Welcome to the CFG Paradigm Pages
The Paradigm Pages were created by the Consortium for Functional Glycomics (CFG) to offer detailed information about 30 exemplary “Paradigm” glycan binding proteins (GBPs) that together encompass nine GBP families studied by the CFG. Each Paradigm GBP is representative of many other GBPs in its family and has clear biological functions that have become better understood through the use of CFG resources. The wiki-based Paradigm Pages are designed to track the progress of the CFG towards our goal to “define paradigms by which protein-carbohydrate interactions mediate cell communication.” CFG investigators are invited to upload and edit information about known progress in understanding each of these Paradigms, with a specific focus on how CFG resources have contributed to progress. To visit the Paradigm Page for each of the selected GBPs, follow the links below.
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The C-type lectin family consists of proteins with diverse overall organization that contain structurally related carbohydrate-recognition domains. Although they generally share a common mechanism for interacting with sugars through a bound calcium ion, the spectrum of ligands bound by different members of the family is diverse and can include both endogenous mammalian oligosaccharides as well a sugar-containing structures on pathogenic micro-organisms. The biological functions of the C-type lectins are correspondingly diverse, but many of the best understood examples are membrane receptors found on the surface of cells of the immune system, which mediate interactions of these cells with each other and with viruses, bacteria, fungi and parasites, while other members of the family are soluble mediators of innate immunity. Outside the immune system, members of this group participate in clearance of circulating glycoproteins.
Galectins are a family of glycan-binding proteins that are expressed in all multicellular organisms, in virtually every cell and tissue, and that vary considerably in function. There are 15 overall genes encoding galectins in different animals and 11 are expressed in humans. All galectins share a consensus sequence of about 130 amino acids and a homologous carbohydrate recognition domain (CRD) that specifically binds many different types of glycans, including those containing b-galactosides and poly-N-acetyllactosamines, but also including blood group antigens, and sialic acid- or sulfate-containing structures found in O- and N-glycans. The jellyroll-like conformation of the CRD, the hallmark of the galectin family, is composed of two anti-parallel b-sheets that establish a b-sandwich Differences in ligand specificity among this family are determined by specific amino acids in the CRDs, allowing recognition of different modifications of galactose-containing glycans, thus defining the affinity of a particular galectin for specific glycoprotein or glycolipid receptors in a certain tissue or cell type. Galectins are synthesized in the cytoplasm and secreted via a non-classical secretion pathway, so that galectins are found in a variety of intracellular compartments, as well as in the extracellular milieu of almost every cell and tissue type. There are three structural subfamilies of galectins - the prototype, the chimeric, and the tandem repeat. The three paradigmatic galectins described below represent the three structural subfamilies. The prototypical galectin subfamily include galectins-1, -2, -7, -10, -13, and -14; the chimeric galectin subfamily has a single representative galectin-3; and the tandem repeat galectin subfamily includes galectins-4, -8, -9, and -12. Recognition of cell surface glycans by many of the galectins, which is associated with oligomerization and lattice formation of the receptors, induces signaling pathways that are being well defined in leukocytes and epithelial cells. In addition, galectins are important in innate immune responses and can directly recognize glycans on pathogens and provide protection independently of antibodies.
Sialic acid-binding immunoglobulin (Ig)-like lectins, or Siglecs, are a family of type 1 membrane proteins containing an extracellular V-set Ig domain and a variable number of C2-set Ig domains. Siglecs are expressed mainly by cells in the hematopoietic and immune systems, with MAG (Siglec-4) being a major exception due to its exclusive expression by cells of the nervous system. The V-set Ig domain of all siglecs mediates binding to sialylated oligosaccharides via a template centered around a conserved arginine on the F b strand. Extended specificity is mediated by variable residues on interstrand loops, such as the C-C' loop. Many siglecs contain one or more immunoreceptor tyrosine-based inhibitory motifs (ITIMS) that are important for regulating intracellular signaling functions and endocytosis. A recently characterized subset of siglecs can also associate via a basic residue in their transmembrane domains with transmembrane adaptors containing immunoreceptor tyrosine-based activation motifs (ITAMs). Siglecs can be divided into two groups based on sequence similarity. Group 1 contains Siglecs-1, -2, -4 and -15, which are distantly related to one another but well conserved in mammals. The other group includes CD33 and the CD33-related Siglecs which are highly related to each other and whose composition varies considerably amongst mammalian species. The paradigms have been selected on the basis of distinct functions, and include each of the 4 siglecs in group 1 and a representative human/murine pair for the ITIM-containing CD33-related siglecs.
GBPs Mediating Intracellular Trafficking & Other Mammalian GBPs
Both calreticulin and the cation-dependent mannose-6-phosphate receptor are glycan-binding proteins recognizing discrete and specific carbohydrates involved in intracellular trafficking of membrane and secretory glycoproteins. In the case of calreticulin, glycan binding is associated with the quality control apparatus ensuring that only properly folded proteins will exit the endoplasmic reticulum. In the case of the cation-dependent mannose-6-phosphate receptor, phosphorylated mannose residues are recognized, allowing lysosomal proteins to be properly targeted. These paradigms are important for understanding diseases of protein misfolding and many lysosomal storage disorders. The ficolins are a class of glycan-binding proteins with affinity for N-acetyl residues that have distinct fold from other known lectins yet mediate pathogen recognition. Polymorphisms in ficoloin genes may also have pathophysiological implications.
Bacterial Adhesins and Lectins
Infection by bacteria is generally initiated by the specific recognition of host epithelial surfaces by adhesins and lectins. These GBPs are therefore virulence factors that play a role in the first step of adhesion and invasion. The GBPs are called adhesins when they are part of organelles, such as fimbriae and flagella. They are referred to as lectins when they are soluble, and lectin-domain when attached to other proteins, which are often hydrolytic enzymes also involved in the infection process. The human targets for bacterial adhesins and lectins are mostly fucosylated human histo-blood group and/or sialylated epitopes. Defining the biological role of bacterial adhesins and lectins together with their structure and specificity is a prerequisite for the development of strategies for inhibiting their binding to human tissues.
Toxigenic bacteria, which include some species of Escherichia, Shigella, Vibrio, and Clostridium, release protein toxins that alter essential host processes, including endocytic pathways, cell signaling and cytoskeletal reorganization. These toxins are key virulence factors that damage host tissues, and aid the spread of bacteria and evasion of immune clearance. Many bacterial toxins have been shown to bind host glycans. Glycan receptor specificity is critical for the pathogenic process, as it determines host susceptibility, tissue tropism, and the nature and spectrum of the resultant pathology. With contributions from the CFG, knowledge of the molecular and structural bases for toxin-glycan interactions is providing a rational framework for design of specific toxin inhibitors with considerable potential as anti-infective therapeutic agents.
Capsid Virus GBPs
A significant number of non-enveloped capsid viruses use glycans as cell attachment receptors. In some cases, viruses exclusively engage glycan structures at the cell surface, while in other cases glycans serve as co-receptors, and viruses also bind to proteins. The carbohydrate structures recognized by capsid viruses are diverse, ranging from gangliosides and other glycolipids to protein-bound glycans. Changes in carbohydrate binding specificity among family members of the same virus can often lead to altered tropism and pathogenicity. Thus, the elucidation of parameters that guide the specificity of interactions with glycans are of critical importance for understanding the complex biology of capsid viruses. The three paradigms listed below represent virus families whose glycan binding properties have been successfully studied by CFG investigators.
Enveloped Virus GBPs
Enveloped viruses initiate infection by using their surface glycoproteins to attach to receptors on the cell surface. These receptors may be proteins, lipids or glycans. Protein receptors may be cell specific, to direct the virus into only its target tissue (e.g. CD4 for HIV). Glycan receptors may provide broader cell specificity, or be just as specific as protein receptors, but historically the lack of glycan reagents has precluded definitive studies. The CFG, and especially the CFG glycan microarray, has allowed definition of glycan receptor specificity. The influenza viruses and parainfluenza viruses are the two main families of enveloped viruses that use glycan binding proteins for their attachment to host cells.
Eukaryotic Microbial GBPs
Eukaryotic microbes present a tremendous diversity of GBPs, many of which are crucial for microbial interactions within their own species or with other cell types. These relatively under-studied GBPs, both soluble and surface-displayed, include a variety of lectins and adhesins that are crucial for developmental processes, establishment of microbial communities, and interactions with the external environment. In the case of pathogenic organisms these GBPs can be key in host interactions, as in the case of the fungal adhesin paradigm below. The cyanovirin family provides another fascinating case with potential impact on human health.