Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
Accepted on February 17, 2001;
Abstract
Classes of intracellular lectins that recognize core-type structures and mediate intracellular glycoprotein trafficking are present in vertebrates, model invertebrates such as Caenorhabditis elegans and Drosophila melanogaster, plants, and yeasts. Lectins that recognize more complex structures at the cell surface, such as C-type lectins and galectins, are also found in invertebrate organisms as well as vertebrates, but the functions of these proteins have evolved differently in different animal lineages.
Key words: carbohydrate-recognition domain/genomics/evolution/lectins
Introduction
Complex oligosaccharide structures displayed at cell surfaces, incorporated into the extracellular matrix, and attached to secreted glycoproteins can serve structural roles, mediate movement of glycoconjugates to the cell surface, or act as markers that mediate cellcell and cell-matrix recognition events. The nonstructural roles of sugars generally require the participation of sugar-binding lectins (Drickamer and Taylor, 1998). Lectins are often complex, multidomain proteins, but sugar-binding activity can usually be ascribed to a single protein module within the lectin polypeptide. Such a module is designated a carbohydrate-recognition domain (CRD). CRDs in vertebrate lectins fall into a number of structurally distinct families of protein modules. Some of the best characterized of these CRD groups are summarized in Table I. The list is by no means complete, as sugar-binding activity has also been described for other protein modules that have folds not represented in this list. For example, several structurally distinct types of proteins have been shown to bind glycosaminoglycans. Although it has been proposed that these proteins might share a common local binding motif (Cardin and Weintraub, 1989
), such a motif would have to be presented in the context of many different protein structures. For reasons of space, this survey of potential CRDs in model organisms discussed is restricted to the structural categories shown in Table I.
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Comparisons of CRDs in each structural group allow the generation of amino acid sequence profiles or motifs that can be used to screen sequence databases for related protein modules. The conserved residues that define these profiles generally reflect the requirements for specific amino acid residues, mostly found in the protein interior, that determine a basic protein fold. Each profile thus serves to identify protein modules that are similar in overall structure to CRDs in a particular group. In many cases, however, such modules serve functions other than sugar binding. Sugar-binding to a bona fide CRD generally occurs in a shallow indentation on the protein surface. For each type of CRD, sugar-binding activity is thus determined by a second set of residues that function within the context of the structural fold associated with that type of CRD. Screening of genomic sequences for potential lectins is thus a two-step process. First, protein modules that have CRD-like folds are identified by profile analysis. The sequences of these domains are then examined for residues that form sugar-binding sites in known lectins to allow informed speculation about which of them may actually mediate carbohydrate binding.
The genomic sequences of the single-celled yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, the nematode Caenorhabditis elegans (Consortium, 1998) and the fruit fly Drosophila melanogaster (Adams et al., 2000
) can provide insight into lectin functions that can be understood by analysis of these model organisms. Using an approach previously employed for the C-type CRDs of C. elegans (Drickamer and Dodd, 1999
), sequence databases have been screened with various CRD profiles to identify protein containing potential CRDs. Sequence alignments have then been used to compare these modules to vertebrate CRDs to identify which ones are likely to bind sugars. The alignments that form the basis for the conclusions summarized here will be found at <http://ctld.glycob.ox.ac.uk>. Further examination of the complete sequences of the proteins, using hydropathy plots and a comprehensive set of protein module profiles, provides insight into their overall domain organization. The presence of other types of protein modules, such as membrane anchors, often suggests possible functions of the CRD-containing proteins. Comparison of the different structural classes of lectins in vertebrates, invertebrates, yeasts, bacteria, and plants also provides a basis for understanding the coevolution of glycan structures and glycan recognition processes.
Lectins in the endoplasmic reticulum: calnexin and calreticulin
Calnexin and calreticulin form part of the quality control system for glycoproteins in the endoplasmic reticulum (Trombetta and Helenius, 1998; Parodi, 2000
). They bind to terminal glucose residues on N-linked oligosaccharides and retain misfolded glycoproteins in the endoplasmic reticulum. Calnexin is a transmembrane protein and calreticulin is a soluble protein retained in the lumen by a C-terminal retention signal. The luminal N-terminal portion of calnexin is very similar to calreticulin, although one of the repeated segments of calnexin is absent from calreticulin.
Homologues of calnexin and calreticulin have been identified in unicellular as well as multicellular eukaryotes. Based on overall sequence similarity and the absence of a membrane anchor from calreticulin, the homologues identified in yeasts resemble calnexin most closely (Parlati et al., 1995). Homologues of both proteins are found in C. elegans as well as Drosophila. Pairwise comparisons show close similarity between calnexins from distant species: S. pombe and human calnexin sequences are 43% identical (Figure 1A). Recent independent duplications in the lineages leading to mammals and Drosophila have generated multiple forms of the membrane-anchored protein in these species. Calnexin and calreticulin do not appear to be part of a larger family of proteins.
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L-type lectins in plants and animals
A second family of lectins involved in protein sorting in luminal compartments of animal cells is composed of two members. ERGIC-53 is localized to the endoplasmic reticulumGolgi intermediate compartment (Itin et al., 1996) and VIP-36 is found in Golgi and post-Golgi portions of the secretory pathway (Fiedler and Simons, 1994
). Both ERGIC-53 and VIP-36 are type I transmembrane proteins. The luminal portions of these proteins correspond to the single folded domain of the soluble lectins found in abundance in the seeds of leguminous plants (Sharon and Lis, 1990
). For this reason, they are designated L-type CRDs.
Plant and animal L-type lectins have divergent sequences and different molecular properties: the plant lectins are secreted, soluble proteins and are found at high level in specialized tissues, and the animal L-type lectins are membrane-bound luminal proteins and are found at low levels in many different cell types. These differences reflect the fact that plant and animal L-type lectins are likely to serve different functions. Nevertheless, it seems likely that the L-type CRDs have retained similar mechanisms of sugar binding. Certain key residues in four loop regions that contribute to the binding sites in the plant proteins (Sharma and Surolia, 1997; Rini, 1995
) are conserved in all of the animal and plant L-type CRDs.
ERGIC-53 and VIP-36 orthologues are both found in C. elegans and Drosophila (Figure 2). These proteins contain the key sugar-binding residues and seem likely to serve sorting functions like ERGIC-53 and VIP-36. In contrast, the EMP47 gene product in S. cerevisiae is a relatively divergent homologue of the L-type plant and animal lectins. Virtually all of the key residues that form the sugar-binding sites in the legume lectins are absent from the yeast protein, suggesting that it probably lacks sugar-binding activity and serves a different function. The presence of an homologous protein in yeast indicates that the L-type CRD fold is ancient, but the sequence comparisons suggest that a sugar-binding L-type CRD first appeared in the common precursor of plants and animals.
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A third family of lectins involved in intracellular trafficking consists of two types of receptors that recognize mannose 6-phosphate residues on oligosaccharides of hydrolases that must be directed from the Golgi apparatus to their lysosomal destination. The cation-dependent mammalian mannose 6-phosphate receptor contains a single P-type CRD, and the cation-independent receptor contains 15 homologous domains, 2 of which have mannose 6-phosphate-binding activity (Figure 3) (Dahms et al., 1989). Because the binding sites for the sugar ligand and the divalent metal ion cofactor are formed mostly from backbone amide and carbonyl groups, only five amino acid side chains in the sugar-binding subsite are common to the domains that interact with mannose 6-phosphate (Roberts et al., 1998
). Overall, the sugar-binding P-type CRDs are no more closely related to each other than they are to the non-binding domains.
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C-type lectin-like proteins
C-type lectins are the most diverse family of animal lectins. These lectins are generally multidomain proteins, in which C-type CRDs provide Ca2+-dependent sugar-recognition activity and a variety of other modules then initiate a broad range of biological processes, such as adhesion, endocytosis, and pathogen neutralization (Drickamer and Taylor, 1993; Weis et al., 1998
). The domain organizations of some of the vertebrate C-type lectins are summarized in Figure 4A. The sugar-binding sites in vertebrate C-type CRDs are formed in part by a bound Ca2+, which must be present for sugar binding to occur. The C-type CRDs form a subgroup of a larger family of protein domains that share a common protein fold and are designated C-type lectin-like domains (CTLDs) (Weis et al., 1998
). Currently about a hundred human proteins that contain CTLDs have been described, and roughly half of these have been proposed to function as C-type CRDs. Many CTLDs bind to protein ligands rather than to sugars, and only some of these binding interactions are Ca2+-dependent.
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In general, the Drosophila CTLD sequences are more closely related to each other than they are to CTLDs from C. elegans or vertebrates, a finding that is consistent with the idea that there has been a largely independent radiation of the CTLDs in different animal lineages. The only exceptions to this rule are the two Drosophila proteins in group E, one of which is the product of the furrowed gene (Leshko-Lindsay and Corces, 1997), which are distantly related to the product of the C54G4.4 locus in C. elegans. In addition to the weak similarity in the CTLD sequences, these three proteins share a similar domain organization, suggesting that they may have related functions.
A comprehensive analysis of the C. elegans genome identified 19 of the 183 CTLDs that contain most of the five residues needed to form the primary Ca2+-binding site in vertebrate C-type CRDs (Drickamer and Dodd, 1999). Of these, seven have sequences consistent with formation of mannose- or N-acetylglucosamine-binding sites similar to those in vertebrate C-type CRDs. A similar analysis of the 32 Drosophila CTLDs reveals that only 6 show conservation of potential Ca2+-liganding residues at positions that correspond to the five residues that form the primary Ca2+- and sugar-binding site in mammalian C-type CRDs (Weis et al., 1992
). In two cases, the pattern of Ca2+-liganding residues is identical to that seen in mannose-binding C-type CRDs, and in two cases it corresponds to the arrangement seen in galactose-binding C-type CRDs. A protein product of one of the genes predicted to encode a galactose-binding CTLD has in fact been characterized as a galactose-binding lectin (Haq et al., 1996
), providing evidence for the utility of the comparative approach to identification of potential binding activity.
The presence of the Ca2+- and sugar-binding site residues in conserved positions in a subset of CTLDs in mammals, C. elegans, and Drosophila might suggest that at least one CTLD present in their common progenitor contained these residues. However, the potential galactose- or mannose-binding C-type CRDs in these different species are less similar in overall sequence than are the various CTLDs within each species. Thus, it appears that the sugar-binding activity originated independently in each lineage (Figure 4C). Although this sequence of events might seem unlikely, it should be noted that the number of residues required to generate a sugar-binding site in the CTLD framework is quite small.
Galectins
Although mammalian galectins lack conventional signal sequences, they reach the cell surface by a novel mechanism and bind to glycoconjugates in the plasma membrane and in the extracellular matrix (Barondes et al., 1994). The galectins consist of globular galectin-type CRDs with relatively minor accessory domains (Cooper and Barondes, 1999
). A galectin-type CRD comprises a ß sandwich similar in overall topology to the L-type CRDs. However, the lack of sequence similarity and the different way in which sugar-binding sites are constructed in these two families of domains suggest that this topological similarity results from convergent evolution. Most galectins contain multiple sugar-binding sites, due to the presence of two galectin-type CRDs in a single polypeptide or as a result of dimerization (Figure 5). A common function of the galectins may be to crosslink N-acetyllactosamine-containing structures found at cell surfaces and in the extracellular matrix. Studies of knockout mice suggest that multiple galectins provide distinct but overlapping functions (Colnot et al., 1998
).
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The overall sequences of the mammalian galectin-type CRDs are marginally more similar to each other than they are to sequences of any of the invertebrate galectins. In other words, no invertebrate galectin is particularly similar to any one mammalian protein. Some of the invertebrate proteins also contain N- or C-terminal extensions that are different from those found in any known mammalian galectins. These results suggest independent radiation of galectins in the vertebrate and invertebrate lineages. Thus, some of the invertebrate galectins may perform functions that are distinct from the functions of mammalian galectins.
I-type lectins
The siglec family of cell surface adhesion receptors are sialic acidbinding proteins that contain I-type CRDs derived from the immunoglobulin fold (Crocker et al., 1998). The evolution of sugar-binding activity in these I-type CRDs is best considered in the context of the evolution of immunoglobulin superfamily modules (Teichmann and Chothia, 2000). It has been noted that evolution of the siglecs parallels the appearance of sialic acidcontaining ligands at cell surfaces (Angata and Varki, 2000).
Ricin-like domains
The ricin-like or R-type CRDs are the only sugar-binding protein modules from animal lectins that have also been found in bacteria. The galactose-binding B chain of the plant toxin ricin is formed of two homologous domains, each consisting of three lobes arranged as a ß-trefoil around a threefold axis (Rutenber and Robertus, 1991; Murzin et al., 1992
). Many bacterial hydrolases resemble the ricin precursor, in which N-terminal hydrolytic domains are attached to C-terminal R-type CRDs (Figure 6) (Fujimoto et al., 2000
). In mammals, UDP-N-acetylgalactosamine: polypeptide N-acetylgalactosaminyltransferases that initiate synthesis of O-linked oligosaccharides in the cis Golgi have a related organization (Clausen and Bennett, 1996
). The C-terminal R-type CRDs in these proteins probably direct them to substrates (Hassan et al., 2000
; Fujimoto et al., 2000
). In contrast, proteins in the macrophage mannose receptor family contain R-type CRDs that are combined with a different set of protein modules (Taylor, 1997
). In the mannose receptor, this domain interacts with sulfated N-acetylgalactosamine residues on glycoprotein hormones, leading to their clearance from the circulation (Fiete et al., 1998
).
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Discussion
Three general patterns emerge from the comparative analysis of lectins summarized in Figures 7 and 8. First, sugar-binding activities evolved from core recognition toward recognition of terminal elaborations (Drickamer and Taylor, 1998). Second, biological functions associated with sugar binding evolved from intracellular to extracellular. Third, both within and between species, the diversity of the lectins, the sugars that they recognize, and the biological functions associated with this recognition is greatest for the extracellular lectins that have evolved most recently.
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Relatively simple invertebrate organisms may serve as useful models for some (but not all) of the functions of sugar-binding proteins in mammals. The early intracellular sorting events involving calnexin and L-type lectins as well as the role of R-type CRDs in glycosyltransferases are likely to be quite similar, whereas later sorting events involving the mannose 6-phosphate receptors will probably be different. At the cell surface, the role of some of the galectins may be similar in all animals, so that genetic and developmental analysis of the model invertebrates is likely to illuminate studies of the vertebrate proteins as well. In contrast, the greater diversity of invertebrates and vertebrates proteins containing CTLDs suggests that these proteins probably participate in more specialized functions of glycans that are unique to different groups of animals.
Acknowledgments
This work was funded by grant 041845 from the Wellcome Trust. We thank Maureen Taylor for critical reading of the manuscript. Use of SRS software and FASTA searching provided on the European Bioinformatics Institute Web site (<http://ebi.ac.uk>), the profile scanning software of the Swiss Institute for Experimental Cancer Research (<http://www.isrec.isb-sib.ch/software/PFSCAN_form.html>) and the sequence analysis software on the ExPASy Molecular Biology Server provided by the Swiss Institute of Bioinformatics (<http://www.expasy.ch/cgi-bin/protscale.pl>) is acknowledged.
Abbreviations
CRD, carbohydrate-recognition domain; CTLD, C-type lectin-like domain.
Footnotes
1 Present address: Wellcome Trust Centre for the Study of Molecular Mechanisms in Disease, Cambridge University, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK
2 To whom correspondence should be addressed
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