Structural evidence for a proline-specific glycopeptide recognition domain in an O-glycopeptidase

'Nunchuck' proteins: Short flexible linkers resist proteolysis by facilitating motions in flanking domains to inhibit the approach of proteases

Peptides linking well-folded and non-interacting domains in fusion proteins can undergo proteolytic degradation. This leads to physical separation of the domains that were originally sought to be joined. In order to identify characteristics that determine linker degradation propensity, we selected a pair of thermostable, proteolytically-resistant domains, and joined them using five different linkers. We then assessed linker degradation propensities through size-exclusion chromatography, and denaturing and non-denaturing electrophoresis. The domains used were Coh2, an all-beta cohesin from C. thermocellum CipA, and BSX, a beta/alpha barrel xylanase from Bacillus sp. NG-27, while the linkers used were Rigid (3 repeats of N-EAAAK-C), Flexible (two repeats of N-SGGGG-C), Nat-full (42 residues of a Coh2-adjacent linker from CipA), Nat-half (a 21 residues-long derivative of Nat-full) and Nat-quarter (a 9 residues-long derivative of Nat-full). Both with proteolysis effected by proteases present in the environment, and with an exogenously-added protease (Subtilisin A), we found that Flexible underwent little or no degradation, whereas linkers of comparable length like Nat-quarter or Rigid underwent extensive degradation, as did longer linkers like Nat-Half and Nat-Full. Our analyses disfavor the likelihood of the sequence of Flexible being naturally resistant to proteolysis, and instead favor the explanation that the flexibility of Flexible facilitates movements of Coh2 relative to BSX which then serve to sterically prevent the approach of proteases. Thus, the construct incorporating Flexible appears to behave like a 'nunchuck' in which rods/spheres flanking a chain collide with approaching swords that are capable of severing the chain, to prevent severance.

Structure and Antidiabetic Activity of a Glycoprotein from Porphyra haitanensis

A novel antidiabetic glycoprotein (PG) was isolated and purified from Porphyra haitanensis, and its structure and inhibiting activity on α-amylase and α-glucosidase were analyzed. The purity of the PG was 95.29 ± 0.21%, and its molecular weight was 163.024 ± 5.55 kDa. The PG had a tetramer structure with α- and β-subunits, and it contained 54.12 ± 0.86% protein (with highly hydrophobic amino acids) and 41.19% ± 0.64% carbohydrate (composed of galactose). The PG was linked via an O-glycosidic bond, exhibiting an α-helical structure and high stability. In addition, the PG inhibited the activities of α-amylase and α-glucosidase, by changing the enzyme's structure toward the PG's structure in a noncompetitive inhibition mode. Molecular docking results showed that the PG inhibited α-amylase activity by hydrophobic interaction, whereas it inhibited α-glucosidase activity by hydrogen bonds and hydrophobic interaction. Overall, the PG was linked to polysaccharides via O-glycosidic bonds, showing an α-helical configuration and a hydrophobic effect, which altered the configuration of α-amylase and α-glucosidase and exerted hypoglycemic activity. This study provides insights into analyzing the structure and antidiabetic activity of glycoproteins.

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key regulators in cellular immunity. However, their dense O-glycosylation remains enigmatic, primarily due to the challenges associated with studying mucin domains. Here, we demonstrate that the mucinase SmE has a unique ability to cleave at residues bearing very complex glycans. SmE enables improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we perform molecular dynamics (MD) simulations of TIM-3 and -4 to understand how glycosylation affects structural features of these proteins. Finally, we use these models to investigate the functional relevance of glycosylation for TIM-3 function and ligand binding. Overall, we present a powerful workflow to better understand the detailed molecular structures and functions of the mucinome.

Characterization of a new family of 6-sulfo-N-acetylglucosaminidases

Sulfation is widespread in nature and plays an important role in modulating biological function. Among the strategies developed by microbes to access sulfated oligosaccharides as a nutrient source is the production of 6-sulfoGlcNAcases to selectively release 6-sulfoGlcNAc from target oligosaccharides. Thus far, all 6-sulfoGlcNAcases identified have belonged to the large GH20 family of β-hexosaminidases. Ηere, we identify and characterize a new, highly specific non-GH20 6-sulfoGlcNAcase from Streptococcus pneumoniae TIGR4, Sp_0475 with a greater than 110,000-fold preference toward N-acetyl-β-D-glucosamine-6-sulfate substrates over the nonsulfated version. Sp_0475 shares distant sequence homology with enzymes of GH20 and with the newly formed GH163 family. However, the sequence similarity between them is sufficiently low that Sp_0475 has been assigned as the founding member of a new glycoside hydrolase family, GH185. By combining results from site-directed mutagenesis with mechanistic studies and bioinformatics we provide insight into the substrate specificity, mechanism, and key active site residues of Sp_0475. Enzymes of the GH185 family follow a substrate-assisted mechanism, consistent with their distant homology to the GH20 family, but the catalytic residues involved are quite different. Taken together, our results highlight in more detail how microbes can degrade sulfated oligosaccharides for nutrients.

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in terms of glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamics (MD) simulations of TIM-3 and -4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.

A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond

Akkermansia muciniphila is key member of the human gut microbiota, impacting many features of host health. A major characteristic of this bacterium is its interaction with host mucin, which is abundant in the gut environment, and its ability to metabolize mucin as a nutrient source. The machinery deployed by A. muciniphila to enable this interaction appears to be extensive and sophisticated, yet it is incompletely defined. The uncharacterized protein AMUC_1438 is encoded by a gene that was previously shown to be upregulated when the bacterium is grown on mucin. This uncharacterized protein has features suggestive of carbohydrate-recognition and peptidase activity, which led us to hypothesize that it has a role in mucin depolymerization. Here we provide structural and functional support for the assignment of AMUC_1438 as a unique O-glycopeptidase with mucin degrading capacity. O-glycopeptidase enzymes recognize glycans but hydrolyze the peptide backbone and are common in host-adapted microbes that colonize or invade mucus layers. Structural, kinetic, and mutagenic analyses point to a metzincin metalloprotease catalytic motif but specific recognition of a GalNAc residue α-linked to serine or threonine (i.e. the Tn-antigen) within the AMUC_1438 active site. The enzyme catalyzes hydrolysis of the bond immediately N-terminal to the glycosylated residue. Additional modelling analyses suggest the presence of a carbohydrate-binding module that may assist in substrate recognition. We anticipate that these results will be fundamental to a wider understanding of the O-glycopeptidase class of enzymes and how they may contribute to host-adaptation.

Current strategies for characterization of mucin-domain glycoproteins

Glycosylation, and especially O-linked glycosylation, remains a critical blind spot in the understanding of post-translational modifications. Due to their nature as proteins defined by a large density and abundance of O-glycosylation, mucins present extra challenges in the analysis of their structure and function. However, recent breakthroughs in multiple areas of research have rendered mucin-domain glycoproteins more accessible to current characterization techniques. In particular, the adaptation of mucinases to glycoproteomic workflows, the manipulation of cellular glycosylation pathways, and the advances in synthetic methods to more closely mimic mucin domains have introduced new and exciting avenues to study mucin glycoproteins. Here, we summarize recent developments in understanding the structure and biological function of mucin domains and their associated glycans, from glycoproteomic tools and visualization methods to synthetic glycopeptide mimetics.

Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences

Akkermansia muciniphila, a mucin-degrading microbe found in the human gut, is often associated with positive health outcomes. The abundance of A. muciniphila is modulated by the presence and accessibility of nutrients, which can be derived from diet or host glycoproteins. In particular, the ability to degrade host mucins, a class of proteins carrying densely O-glycosylated domains, provides a competitive advantage in the sustained colonization of niche mucosal environments. Although A. muciniphila is known to rely on mucins as a carbon and nitrogen source, the enzymatic machinery used by this microbe to process mucins in the gut is not yet fully characterized. Here, we focus on the mucin-selective metalloprotease, Amuc_0627 (AM0627), which is known to cleave between adjacent residues carrying truncated core 1 O-glycans. We showed that this enzyme is capable of degrading purified mucin 2 (MUC2), the major protein component of mucus in the gut. An X-ray crystal structure of AM0627 (1.9 Å resolution) revealed O-glycan–binding residues that are conserved between structurally characterized enzymes from the same family. We further rationalized the substrate cleavage motif using molecular modeling to identify nonconserved glycan-interacting residues. We conclude that mutagenesis of these residues resulted in altered substrate preferences down to the glycan level, providing insight into the structural determinants of O-glycan recognition.

A Broad-Specificity O-Glycoprotease That Enables Improved Analysis of Glycoproteins and Glycopeptides Containing Intact Complex O-Glycans

Characterization of mucin-type O-glycans linked to serine/threonine of glycoproteins is technically challenging, in part, due to a lack of effective enzymatic tools that enable their analysis. Recently, several O-glycan-specific endoproteases that can cleave the protein adjacent to the appended glycan have been described. Despite significant progress in understanding the biochemistry of these enzymes, known O-glycoproteases have specificity constraints, such as inefficient cleavage of glycoproteins bearing sialylated O-glycans, high selectivity for certain types of glycoproteins, or protein sequence bias. These factors limit their analytical application. In this study, we examined the capabilities of an immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa. Peptide sequence selectivity and its impact on IMPa activity were interrogated using an array of synthetic peptides and their glycoforms. We show that IMPa has no specific P1 residue preference and can tolerate most amino acids at the P1 position, except aspartic acid. The enzyme does not cleave between two adjacent O-glycosites, indicating that O-glycosylated serine/threonine is not allowed at position P1. Glycopeptides with as few as two amino acids on either side of an O-glycosite were cleaved by IMPa. Finally, IMPa efficiently cleaved peptides and proteins carrying sialylated and asialylated O-glycans of varying complexity. We present the use of IMPa in a one-step O-glycoproteomic workflow for glycoprofiling of the purified glycoproteins granulocyte colony-stimulating factor and receptor-type tyrosine-protein phosphatase C without the need for glycopeptide enrichment. In these examples, IMPa enabled both the identification of O-glycosites and the range of complex O-glycan structures at each site.

Architecturally complex O-glycopeptidases are customized for mucin recognition and hydrolysis

A challenge faced by peptidases is the recognition of highly diverse substrates. A feature of some peptidase families is the capacity to specifically use post-translationally added glycans present on their protein substrates as a recognition determinant. This is ultimately critical to enabling peptide bond hydrolysis. This class of enzyme is also frequently large and architecturally sophisticated. However, the molecular details underpinning glycan recognition by these O-glycopeptidases, the importance of these interactions, and the functional roles of their ancillary domains remain unclear. Here, using the Clostridium perfringens ZmpA, ZmpB, and ZmpC M60 peptidases as model proteins, we provide structural and functional insight into how these intricate proteins recognize glycans as part of catalytic and noncatalytic substrate recognition. Structural, kinetic, and mutagenic analyses support the key role of glycan recognition within the M60 domain catalytic site, though they point to ZmpA as an apparently inactive enzyme. Wider examination of the Zmp domain content reveals noncatalytic carbohydrate binding as a feature of these proteins. The complete three-dimensional structure of ZmpB provides rare insight into the overall molecular organization of a highly multimodular enzyme and reveals how the interplay of individual domain function may influence biological activity. O-glycopeptidases frequently occur in host-adapted microbes that inhabit or attack mucus layers. Therefore, we anticipate that these results will be fundamental to informing more detailed models of how the glycoproteins that are abundant in mucus are destroyed as part of pathogenic processes or liberated as energy sources during normal commensal lifestyles.

Classification, structural biology, and applications of mucin domain-targeting proteases

Epithelial surfaces throughout the body are coated by mucins, a class of proteins carrying domains characterized by a high density of O-glycosylated serine and threonine residues. The resulting mucosal layers form crucial host-microbe interfaces that prevent the translocation of microbes while also selecting for distinct bacteria via the presented glycan repertoire. The intricate interplay between mucus production and breakdown thus determines the composition of the microbiota maintained within these mucosal environments, which can have a large influence on the host during both homeostasis and disease. Most research to date on mucus breakdown has focused on glycosidases that trim glycan structures to release monosaccharides as a source of nutrients. More recent work has uncovered the existence of mucin-type O-glycosylation-dependent proteases that are secreted by pathogens, commensals, and mutualists to facilitate mucosal colonization and penetration. Additionally, immunoglobulin A (IgA) proteases promote bacterial colonization in the presence of neutralizing secretory IgA through selective cleavage of the heavily O-glycosylated hinge region. In this review, we summarize families of O-glycoproteases and IgA proteases, discuss known structural features, and review applications of these enzymes to glycobiology.