics or sensors selective for specific glycans. To discover reagents that can selectively interact with specific bacterial glycans, a system for both the chemoenzymatic preparation and immobilization of these materials would be ideal. Bacterial glycans are typically synthesized in nature on the C55 polyisoprenoid bactoprenyl (or undecaprenyl) phosphate. However, this long-chain isoprenoid can be difficult to work with in vitro. Here, we describe the addition of a chemically functional benzylazide tag to polyisoprenoids. We have found that both the organic-soluble and water-soluble benzylazide isoprenoid can serve as a substrate for the well-characterized system responsible for Campylobacter jejuni N-linked heptasaccharide assembly. Using the organic-soluble analogue, we demonstrate the use of an N-acetyl-glucosamine epimerase that can be used to lower the cost of glycan assembly, and using the water-soluble analogue, we demonstrate the immobilization of the C. jejuni heptasaccharide on magnetic beads. These conjugated beads are then shown to interact with soybean agglutinin, a lectin known to interact with N-acetyl-galactosamine in the C. jejuni heptasaccharide. The methods provided could be used for a wide variety of applications including the discovery of new glycan-interacting partners.

Chemical tools to study bacterial glycans: a tale from discovery of glycoproteins to disruption of their function

Bacteria coat themselves with a dense array of cell envelope glycans that enhance bacterial fitness and promote survival. Despite the importance of bacterial glycans, their systematic study and perturbation remains challenging. Chemical tools have made important inroads toward understanding and altering bacterial glycans. This review describes how pioneering discoveries from Prof. Carolyn Bertozzi's laboratory inspired our laboratory to develop sugar probes to facilitate the study of bacterial glycans. As described below, we used metabolic glycan labelling to install bioorthogonal reporters into bacterial glycans, ultimately permitting the discovery of a protein glycosylation system, the identification of glycosylation genes, and the development of metabolic glycan inhibitors. Our results have provided an approach to screen bacterial glycans and gain insight into their function, even in the absence of detailed structural information.

Metabolic glycoengineering - exploring glycosylation with bioorthogonal chemistry

Glycans are involved in numerous biological recognition events. Being secondary gene products, their labeling by genetic methods - comparable to GFP labeling of proteins - is not possible. To overcome this limitation, metabolic glycoengineering (MGE, also known as metabolic oligosaccharide engineering, MOE) has been developed. In this approach, cells or organisms are treated with synthetic carbohydrate derivatives that are modified with a chemical reporter group. In the cytosol, the compounds are metabolized and incorporated into newly synthesized glycoconjugates. Subsequently, the reporter groups can be further derivatized in a bioorthogonal ligation reaction. In this way, glycans can be visualized or isolated. Furthermore, diverse targeting strategies have been developed to direct drugs, nanoparticles, or whole cells to a desired location. This review summarizes research in the field of MGE carried out in recent years. After an introduction to the bioorthogonal ligation reactions that have been used in in connection with MGE, an overview on carbohydrate derivatives for MGE is given. The last part of the review focuses on the many applications of MGE starting from mammalian cells to experiments with animals and other organisms.

Glycoconjugate vaccines against antimicrobial resistant pathogens

INTRODUCTION

Antimicrobial resistance (AMR) is responsible for the death of millions worldwide and stands as a major threat to our healthcare systems, which are heavily reliant on antibiotics to fight bacterial infections. The development of vaccines against the main pathogens involved is urgently required as prevention remains essential against the rise of AMR.

AREAS COVERED

A systematic research review was conducted on MEDLINE database focusing on the six AMR pathogens defined as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli), which are considered critical or high priority pathogens by the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC). The analysis was intersecated with the terms carbohydrate, glycoconjugate, bioconjugate, glyconanoparticle, and multiple presenting antigen system vaccines.

EXPERT OPINION

Glycoconjugate vaccines have been successful in preventing meningitis and pneumoniae, and there are high expectations that they will play a key role in fighting AMR. We herein discuss the recent technological, preclinical, and clinical advances, as well as the challenges associated with the development of carbohydrate-based vaccines against leading AMR bacteria, with focus on the ESKAPE pathogens. The need of innovative clinical and regulatory approaches to tackle these targets is also highlighted.

Termination of Poly-N-acetylglucosamine (PNAG) Polymerization with N-Acetylglucosamine Analogues

Bacteria require polysaccharides for structure, survival, and virulence. Despite their central role in microbiology, few tools are available to manipulate their production. In E. coli, the glycosyltransferase complex PgaCD produces poly-N-acetylglucosamine (PNAG), an extracellular matrix polysaccharide required for biofilm formation. We report that C6-substituted (H, F, N₃, SH, NH₂) UDP-GlcNAc substrate analogues are inhibitors of PgaCD. In vitro, the inhibitors cause PNAG chain termination, consistent with the mechanism of PNAG polymerization from the nonreducing terminus. In vivo, expression of the GlcNAc-1-kinase NahK in E. coli provided a non-native GlcNAc salvage pathway that produced the UDP-GlcNAc analogue inhibitors in situ. The 6-fluoro and 6-deoxy derivatives were potent inhibitors of biofilm formation in the transformed strain, providing a tool to manipulate this key exopolysaccharide. Characterization of the UDP-GlcNAc pool and quantification of PNAG generation support PNAG termination as the primary in vivo mechanism of biofilm inhibition by 6-fluoro UDP-GlcNAc.

Expanding the Substrate Scope of a Bacterial Nucleotidyltransferase via Allosteric Mutations

Bacterial glycoconjugates, such as cell surface polysaccharides and glycoproteins, play important roles in cellular interactions and survival. Enzymes called nucleotidyltransferases use sugar-1-phosphates and nucleoside triphosphates (NTPs) to produce nucleoside diphosphate sugars (NDP-sugars), which serve as building blocks for most glycoconjugates. Research spanning several decades has shown that some bacterial nucleotidyltransferases have broad substrate tolerance and can be exploited to produce a variety of NDP-sugars in vitro. While these enzymes are known to be allosterically regulated by NDP-sugars and their fragments, much work has focused on the effect of active site mutations alone. Here, we show that rational mutations in the allosteric site of the nucleotidyltransferase RmlA lead to expanded substrate tolerance and improvements in catalytic activity that can be explained by subtle changes in quaternary structure and interactions with ligands. These observations will help inform future studies on the directed biosynthesis of diverse bacterial NDP-sugars and downstream glycoconjugates.

Selective Exoenzymatic Labeling of Lipooligosaccharides of Neisseria gonorrhoeae with α2,6-Sialoside Analogues

The interactions between bacteria and their host often rely on recognition processes that involve host or bacterial glycans. Glycoengineering techniques make it possible to modify and study the glycans on the host's eukaryotic cells, but only a few are available for the study of bacterial glycans. Here, we have adapted selective exoenzymatic labeling (SEEL), a chemical reporter strategy, to label the lipooligosaccharides of the bacterial pathogen Neisseria gonorrhoeae, using the recombinant glycosyltransferase ST6Gal1, and three synthetic CMP-sialic acid derivatives. We show that SEEL treatment does not affect cell viability and can introduce an α2,6-linked sialic acid with a reporter group on the lipooligosaccharides by Western blot, flow cytometry and fluorescent microscopy. This new bacterial glycoengineering technique allows for the precise modification, here with α2,6-sialoside derivatives, and direct detection of specific surface glycans on live bacteria, which will aid in further unravelling the precise biological functions of bacterial glycans.

Amyloid-Mediated Remineralization in Pit and Fissure for Caries Preventive Therapy

The pits and fissures of teeth have high caries susceptibility, and sealing these areas is considered as an effective method to prevent caries. However, long-term caries prophylaxis cannot be maintained because of the negative effects derived from the technical sensitivity and disadvantages of sealing materials. Herein, a new strategy is proposed to occlude fossae by amyloid-mediated biomimetic remineralization. In contrast to conventional inward blocking from the outside of fossae, amyloid-mediated biomimetic mineralization delivers an amyloid-like protein nanofilm into the deepest zone of the fossae and induces the formation of remineralized enamel inside. Such assembly from lysozyme conjugated with poly (ethylene glycol) enriches the interface with strongly bonded ionsand directs in situ nucleation to achieve enamel epitaxial growth. Not only is the structure of the enamel-like crystalline hydroxyapatite layer but also its mechanical stability is similar to that of natural enamel. Furthermore, the layer shows good biocompatibility and antibacterial properties. On the basis of the findings, it is demonstrated that amyloid-like protein aggregation may provide an enamel remineralization strategy to modify the current clinically available methods of pit and fissure sealing and shows great promise in preventing caries.

Development of a GalNAc-Tyrosine-Specific Monoclonal Antibody and Detection of Tyrosine O-GalNAcylation in Numerous Human Tissues and Cell Lines

Glycosylation is a vital post-translational modification involved in a range of biological processes including protein folding, signaling, and cell-cell interactions. In 2011, a new type of O-linked glycosylation was discovered, wherein the side-chain oxygen of tyrosine is modified with a GalNAc residue (GalNAc-Tyr). At present, very little is known about GalNAc-Tyr prevalence, function, or biosynthesis. Herein, we describe the design and synthesis of a GalNAc-Tyr-derived hapten and its use in generating a GalNAc-Tyr selective monoclonal antibody. The antibody, G10C, has an unusually high affinity (app KD = 100 pM) and excellent selectivity for GalNAc-Tyr. We also obtained a crystal structure of the G10C Fab region in complex with 4-nitrophenyl-N-acetyl-α-d-galactosaminide (a small molecule mimic of GalNAc-Tyr) providing insights into the structural basis for high affinity and selectivity. Using this antibody, we discovered that GalNAc-Tyr is widely expressed in most human tissues, indicating that it is a ubiquitous and underappreciated post-translational modification. Localization to specific cell types and organ substructures within those tissues indicates that GalNAc-Tyr is likely regulated in a cell-specific manner. GalNAc-Tyr was also observed in a variety of cell lines and primary cells but was only present on the external cell surface in certain cancer cell lines, suggesting that GalNAc-Tyr localization may be altered in cancer cells. Collectively, the results shed new light on this under-studied form of glycosylation and provide access to new tools that will enable expanded biochemical and clinical investigations.

HP0953 - hypothetical virulence factor overexpresion and localization during Helicobacter pylori infection of gastric epithelium

BACKGROUND

The high prevalence and persistence of Helicobacter pylori (H. pylori) infection, as well as the diversity of pathologies related to it, suggest that the virulence factors used by this microorganism are varied. Moreover, as its proteome contains 340 hypothetical proteins, it is important to investigate them to completely understand the mechanisms of its virulence and survival. We have previously reported that the hypothetical protein HP0953 is overexpressed during the first hours of adhesion to inert surfaces, under stress conditions, suggesting its role in the environmental survival of this bacterium and perhaps as a virulence factor.

AIM

To investigate the expression and localization of HP0953 during adhesion to an inert surface and against gastric (AGS) cells.

METHODS

Expression analysis was performed for HP0953 during H. pylori adhesion. HP0953 expression at 0, 3, 12, 24, and 48 h was evaluated and compared using the Kruskal-Wallis equality-of-populations rank test. Recombinant protein was produced and used to obtain polyclonal antibodies for immunolocalization. Immunogold technique was performed on bacterial sections during adherence to inert surfaces and AGS cells, which was analyzed by transmission electron microscopy. HP0953 protein sequence was analyzed to predict the presence of a signal peptide and transmembrane helices, both provided by the ExPASy platform, and using the GLYCOPP platform for glycosylation sites. Different programs, via, I-TASSER, RaptorX, and HHalign-Kbest, were used to perform three-dimensional modeling.

RESULTS

HP0953 exhibited its maximum expression at 12 h of infection in gastric epithelium cells. Immunogold technique revealed HP0953 localization in the cytoplasm and accumulation in some peripheral areas of the bacterial body, with greater expression when it is close to AGS cells. Bioinformatics analysis revealed the presence of a signal peptide that interacts with the transmembrane region and then allows the release of the protein to the external environment. The programs also showed a similarity with the Tip-alpha protein of H. pylori. Tip-alpha is an exotoxin that penetrates cells and induces tumor necrosis factor alpha production, and HP0953 could have a similar function as posttranslational modification sites were found; modifications in turn require enzymes located in eukaryotic cells. Thus, to be functional, HP0953 may necessarily need to be translocated inside the cell where it can trigger different mechanisms producing cellular damage.

CONCLUSION

The location of HP0953 around infected cells, the probable posttranslational modifications, and its similarity to an exotoxin suggest that this protein is a virulence factor.

A De Novo Route to 3,6-Dideoxy Sugars

We report the de novo asymmetric synthesis of the 3,6-dideoxy sugars abequose, paratose, and tyvelose from 2-acetylfuran. Conversion of this readily available ketone to a pyranone derivative was followed by transformation to either an α- or β-glycoside via diasteroselective acylation. Michael addition at C2 controlled primarily by the C1 configuration in the glycoside produced 3,6-dideoxy-4-keto sugars, which could be reduced and converted to either fully deprotected monosaccharides or to immediate precursors of glycosyl donors.

Synthesis and Application of Rare Deoxy Amino l-Sugar Analogues to Probe Glycans in Pathogenic Bacteria

Bacterial cell envelope glycans are compelling antibiotic targets as they are critical for strain fitness and pathogenesis yet are virtually absent from human cells. However, systematic study and perturbation of bacterial glycans remains challenging due to their utilization of rare deoxy amino l-sugars, which impede traditional glycan analysis and are not readily available from natural sources. The development of chemical tools to study bacterial glycans is a crucial step toward understanding and altering these biomolecules. Here we report an expedient methodology to access azide-containing analogues of a variety of unusual deoxy amino l-sugars starting from readily available l-rhamnose and l-fucose. Azide-containing l-sugar analogues facilitated metabolic profiling of bacterial glycans in a range of Gram-negative bacteria and revealed differential utilization of l-sugars in symbiotic versus pathogenic bacteria. Further application of these probes will refine our knowledge of the glycan repertoire in diverse bacteria and aid in the design of novel antibiotics.

A ratiometric fluorescent probe for sensing hypochlorite in physiological saline, bovine serum albumin and fetal bovine/calf serum

HClO/ClO^-, as one of important reactive oxygen species, is a highly reactive unavoidable by-product generated from normal cell metabolism. In recent years, efficient method for detectiing HClO/ClO^- is of great important to research its pathological or physiological function in bio-systems. In this work, we have constructed a fluorescent probe (P-Hc) with ratiometric signal for sensing HClO/ClO^- in aqueous solution, physiological saline and different serums based on 2-(benzo[d]thiazol-2-yl)phenol dye. The structure of P-Hc was characterized by NMR and HRMS spectrum. The sensing mechanism has also been verified by ¹H NMR spectrum. The P-Hc displays good sensitivity and selectivity for HClO/ClO^- with a limit of detection (LOD) of 2.03 × 10^-6 M. Furthermore, P-Hc has been applied for sensing HClO/ClO^- in physiological saline and different serums. Thus, P-Hc may provide a novel method for ratiometric fluorescent sensing HClO/ClO^- in bio-samples.

Chemical Reporters for Bacterial Glycans: Development and Applications

Bacteria possess an extraordinary repertoire of cell envelope glycans that have critical physiological functions. Pathogenic bacteria have glycans that are essential for growth and virulence but are absent from humans, making them high-priority targets for antibiotic, vaccine, and diagnostic development. The advent of metabolic labeling with bioorthogonal chemical reporters and small-molecule fluorescent reporters has enabled the investigation and targeting of specific bacterial glycans in their native environments. These tools have opened the door to imaging glycan dynamics, assaying and inhibiting glycan biosynthesis, profiling glycoproteins and glycan-binding proteins, and targeting pathogens with diagnostic and therapeutic payload. These capabilities have been wielded in diverse commensal and pathogenic Gram-positive, Gram-negative, and mycobacterial species─including within live host organisms. Here, we review the development and applications of chemical reporters for bacterial glycans, including peptidoglycan, lipopolysaccharide, glycoproteins, teichoic acids, and capsular polysaccharides, as well as mycobacterial glycans, including trehalose glycolipids and arabinan-containing glycoconjugates. We cover in detail how bacteria-targeting chemical reporters are designed, synthesized, and evaluated, how they operate from a mechanistic standpoint, and how this information informs their judicious and innovative application. We also provide a perspective on the current state and future directions of the field, underscoring the need for interdisciplinary teams to create novel tools and extend existing tools to support fundamental and translational research on bacterial glycans.

Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides

Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.