Glycan-mediated molecular interactions in bacterial pathogenesis

New insights in amino sugar metabolism by the gut microbiome

Gut microorganisms inhabiting the intestinal tract play key roles in host's health and disease. A properly functioning gut microbiome requires the availability of adequate carbon, nitrogen and energy sources. One of the main sources of energy for intestinal bacteria are glycans, of which amino sugars are important components. Amino sugars are a class of carbohydrates in which one or more hydroxyl groups are substituted with amino groups. However, bacterial utilization of amino sugars and their impact on the gut microbiome and host health have not been thoroughly assessed. In this review, we summarize the latest discoveries about amino sugar metabolism by gut microbes, paying particular attention to the metabolism of N-acetyl-galactosamine (GalNAc), one of the most abundant amino sugars in the intestine, and its potential implications for microbial functionality and host health.

Protein glycopatterns for natural regulation of microbiota in lung adenocarcinoma

Despite medical advancements, lung cancer remains a leading cause of mortality, necessitating a deeper understanding. Recent studies show that protein glycopatterns and lung microbiome are crucial in lung cancer development, but their relationship in adenocarcinoma remains unexplored. Therefore, this study evaluated protein glycopatterns and microbial changes between lung adenocarcinoma (n = 70) and paracancerous tissues (n = 70) through lectin microarrays and 16S rDNA sequencing. Further, we explored the impact of protein glycopatterns against a decreased abundant microbiota using extracted glycoproteins reflecting high expression protein glycopatterns observed in lung adenocarcinoma tissues. The results demonstrated a significant up-regulation of protein glycopatterns in tumor tissues, including WGA binding to multivalent Sia/(GlcNAc)n (P = 0.0078) and Jacalin binding to T/Tn antigens (P = 0.0313). Meanwhile, two bacterial species of the genus Sphingomonas showed a significant decrease (P < 0.01) in adenocarcinoma as compared to paracancerous tissue. Interestingly, adhesion assay results showed glycoproteins (25-100 μg/ml) with multivalent Sia and (GlcNAc)n structures extracted by WGA-magnetic particle conjugates significantly reduce (P < 0.0001) Sphingomonas mucosissima adhesion and toxicity to lung cancer cells (A-549). The findings indicated that protein glycopatterns could inhibit cancer-instigating oncomicrobes to intercept cancer progression, offering insights into molecular mechanisms driving disease progression and aiding to develop new treatment strategies.

EASyMap-Guided Stepwise One-Pot Multienzyme (StOPMe) Synthesis and Multiplex Assays Identify Functional Tetraose-Core-Human Milk Oligosaccharides

Carbohydrates are biologically and medicinally important molecules that are attracting growing attention to their synthesis and applications. Unlike the biosynthetic processes for nucleic acids and proteins, carbohydrate biosynthesis is not template-driven, more challenging, and often leads to product variations. In lieu of templates for carbohydrate biosynthesis, we describe herein a new concept of designing enzyme assembly synthetic maps (EASyMaps) as blueprints to guide glycosyltransferase-dependent stepwise one-pot multienzyme (StOPMe) synthesis to systematically access structurally diverse carbohydrates in a target-oriented manner. The strategy is demonstrated for the construction of a comprehensive library of tetraose-core-containing human milk oligosaccharides (HMOs) presenting diverse functional important glycan epitopes shared by more complex HMOs. The tetraose-core-HMOs are attractive candidates for large-scale production and for the development of HMO-based nutraceuticals. To achieve the preparative-scale synthesis of targets containing a Neu5Acα2-6GlcNAc component, a human α2-6-sialyltransferase hST6GALNAC5 is successfully expressed in E. coli. Neoglycoproteins with controlled glycan valencies are prepared and immobilized on fluorescent magnetic beads. Multiplex bead assays reveal ligands of glycan-binding proteins from plants, influenza viruses, human, and bacteria, identifying promising HMO targets for functional applications. The concept of designing EASyMaps as blueprints to guide StOPMe synthesis in a systematic target-oriented manner is broadly applicable beyond the synthesis of HMOs. The efficient StOPMe process is suitable for the large-scale production of complex carbohydrates and can be potentially adapted for automation.

Decoding Sugars: Mass Spectrometric Advances in the Analysis of the Sugar Alphabet

Monosaccharides play a central role in metabolic networks and in the biosynthesis of glycomolecules, which perform essential functions across all domains of life. Thus, identifying and quantifying these building blocks is crucial in both research and industry. Routine methods have been established to facilitate the analysis of common monosaccharides. However, despite the presence of common metabolites, most organisms utilize distinct sets of monosaccharides and derivatives. These molecules therefore display a large diversity, potentially numbering in the hundreds or thousands, with many still unknown. This complexity presents significant challenges in the study of glycomolecules, particularly in microbes, including pathogens and those with the potential to serve as novel model organisms. This review discusses mass spectrometric techniques for the isomer-sensitive analysis of monosaccharides, their derivatives, and activated forms. Although mass spectrometry allows for untargeted analysis and sensitive detection in complex matrices, the presence of stereoisomers and extensive modifications necessitates the integration of advanced chromatographic, electrophoretic, ion mobility, or ion spectroscopic methods. Furthermore, stable-isotope incorporation studies are critical in elucidating biosynthetic routes in novel organisms.

Carbohydrate Structure Database: current state and recent developments

Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D modeler, NMR simulator, NMR-based structure predictor, and other tools.

Host-intestinal microbiota interactions in Edwardsiella piscicida-induced lethal enteritis in big-belly seahorses: Novel insights into the role of Carbohydrate-Active enzymes and host transcriptional responses

Edwardsiella piscicida-induced lethal enteritis is a major threat to the sustainable development of seahorse aquaculture. The roles of Carbohydrate-Active enzymes (CAZymes) in interactions between the pathogen and the host are poorly understood. In this study, we found that 22 key CAZymes encoded by E. piscicida might involve in the coordination of five key stages of infection. Specifically, during the motility, adherence, and invasion stages, 10 CAZymes, including CE4, PL8, and CBM48, may significantly increase the activities of Lipid metabolism-associated pathways of the intestinal microbiota (P < 0.01), facilitating pathogen invasion of the host intestinal epithelium. During the replication stage, 11 CAZymes, including GH20, GT4, and GH3, may significantly increase activities of pathways associated with Carbohydrate metabolism (P < 0.01) to promote replication and proliferation of the pathogen. And for avoiding host defenses, GH2 and GH1 may enhance activities of both Carbohydrate and Amino acid metabolic pathways (P < 0.01), facilitating infection and immune evasion. Conjoint analysis showed that E. piscicida might mainly rely on Carbohydrate metabolism for infection, while the host might activate Amino acid metabolic pathways for self-defense. In addition, expressions of 10 key genes, Aldh9a1b, Aoc1, Tpi1b, PCK1, Ldha, Me1, Gla, Cel.2, Ugdh, and Mao, were significantly altered (P < 0.01) and may be used for characterizing host responses to E. piscicida infection. Activities of both Glycolysis/Gluconeogenesis and Tryptophan metabolism were found oppositely changed (P < 0.01) between pathogen and host, respectively, representing the primary focuses of the competition. Overall, this study provides new insights into E. piscicida-mediated intestinal enteritis in fish for the first time from the perspective of CAZymes, as well as a theoretical reference for the prevention and control of these diseases in the aquaculture of seahorses and other fish.

Injectable immunoregulatory hydrogels sequentially drive phenotypic polarization of macrophages for infected wound healing

Regulating macrophage phenotypes to reconcile the conflict between bacterial suppression and tissue regeneration is ideal for treating infectious skin wounds. Here, an injectable immunoregulatory hydrogel (SrmE20) that sequentially drives macrophage phenotypic polarization (M0 to M1, then to M2) was constructed by integrating anti-inflammatory components and proinflammatory solvents. In vitro experiments demonstrated that the proinflammatory solvent ethanol stabilized the hydrogel structure, maintained the phenolic hydroxyl group activity, and achieved macrophages' proinflammatory transition (M0 to M1) to enhance antibacterial effects. With ethanol depletion, the hydrogel's cations and phenolic hydroxyl groups synergistically regulated macrophages' anti-inflammatory transition (M1 to M2) to initiate regeneration. In the anti-contraction full-thickness wound model with infection, this hydrogel effectively eliminated bacteria and even achieved anti-inflammatory M2 macrophage accumulation at three days post-surgery, accelerated angiogenesis and collagen deposition. By sequentially driving macrophage phenotypic polarization, this injectable immunoregulatory hydrogel will bring new guidance for the care and treatment of infected wounds.

Smart self-defensive coatings with bacteria-triggered antimicrobial response for medical devices

Bacterial colonization and biofilm formation on medical devices represent one of the most urgent and critical challenges in modern healthcare. These issues not only pose serious threats to patient health by increasing the risk of infections but also exert a considerable economic burden on national healthcare systems due to prolonged hospital stays and additional treatments. To address this challenge, there is a need for smart, customized biomaterials for medical device fabrication, particularly through the development of surface modification strategies that prevent bacterial adhesion and the growth of mature biofilms. This review explores three bioinspired approaches through which antibacterial and antiadhesive coatings can be engineered to exhibit smart, stimuli-responsive features. This responsiveness is greatly valuable as it provides the coatings with a controlled, on-demand antibacterial response that is activated only in the presence of bacteria, functioning as self-defensive coatings. Such coatings can be designed to release antibacterial agents or change their surface properties/conformation in response to specific stimuli, like changes in pH, temperature, or the presence of bacterial enzymes. This targeted approach minimizes the risk of developing antibiotic resistance and reduces the need for continuous, high-dose antibacterial treatments, thereby preserving the natural microbiome and further reducing healthcare costs. The final part of the review reports a critical analysis highlighting the potential improvements and future evolutions regarding antimicrobial self-defensive coatings and their validation.

Comprehensive characterization of bacterial glycoconjugate vaccines by liquid chromatography - mass spectrometry

Bacterial pathogens can cause a broad range of infections with detrimental effects on health. Vaccine development is essential as multi-drug resistance in bacterial infections is a rising concern. Recombinantly produced proteins carrying O-antigen glycosylation are promising glycoconjugate vaccine candidates to prevent bacterial infections. However, methods for their comprehensive structural characterization are lacking. Here, we present a bottom-up approach for their site-specific characterization, detecting N-glycopeptides by nano reversed-phase liquid chromatography-mass spectrometry (RP-LC-MS). Glycopeptide analyses revealed information on partial site-occupancy and site-specific glycosylation heterogeneity and helped corroborate the polysaccharide structures and their modifications. Bottom-up analysis was complemented by intact glycoprotein analysis using nano RP-LC-MS allowing the fast visualization of the polysaccharide distribution in the intact glycoconjugate. At the glycopeptide level, the model glycoconjugates analyzed showed different repeat unit (RU) distributions that spanned from 1 to 21 RUs attached to each of the different glycosylation sites. Interestingly, the intact glycoprotein analysis displayed a RU distribution ranging from 1 to 28 RUs, showing the predominant species when the different glycopeptide distributions are combined in the intact glycoconjugate. The complete workflow based on LC-MS measurements allows detailed and comprehensive analysis of the glycosylation state of glycoconjugate vaccines.

The immune interactions of gut glycans and microbiota in health and disease

The human digestive system harbors a vast diversity of commensal bacteria and maintains a symbiotic relationship with them. However, imbalances in the gut microbiota accompany various diseases, such as inflammatory bowel diseases (IBDs) and colorectal cancers (CRCs), which significantly impact the well-being of populations globally. Glycosylation of the mucus layer is a crucial factor that plays a critical role in maintaining the homeostatic environment in the gut. This review delves into how the gut microbiota, immune cells, and gut mucus layer work together to establish a balanced gut environment. Specifically, the role of glycosylation in regulating immune cell responses and mucus metabolism in this process is examined.

The role of galectins in the regulation of autophagy and inflammasome in host immunity

Galectins, a family of glycan-binding proteins have been shown to bind a wide range of glycans. In the cytoplasm, these glycans can be endogenous (or "self"), originating from damaged endocytic vesicles, or exogenous (or "non-self"), found on the surface of invading microbial pathogens. Galectins can detect these unusual cytosolic exposures to glycans and serve as critical regulators in orchestrating immune responses in innate and adaptive immunity. This review provides an overview of how galectins modulate host cellular responses, such as autophagy, xenophagy, and inflammasome-dependent cell death program, to infection.

Glycoconjugates: Advances in modern medicines and human health

Glycans and their glycoconjugates are complex biomolecules that are crucial for various biological processes. Glycoconjugates are found in all domains of life. They are covalently linked to key biomolecules such as proteins and lipids to play a pivotal role in cell signaling, adhesion, and recognition. The diversity of glycan structures and the associated complexity of glycoconjugates is the reason for their role in intricate biosynthetic pathways. Glycoconjugates play an important role in various diseases where they are actively involved in the immune response as well as in the pathogenicity of infectious diseases. In addition, various autoimmune diseases have been linked to glycosylation defects of different biomolecules, making them an important molecule in the field of medicine. The glycoconjugates have been explored for the development of therapeutics and vaccines, representing a breakthrough in medical science. They also hold significance in research studies to understand the mechanisms behind various biological processes. Finally, glycoconjugates have found an emerging role in various industrial and environmental applications which have been discussed here.

Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi

Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S. Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control Vi polymerization or acetylation is enough to result in different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper Vi capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo Vi capsule variants have primarily been identified in Africa, whereas the hyper Vi capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria.

ZNT5-6 and ZNT7 play an integral role in protein N-glycosylation by supplying Zn2+ to Golgi α-mannosidase II

The stepwise addition of monosaccharides to N-glycans attached to client proteins to generate a repertoire of mature proteins involves a concerted action of many glycosidases and glycosyltransferases. Here, we report that Golgi α-mannosidase II (GMII), a pivotal enzyme catalyzing the first step in the conversion of hybrid- to complex-type N-glycans, is activated by Zn2+ supplied by the early secretory compartment-resident ZNT5-ZNT6 heterodimers (ZNT5-6) and ZNT7 homodimers (ZNT7). Loss of ZNT5-6 and ZNT7 function results in marked accumulation of hybrid-type and complex/hybrid glycans with concomitant reduction of complex- and high-mannose-type glycans. In cells lacking the ZNT5-6 and ZNT7 functions, the GMII activity is substantially decreased. In contrast, the activity of its homolog, lysosomal mannosidase (LAMAN), is not decreased. Moreover, we show that the growth of pancreatic cancer MIA PaCa-2 cells lacking ZNT5-6 and ZNT7 is significantly decreased in a nude mouse xenograft model. Our results indicate the integral roles of ZNT5-6 and ZNT7 in N-glycosylation and highlight their potential as novel target proteins for cancer therapy.

Recent trends and challenges to overcome Pseudomonas aeruginosa infections

INTRODUCTION

Pseudomonas aeruginosa (PA) is a Gram-negative bacterium that can cause a wide range of severe infections in immunocompromised patients. The most difficult challenge is due to its ability to rapidly develop multi drug-resistance. New strategies are urgently required to improve the outcome of patients with PA infections. The present patent review highlights the new molecules acting on different targets involved in the antibiotic resistance.

AREA COVERED

This review offers an insight into new potential PA treatment disclosed in patent literature. From a broad search of documents claiming new PA inhibitors, we selected and summarized molecules that showed in vitro and in vivo activity against PA spp. in the period 2020 and 2023. We collected the search results basing on the targets explored.

EXPERT OPINION

This review examined the main patented compounds published in the last three years, with regard to the structural novelty and the identification of innovative targets. The main areas of antibiotic resistance have been explored. The compounds are structurally unrelated to earlier antibiotics, characterized by a medium-high molecular weight and the presence of heterocycle rings. Peptides and antibodies have also been reported as potential alternatives to chemical treatment, hereby expanding the therapeutic possibilities in this field.

Molecular insights into FucR transcription factor to control the metabolism of L-fucose in Bifidobacterium longum subsp. infantis

Bifidobacterium longum subsp. infantis commonly colonizes the human gut and is capable of metabolizing L-fucose, which is abundant in the gut. Multiple studies have focused on the mechanisms of L-fucose utilization by B. longum subsp. infantis, but the regulatory pathways governing the expression of these catabolic processes are still unclear. In this study, we have conducted a structural and functional analysis of L-fucose metabolism transcription factor FucR derived from B. longum subsp. infantis Bi-26. Our results indicated that FucR is a L-fucose-sensitive repressor with more α-helices, fewer β-sheets, and β-turns. Transcriptional analysis revealed that FucR displays weak negative self-regulation, which is counteracted in the presence of L-fucose. Isothermal titration calorimetry indicated that FucR has a 2:1 stoichiometry with L-fucose. The key amino acid residues for FucR binding L-fucose are Asp280 and Arg331, with mutation of Asp280 to Ala resulting in a decrease in the affinity between FucR and L-fucose with the Kd value from 2.58 to 11.68 μM, and mutation of Arg331 to Ala abolishes the binding ability of FucR towards L-fucose. FucR specifically recognized and bound to a 20-bp incomplete palindrome sequence (5'-ACCCCAATTACGAAAATTTTT-3'), and the affinity of the L-fucose-loaded FucR for the DNA fragment was lower than apo-FucR. The results provided new insights into the regulating L-fucose metabolism by B. longum subsp. infantis.

The three-sided right-handed β-helix is a versatile fold for glycan interactions

Interactions between proteins and glycans are critical to various biological processes. With databases of carbohydrate-interacting proteins and increasing amounts of structural data, the three-sided right-handed β-helix (RHBH) has emerged as a significant structural fold for glycan interactions. In this review, we provide an overview of the sequence, mechanistic, and structural features that enable the RHBH to interact with glycans. The RHBH is a prevalent fold that exists in eukaryotes, prokaryotes, and viruses associated with adhesin and carbohydrate-active enzyme (CAZyme) functions. An evolutionary trajectory analysis on structurally characterized RHBH-containing proteins shows that they likely evolved from carbohydrate-binding proteins with their carbohydrate-degrading activities evolving later. By examining three polysaccharide lyase and three glycoside hydrolase structures, we provide a detailed view of the modes of glycan binding in RHBH proteins. The 3-dimensional shape of the RHBH creates an electrostatically and spatially favorable glycan binding surface that allows for extensive hydrogen bonding interactions, leading to favorable and stable glycan binding. The RHBH is observed to be an adaptable domain capable of being modified with loop insertions and charge inversions to accommodate heterogeneous and flexible glycans and diverse reaction mechanisms. Understanding this prevalent protein fold can advance our knowledge of glycan binding in biological systems and help guide the efficient design and utilization of RHBH-containing proteins in glycobiology research.

Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi

Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S . Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control the length or acetylation of Vi is enough to create different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper-capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo-capsule variants have primarily been identified in Africa, whereas the hyper-capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria.

Combating bacterial infections with host defense peptides: Shifting focus from bacteria to host immunity

The increasing prevalence of multidrug-resistant bacterial infections necessitates the exploration of novel paradigms for anti-infective therapy. Antimicrobial peptides (AMPs), also known as host defense peptides (HDPs), have garnered extensive recognition as immunomodulatory molecules that leverage natural host mechanisms to enhance therapeutic benefits. The unique immune mechanism exhibited by certain HDPs that involves self-assembly into supramolecular nanonets capable of inducing bacterial agglutination and entrapping is significantly important. This process effectively prevents microbial invasion and subsequent dissemination and significantly mitigates selective pressure for the evolution of microbial resistance, highlighting the potential of HDP-based antimicrobial therapy. Recent advancements in this field have focused on developing bio-responsive materials in the form of supramolecular nanonets. A comprehensive overview of the immunomodulatory and bacteria-agglutinating activities of HDPs, along with a discussion on optimization strategies for synthetic derivatives, is presented in this article. These optimized derivatives exhibit improved biological properties and therapeutic potential, making them suitable for future clinical applications as effective anti-infective therapeutics.

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.

Respiratory viruses interacting with cells: the importance of electrostatics

The COVID-19 pandemic has rekindled interest in the molecular mechanisms involved in the early steps of infection of cells by viruses. Compared to SARS-CoV-1 which only caused a relatively small albeit deadly outbreak, SARS-CoV-2 has led to fulminant spread and a full-scale pandemic characterized by efficient virus transmission worldwide within a very short time. Moreover, the mutations the virus acquired over the many months of virus transmission, particularly those seen in the Omicron variant, have turned out to result in an even more transmissible virus. Here, we focus on the early events of virus infection of cells. We review evidence that the first decisive step in this process is the electrostatic interaction of the spike protein with heparan sulfate chains present on the surface of target cells: Patches of cationic amino acids located on the surface of the spike protein can interact intimately with the negatively charged heparan sulfate chains, which results in the binding of the virion to the cell surface. In a second step, the specific interaction of the receptor binding domain (RBD) within the spike with the angiotensin-converting enzyme 2 (ACE2) receptor leads to the uptake of bound virions into the cell. We show that these events can be expressed as a semi-quantitative model by calculating the surface potential of different spike proteins using the Adaptive Poison-Boltzmann-Solver (APBS). This software allows visualization of the positive surface potential caused by the cationic patches, which increased markedly from the original Wuhan strain of SARS-CoV-2 to the Omicron variant. The surface potential thus enhanced leads to a much stronger binding of the Omicron variant as compared to the original wild-type virus. At the same time, data taken from the literature demonstrate that the interaction of the RBD of the spike protein with the ACE2 receptor remains constant within the limits of error. Finally, we briefly digress to other viruses and show the usefulness of these electrostatic processes and calculations for cell-virus interactions more generally.

Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods

Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.

L-Fucose is involved in human-gut microbiome interactions

L-Fucose is one of the key metabolites in human-gut microbiome interactions. It is continuously synthesized by humans in the form of fucosylated glycans and fucosyl-oligosaccharides and delivered into the gut throughout their lifetime. Gut microorganisms metabolize L-fucose and produce short-chain fatty acids, which are absorbed by epithelial cells and used as energy sources or signaling molecules. Recent studies have revealed that the carbon flux in L-fucose metabolism by gut microorganisms is distinct from that in other sugar metabolisms because of cofactor imbalance and low efficiencies in energy synthesis of L-fucose metabolism. The large amounts of short-chain fatty acids produced during microbial L-fucose metabolism are used by epithelial cells to recover most of the energy used up during L-fucose synthesis. In this review, we present a detailed overview of microbial L-fucose metabolism and a potential solution for disease treatment and prevention using genetically engineered probiotics that modulate fucose metabolism. Our review contributes to the understanding of human-gut microbiome interactions through L-fucose metabolism. KEY POINTS: • Fucose-metabolizing microorganisms produce large amounts of short-chain fatty acids • Fucose metabolism differs from other sugar metabolisms by cofactor imbalance • Modulating fucose metabolism is the key to control host-gut microbiome interactions.

Adenosine Triphosphate-Responsive Glyconanorods through Self-Assembly of β-Cyclodextrin-Based Glycoconjugates for Targeted and Effective Bacterial Sensing and Killing

Polymer-based nanomaterials have exhibited promising alternative avenues to combat the globe challenge of multidrug-resistant bacterial infection. However, most of the reported polymeric nanomaterials have facially linear amphiphilic structures with positive net charges, which may lead to nonspecific binding, high hemolysis, and uncontrollable self-organization, limiting their practical applications. In this contribution, we report a one-dimensional glyconanorod (GNR) through self-assembly of well-defined β-cyclodextrin-based glycoconjugates (RMan) featuring hydrophobic carbon-based chains and amide rhodamines with an adenosine triphosphate (ATP)-recognition site and targeted and hydrophilic mannoses and positively net-charged ethylene amine groups. The GNRs show superior targeting sensing and killing for Gram-negative Escherichia coli (E. coli) dominantly through the multivalent recognition between mannoses on the nanorod and the lectin on the surface of E. coli. Moreover, red fluorescence was light on due to the hydrogen bonding between amide rhodamine and ATP. Benefiting from the designs, the GNRs are capable of possessing a higher therapeutic index and of encapsulating other antibiotics. They exhibit an enhanced effect against E. coli strains. Intriguingly, the GNRs displayed a more reduced hemolysis effect and lower cytotoxicity compared to that of ethylene glyco-modified nanorods. These results reveal that the glyconanomaterials not only feature superior and targeted bacterial sensing and antibacterial activity, but also better biocompatibility compared with the widely used PEG-covered nanomaterials. Furthermore, the in vivo studies demonstrate that the targeted and ATP-responsive GNRs complexed with antibiotics showed better treatment using a mouse model of abdominal sepsis following intraperitoneal E. coli infection. The present work describes a targeted and effective sensing and antibacterial platform based on glycoconjugates that have potential applications for the treatment of infections caused by pathogenic microorganisms.

A Rapid Protocol for Preparing 8-Aminopyrene-1,3,6-Trisulfonate-Labeled Glycans for Capillary Electrophoresis-Based Enzyme Assays

Purified glycan standards are required for glycan arrays, characterizing substrate specificities of glycan-active enzymes, and to serve as retention-time or mobility standards for various separation techniques. This chapter describes a method for the rapid separation, and subsequent desalting, of glycans labeled with the highly fluorescent fluorophore 8-aminopyrene-1,3,6-trisulfonate (APTS). By using fluorophore-assisted carbohydrate electrophoresis (FACE) on polyacrylamide gels, a technique amenable to equipment readily available in most molecular biology laboratories, many APTS-labeled glycans can be simultaneously resolved. Excising specific gel bands containing the desired APTS-labeled glycans, followed by glycan elution from the gel by simple diffusion and subsequent solid-phase extraction (SPE)-based desalting, affords a single glycan species free of excess labeling reagents and buffer components. The described protocol also offers a simple, rapid method for the simultaneous removal of excess APTS and unlabeled glycan material from reaction mixtures. This chapter describes a FACE/SPE procedure ideal for preparing glycans for capillary electrophoresis (CE)-based enzyme assays, as well as for the purification of rare, commercially unavailable glycans from tissue culture samples.

Glycan Conformation in the Heavily Glycosylated Protein, CEACAM1

Glycans attached to glycoproteins can contribute to stability, mediate interactions with other proteins, and initiate signal transduction. Glycan conformation, which is critical to these processes, is highly variable and often depicted as sampling a multitude of conformers. These conformers can be generated by molecular dynamics simulations, and more inclusively by accelerated molecular dynamics, as well as other extended sampling methods. However, experimental assessments of the contribution that various conformers make to a native ensemble are rare. Here, we use long-range pseudo-contact shifts (PCSs) of NMR resonances from an isotopically labeled glycoprotein to identify preferred conformations of its glycans. The N-terminal domain from human Carcinoembryonic Antigen Cell Adhesion Molecule 1, hCEACAM1-Ig1, was used as the model glycoprotein in this study. It has been engineered to include a lanthanide-ion-binding loop that generates PCSs, as well as a homogeneous set of three ¹³C-labeled N-glycans. Analysis of the PCSs indicates that preferred glycan conformers have extensive contacts with the protein surface. Factors leading to this preference appear to include interactions between N-acetyl methyls of GlcNAc residues and hydrophobic surface pockets on the protein surface.

N-glycosylation of cervicovaginal fluid reflects microbial community, immune activity, and pregnancy status

Human cervicovaginal fluid (CVF) is a complex, functionally important and glycan rich biological fluid, fundamental in mediating physiological events associated with reproductive health. Using a comprehensive glycomic strategy we reveal an extremely rich and complex N-glycome in CVF of pregnant and non-pregnant women, abundant in paucimannose and high mannose glycans, complex glycans with 2-4 N-Acetyllactosamine (LacNAc) antennae, and Poly-LacNAc glycans decorated with fucosylation and sialylation. N-glycosylation profiles were observed to differ in relation to pregnancy status, microbial composition, immune activation, and pregnancy outcome. Compared to CVF from women experiencing term birth, CVF from women who subsequently experienced preterm birth showed lower sialylation, which correlated to the presence of a diverse microbiome, and higher fucosylation, which correlated positively to pro-inflammatory cytokine concentration. This study is the first step towards better understanding the role of cervicovaginal glycans in reproductive health, their contribution to the mechanism of microbial driven preterm birth, and their potential for preventative therapy.

An analytical study on the identification of N-linked glycosylation sites using machine learning model

N-linked is the most common type of glycosylation which plays a significant role in identifying various diseases such as type I diabetes and cancer and helps in drug development. Most of the proteins cannot perform their biological and psychological functionalities without undergoing such modification. Therefore, it is essential to identify such sites by computational techniques because of experimental limitations. This study aims to analyze and synthesize the progress to discover N-linked places using machine learning methods. It also explores the performance of currently available tools to predict such sites. Almost seventy research articles published in recognized journals of the N-linked glycosylation field have shortlisted after the rigorous filtering process. The findings of the studies have been reported based on multiple aspects: publication channel, feature set construction method, training algorithm, and performance evaluation. Moreover, a literature survey has developed a taxonomy of N-linked sequence identification. Our study focuses on the performance evaluation criteria, and the importance of N-linked glycosylation motivates us to discover resources that use computational methods instead of the experimental method due to its limitations.

Delivery, structure, and function of bacterial genotoxins

Bacterial genotoxins are peptide or protein virulence factors produced by several pathogens, which make single-strand breaks (SSBs) and/or double-strand DNA breaks (DSBs) in the target host cells. If host DNA inflictions are not resolved on time, host cell apoptosis, cell senescence, and/or even bacterial pathogen-related cancer may occur. Two multi-protein AB toxins, cytolethal distending toxin (CDT) produced by over 30 bacterial pathogens and typhoid toxin from Salmonella Typhi, as well as small polyketide-peptides named colibactin that causes the DNA interstrand cross-linking and subsequent DSBs is the most well-characterized bacterial genotoxins. Using these three examples, this review discusses the mechanisms by which these toxins deliver themselves into the nucleus of the target host cells and exert their genotoxic functions at the structural and functional levels.

How bacteria utilize sialic acid during interactions with the host: snip, snatch, dispatch, match and attach

N -glycolylneuraminic acid (Neu5Gc), and its precursor N-acetylneuraminic acid (Neu5Ac), commonly referred to as sialic acids, are two of the most common glycans found in mammals. Humans carry a mutation in the enzyme that converts Neu5Ac into Neu5Gc, and as such, expression of Neu5Ac can be thought of as a 'human specific' trait. Bacteria can utilize sialic acids as a carbon and energy source and have evolved multiple ways to take up sialic acids. In order to generate free sialic acid, many bacteria produce sialidases that cleave sialic acid residues from complex glycan structures. In addition, sialidases allow escape from innate immune mechanisms, and can synergize with other virulence factors such as toxins. Human-adapted pathogens have evolved a preference for Neu5Ac, with many bacterial adhesins, and major classes of toxin, specifically recognizing Neu5Ac containing glycans as receptors. The preference of human-adapted pathogens for Neu5Ac also occurs during biosynthesis of surface structures such as lipo-oligosaccharide (LOS), lipo-polysaccharide (LPS) and polysaccharide capsules, subverting the human host immune system by mimicking the host. This review aims to provide an update on the advances made in understanding the role of sialic acid in bacteria-host interactions made in the last 5-10 years, and put these findings into context by highlighting key historical discoveries. We provide a particular focus on 'molecular mimicry' and incorporation of sialic acid onto the bacterial outer-surface, and the role of sialic acid as a receptor for bacterial adhesins and toxins.

Neutralization of typhoid toxin by alpaca-derived, single-domain antibodies targeting the PltB and CdtB subunits

Typhoid toxin is secreted by the typhoid fever-causing bacterial pathogen Salmonella enterica serovar Typhi and has tropism for immune cells and brain endothelial cells. Here, we generated a camelid single-domain antibody (VHH) library from typhoid toxoid-immunized alpacas and identified 41 VHHs selected on the glycan receptor-binding PltB and nuclease CdtB. VHHs exhibiting potent in vitro neutralizing activities from each sequence-based family were epitope binned via competition enzyme-linked immunosorbent assays (ELISAs), leading to 6 distinct VHHs, 2 anti-PltBs (T2E7 and T2G9), and 4 anti-CdtB VHHs (T4C4, T4C12, T4E5, and T4E8), whose in vivo neutralizing activities and associated toxin-neutralizing mechanisms were investigated. We found that T2E7, T2G9, and T4E5 effectively neutralized typhoid toxin in vivo, as demonstrated by 100% survival of mice administered a lethal dose of typhoid toxin and with little to no typhoid toxin-mediated upper motor function defect. Cumulatively, these results highlight the potential of the compact antibodies to neutralize typhoid toxin by targeting the glycan-binding and/or nuclease subunits.

The structural basis of Salmonella A2B5 toxin neutralization by antibodies targeting the glycan-receptor binding subunits

Many bacterial pathogens secrete A₍₂₎B₅ toxins comprising two functionally distinct yet complementary “A” and “B” subunits to benefit the pathogens during infection. The lectin-like pentameric B subunits recognize specific sets of host glycans to deliver the toxin into target host cells. Here, we offer the molecular mechanism by which neutralizing antibodies, which have the potential to bind to all glycan-receptor binding sites and thus completely inhibit toxin binding to host cells, are inhibited from exerting this action. Cryogenic electron microscopy (cryo-EM)-based analyses indicate that the skewed positioning of the toxin A subunit(s) toward one side of the toxin B pentamer inhibited neutralizing antibody binding to the laterally located epitopes, rendering some glycan-receptor binding sites that remained available for the toxin binding and endocytosis process, which is strikingly different from the counterpart antibodies recognizing the far side-located epitopes. These results highlight additional features of the toxin-antibody interactions and offer important insights into anti-toxin strategies.

Nguyen et al. find that toxin-neutralizing antibodies targeting glycan-receptor binding B subunits can be split into two classes based on their epitope locations. They describe how these two classes exhibit significantly different neutralizing efficacies, a feature that appears to be shared among A₍₂₎B₅ toxins, and thus they provide insights into anti-toxin strategies.