The human microbiome contains at least as many bacterial cells as human cells. Some bacteria offer benefits, like improving gut barrier function, suppressing pathobiont growth, and modulating immunity. These benefits have popularized probiotics, but probiotic retention is often hindered by low colonization efficiency in the mucosal layer that lines all epithelial cells. Mucins, the primary components of mucus, are essential for the organization and regulation of microbial populations. The molecular mechanisms of mucin-probiotic interactions remain understudied due, in part, to the inability to incisively manipulate native mucin sequences or their glycans. Here, we used synthetic mucins with defined glycan presentations to interrogate glycan-dependent interactions between mucus and three probiotic lactobacilli species. The nutrient conditions under which bacteria were cultured influenced glycan binding preferences, suggesting mucin-probiotic interactions change with nutrient availability. The addition of synthetic mucins to native mucin increased Limosilactobacillus fermentum adherence. Additionally, an increase in glycosidase activity indicated that native and synthetic mucins function as prebiotics, as probiotic bacteria can cleave the displayed O-glycans. Thus, synthetic mucins can cultivate target probiotic bacteria and increase adhesion as binding sites, highlighting their value as tools for elucidating native mucin functions and as promising agents for promoting human health.

Human lectins are critical carbohydrate-binding proteins that recognize diverse glycoconjugates from microorganisms and can play a key role in host-microbe interactions. Despite their importance in immune recognition and microbe binding, the specific glycan ligands and functions of many human lectins remain poorly understood. Using previous proof-of-concept studies on selected lectins as the foundation for this work, we present ten additional glycan analysis probes (GAPs) from a diverse set of human soluble lectins, offering robust tools to investigate glycan-mediated interactions. We describe a protein engineering platform that enables scalable production of GAPs that maintain native-like conformations and oligomerization states, equipped with functional reporter tags for targeted glycan profiling. We demonstrate that the soluble GAP reagents can be used in various applications, including glycan array analysis, mucin-binding assays, tissue staining, and microbe binding in complex populations. These capabilities make GAPs valuable for dissecting interactions relevant to understanding host responses to microbes. The tools can also be used to probe differential microbial and mammalian glycan interactions, which are crucial for understanding the interactions of lectins in a physiological environment where both glycan types exist. GAPs have potential as diagnostic and prognostic tools for detecting glycan alterations in chronic diseases, microbial dysbiosis, and immune-related conditions.

Glycan-binding proteins, or lectins, recognize distinct structural elements of polysaccharides, to mediate myriad biological functions. Targeting glycan-binding proteins involved in human disease has been challenging due to an incomplete understanding of the molecular mechanisms that govern protein-glycan interactions. Bioinformatics and structural studies of glycan-binding proteins indicate that aromatic residues with the potential for CH-pi interactions are prevalent in glycan-binding sites. However, the contributions of these CH-pi interactions to glycan binding and their relevance in downstream function remain unclear. An emblematic lectin, human galectin-3, recognizes lactose and N-acetyllactosamine-containing glycans by positioning the electropositive face of a galactose residue over the tryptophan 181 (W181) indole forming a CH-pi interaction. We generated a suite of galectin-3 W181 variants to assess the importance of these CH-pi interactions to glycan binding and function. As determined experimentally and further validated with computational modeling, variants with smaller or less electron-rich aromatic side chains (W181Y, W181F, W181H) or sterically similar but nonaromatic residues (W181M, W181R) showed poor or undetectable binding to lactose and attenuated ability to bind mucins or agglutinate red blood cells. The latter functions depend on multivalent binding, highlighting that weakened CH-pi interactions cannot be overcome by avidity. Two galectin-3 variants with disrupted hydrogen bonding interactions (H158A and E184A) showed similarly impaired lactose binding. Molecular simulations demonstrate that all variants have decreased binding orientation stability relative to native galectin-3. Thus, W181 collaborates with the endogenous hydrogen bonding network to enhance binding affinity for lactose, and abrogation of these CH-pi interactions is as deleterious as eliminating key hydrogen bonding interactions. These findings underscore the critical roles of CH-pi interactions in carbohydrate binding and lectin function and will aid the development of novel lectin inhibitors.

The oral microbiome is critical to human health and disease, yet the role that host salivary proteins play in maintaining oral health is unclear. A highly expressed gene in human salivary glands encodes the lectin zymogen granule protein 16 homolog B (ZG16B). Despite the abundance of this protein, its interaction partners in the oral microbiome are unknown. ZG16B possesses a lectin fold, but whether it binds carbohydrates is unclear. We postulated that ZG16B would bind microbial glycans to mediate recognition of oral microbes. To this end, we developed a microbial glycan analysis probe (mGAP) strategy based on conjugating the recombinant protein to fluorescent or biotin reporter functionality. Applying the ZG16B-mGAP to dental plaque isolates revealed that ZG16B predominantly binds to a limited set of oral microbes, including Streptococcus mitis, Gemella haemolysans, and, most prominently, Streptococcus vestibularis. S. vestibularis is a commensal bacterium widely distributed in healthy individuals. ZG16B binds to S. vestibularis through the cell wall polysaccharides attached to the peptidoglycan, indicating that the protein is a lectin. ZG16B slows the growth of S. vestibularis with no cytotoxicity, suggesting that it regulates S. vestibularis abundance. The mGAP probes also revealed that ZG16B interacts with the salivary mucin MUC7. Analysis of S. vestibularis and MUC7 with ZG16B using super-resolution microscopy supports ternary complex formation that can promote microbe clustering. Together, our data suggest that ZG16B influences the compositional balance of the oral microbiome by capturing commensal microbes and regulating their growth using a mucin-assisted clearance mechanism.

Enveloped viruses co-opt host glycosylation pathways to decorate their surface proteins. As viruses evolve, emerging strains can modify their glycosylation patterns to influence host interactions and subvert immune recognition. Still, changes in viral glycosylation or their impact on antibody protection cannot be predicted from genomic sequences alone. Using the highly glycosylated SARS-CoV-2 Spike protein as a model system, we present a lectin fingerprinting method that rapidly reports on changes in variant glycosylation state, which are linked to antibody neutralization. In the presence of antibodies or convalescent and vaccinated patient sera, unique lectin fingerprints emerge that distinguish neutralizing versus non-neutralizing antibodies. This information could not be inferred from direct binding interactions between antibodies and the Spike receptor-binding domain (RBD) binding data alone. Comparative glycoproteomics of the Spike RBD of wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) variants reveal O-glycosylation differences as a key determinant of immune recognition differences. These data underscore the interplay between viral glycosylation and immune recognition and reveal lectin fingerprinting to be a rapid, sensitive, and high-throughput assay to distinguish the neutralization potential of antibodies that target critical viral glycoproteins.

Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins' roles in regulating microbiota requires an understanding of which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using the soluble mannose-binding lectin (MBL) and intelectin-1 (hItln1). Although each lectin binds a substantial percentage of the samples (10 to 20%), the microbial interactomes of MBL and hItln1 differ markedly in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1's interaction profile encompasses a broad range of lower-abundance species. Our data uncover stark differences in the commensal recognition properties of human lectins.

Interactions between carbohydrates and the proteins that bind them (lectins) are often some of the first between a host cell and a viral invader. With its highly glycosylated spike protein, SARS-CoV-2 is no exception. Interrogating glycosylation is vital to understand viral infection, yet it has been a challenge. Improvement in methods ranging from mass spectrometry to glycan arrays and modeling simulations are yielding atomic-level information about the glycans that decorate viruses and host cells alike.

Intelectins are ancient carbohydrate binding proteins, spanning chordate evolution and implicated in multiple human diseases. Previous GWAS have linked SNPs in ITLN1 (also known as omentin) with susceptibility to Crohn's disease (CD); however, analysis of possible functional significance of SNPs at this locus is lacking. Using the Ensembl database, pairwise linkage disequilibrium (LD) analyses indicated that several disease-associated SNPs at the ITLN1 locus, including SNPs in CD244 and Ly9, were in LD. The alleles comprising the risk haplotype are the major alleles in European (67%), but minor alleles in African superpopulations. Neither ITLN1 mRNA nor protein abundance in intestinal tissue, which we confirm as goblet-cell derived, was altered in the CD samples overall nor when samples were analyzed according to genotype. Moreover, the missense variant V109D does not influence ITLN1 glycan binding to the glycan β-D-galactofuranose or protein–protein oligomerization. Taken together, our data are an important step in defining the role(s) of the CD-risk haplotype by determining that risk is unlikely to be due to changes in ITLN1 carbohydrate recognition, protein oligomerization, or expression levels in intestinal mucosa. Our findings suggest that the relationship between the genomic data and disease arises from changes in CD244 or Ly9 biology, differences in ITLN1 expression in other tissues, or an alteration in ITLN1 interaction with other proteins.

In humans, a collection of diverse proteins known as lectins are responsible for binding to glycan epitopes. Recognition of extracellular glycan epitopes represents a key facet of the innate immune response in eukaryotes. These epitopes can be used to distinguish cell types, self‐from non‐self, and perhaps even pathogenic from commensal bacteria. Understanding human lectin specificity can uncover mechanisms underlying innate immunity. Additionally, lectins represent attractive reagents for the development of glycan‐reading probes. Here, we demonstrate our efforts to develop and deploy a pipeline for recombinant expression, functionalization, and characterization of a subset of human lectins, including C‐type lectins, ficolins, jacalin‐type lectins, galectins, and intelectins. Target lectins can be efficiently expressed and purified, functionalized with either biotin or a fluorophore via sortase‐mediated ligation under flow, and screened for glycan binding. The success of this pipeline has been validated in preliminary studies showing that the recombinant lectins can engage with glycans from mammalian glycan arrays, bacterial glycan arrays, purified mucins, or human biological samples. These experiments highlight the potential of lectins as valuable molecular probes that fill a gap in the current molecular toolkit for glycan analysis.Support or Funding InformationNIH U01 CA231079‐01

The human microbiota is intimately linked to health and disease. However, identifying community members that contribute to a healthy or dysbiotic state remains a challenge. Host factors regulate microbiome composition by promoting colonization or clearance of microbes. One such factor, soluble lectins, can detect microbes at strain‐level resolution by specific recognition of glycans. Several human lectins expressed at mucosal surfaces can bind microbes, but lectin specificity for microbes is under‐characterized. To this end, we have generated and characterized a suite of fluorescently labeled human soluble lectins to elucidate their microbe‐specificity. Using these probes, we analyzed recognition of bacteria from the human intestinal microbiota, and found that different lectins bind distinct populations. These data support the use of lectins as specific probes of microbial glycosylation. Further, analysis of fecal samples using lectins implicated in clearance of pathogens or promotion of colonization could provide a facile method of profiling the microbiota in health and disease.

Human innate immune lectins that recognize microbial glycans can conduct microbial surveillance and thereby help prevent infection. Structural analysis of soluble lectins has provided invaluable insight into how these proteins recognize their cognate carbohydrate ligands and how this recognition gives rise to biological function. In this opinion, we cover the structural features of lectins that allow them to mediate microbial recognition, highlighting examples from the collectin, Reg protein, galectin, pentraxin, ficolin and intelectin families. These analyses reveal how some lectins (e.g., human intelectin-1) can recognize glycan epitopes that are remarkably diverse, yet still differentiate between mammalian and microbial glycans. We additionally discuss strategies to identify lectins that recognize microbial glycans and highlight tools that facilitate these discovery efforts.

The network of activator protein-protein interactions (PPIs) that underpin transcription initiation is poorly defined, particularly in the cellular context. The transient nature of these contacts and the often low abundance of the participants present significant experimental hurdles. Through the coupling of in vivo covalent chemical capture and shotgun LC-MS/MS (MuDPIT) analysis, we can trap the PPIs of transcriptional activators in a cellular setting and identify the binding partners in an unbiased fashion. Using this approach, we discover that the prototypical activators Gal4 and VP16 target the Snf1 (AMPK) kinase complex via direct interactions with both the core enzymatic subunit Snf1 and the exchangeable subunit Gal83. Further, we use a tandem reversible formaldehyde and irreversible covalent chemical capture approach (TRIC) to capture the Gal4-Snf1 interaction at the Gal1 promoter in live yeast. Together, these data support a critical role for activator PPIs in both the recruitment and positioning of important enzymatic complexes at a gene promoter and represent a technical advancement in the discovery of new cellular binding targets of transcriptional activators.

Transcriptional activators coordinate the dynamic assembly of multiprotein coactivator complexes required for gene expression to occur. Here we combine the power of in vivo covalent chemical capture with p-benzoyl-L-phenylalanine (Bpa), a genetically incorporated photo-crosslinking amino acid, and chromatin immunoprecipitation (ChIP) to capture the direct protein interactions of the transcriptional activator VP16 with the general transcription factor TBP at the GAL1 promoter in live yeast.

ABSTRACT Protein–protein interactions (PPIs) are essential for implementing cellular processes and thus methods for the discovery and study of PPIs are highly desirable. An emerging method for capturing PPIs in their native cellular environment is in vivo covalent chemical capture, a method that uses nonsense suppression to site specifically incorporate photoactivable unnatural amino acids (UAAs) in living cells. However, in one study we found that this method did not capture a PPI for which there was abundant functional evidence, a complex formed between the transcriptional activator Gal4 and its repressor protein Gal80. Here we describe the factors that influence the success of covalent chemical capture and show that the innate reactivity of the two UAAs utilized, ( p‐ benzoylphenylalanine (pBpa) and p ‐azidophenylalanine (pAzpa)), plays a profound role in the capture of Gal80 by Gal4. Based upon these data, guidelines are outlined for the successful use of in vivo photo‐crosslinking to capture novel PPIs and to characterize the interfaces. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 391–397, 2014.

Transcriptional activators are modular, signal responsive proteins that play an essential role in regulating gene expression. When localized to the nucleus, activators engage in a wave of interactions with a suite of multi‐protein coactivator complexes, resulting in their recruitment to the promoter of the gene to be transcribed. While the majority of methods available for studying protein‐protein interactions (PPIs) are ideal for studying those of higher affinity, few are well‐suited for studying PPIs of a more moderate affinity, including activator‐coactivator interactions. Recently, covalent crosslinking using a photoactivatable amino acid (Bpa) has proven to be a powerful method for the in vivo capture of moderate affinity PPIs. Herein we use in vivo photocrosslinking to examine the interaction between the amphipathic activator VP16 and the essential transcription factor TBP in live yeast. Several lines of evidence suggest that TBP is recruited to promoters through a direct interaction with VP16; However, in vivo co‐localization studies suggest that this recruitment occurs through an indirect mechanism. Using this methodology, we find that VP16 does in fact directly interact with TBP and that this interaction is sustained on DNA. We also find that TBP is a shared target of other amphipathic activators, suggesting a common mechanism of recruitment within a single family of activator proteins. Thus, this methodology should be useful in studying regulatory proteins involved in complex interaction networks. This project is funded by NIH‐NIGMS 2R0106553.