Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements

Background

Diversity-generating retroelements (DGRs) provide organisms with a unique means for adaptation to a dynamic environment through massive protein sequence variation. The potential scope of this variation exceeds that of the vertebrate adaptive immune system. DGRs were known to exist only in viruses and bacteria until their recent discovery in archaea belonging to the ‘microbial dark matter’, specifically in organisms closely related to Nanoarchaeota. However, Nanoarchaeota DGR variable proteins were unassignable to known protein folds and apparently unrelated to characterized DGR variable proteins.

Results

To address the issue of how Nanoarchaeota DGR variable proteins accommodate massive sequence variation, we determined the 2.52 Å resolution limit crystal structure of one such protein, AvpA, which revealed a C-type lectin (CLec)-fold that organizes a putative ligand-binding site that is capable of accommodating 10¹³ sequences. This fold is surprisingly reminiscent of the CLec-folds of viral and bacterial DGR variable protein, but differs sufficiently to define a new CLec-fold subclass, which is consistent with early divergence between bacterial and archaeal DGRs. The structure also enabled identification of a group of AvpA-like proteins in multiple putative DGRs from uncultivated archaea. These variable proteins may aid Nanoarchaeota and these uncultivated archaea in symbiotic relationships.

Conclusions

Our results have uncovered the widespread conservation of the CLec-fold in viruses, bacteria, and archaea for accommodating massive sequence variation. In addition, to our knowledge, this is the first report of an archaeal CLec-fold protein.

     

The C-type lectin macrophage galactose-type lectin impedes migration of immature APCs

Dendritic cells (DCs) are the most potent APCs of the immune system that seed the peripheral tissues and lymphoid organs. In an immature state, DCs sample their surroundings for incoming pathogens. Upon Ag encounter, DCs mature and migrate to the lymph node to induce adaptive immune responses. The C-type macrophage galactose-type lectin (MGL), expressed in immature DCs, mediates binding to glycoproteins carrying GalNAc moieties. In the present study, we demonstrate that MGL ligands are present on the sinusoidal and lymphatic endothelium of lymph node and thymus, respectively. MGL binding strongly correlated with the expression of the preferred MGL ligand, alpha-GalNAc-containing glycan structures, as visualized by staining with the alpha-GalNAc-specific snail lectin Helix pomatia agglutinin. MGL(+) cells were localized in close proximity of the endothelial structures that express the MGL ligand. Strikingly, instead of inducing migration, MGL mediated retention of human immature DCs, as blockade of MGL interactions enhanced DC trafficking and migration. Thus, MGL(+) DCs are hampered in their migratory responses and only upon maturation, when MGL expression is abolished; these DCs will be released from their MGL-mediated restraints.     

Preferences for uptake of carbohydrate-coated liposomes by C-type lectin receptors as antigen-uptake receptors

We evaluated the carbohydrate preferences of the C-type lectin receptors (CLRs) SIGNR1, SIGNR3, and Langerin as pathogen-uptake receptors based on uptake of liposomes consisting of cholesterol, DPPC, and various neoglycolipids at molar ratios of 10:10:1 and 10:7:4, respectively, using non-phagocytic CHO cells that express these receptors transiently. SIGNR1-expressing cells ingested liposomes coated with neoglycolipids with terminal mannose residues, such as Man2-, Man3-, and Man5-DPPE, and with a terminal N-acetylglucosamine. SIGNR1 mediated uptake of Man3-DPPE-coated liposomes most efficiently. Uptake of liposomes with lower neoglycolipid content by SIGNR3- or Langerin-expressing cells was slight or negligible, but uptake into these cells was detected for liposomes with higher neoglycolipid content. SIGNR1-expressing cells clearly ingested liposomes coated with Lewis X antigen, whereas SIGNR3- or Langerin-expressing cells barely ingested these liposomes, even at the higher neoglycolipid content. In contrast, SIGNR3 or Langerin, but not SIGNR1, mediated uptake of liposomes coated with blood group H antigen. These results indicate that CLRs with similar carbohydrate-recognition characteristics have distinct properties as pathogen-uptake receptors for carbohydrate-decorated particles.     

Protein 3D structure computed from evolutionary sequence variation

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å C_α-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.     

Amino acid sequence and characterization of C-type lectin purified from the snake venom of Crotalus ruber

Galactoside-binding lectin was purified from the snake venom of Crotalus ruber by affinity chromatography on a lactose-agarose column, and the complete amino acid sequence was determined. The C. ruber venom lectin (CRL) showed a single band of 28 kDa by SDS-polyacrylamide electrophoresis under non-reducing conditions, but it showed a single band of 15 kDa under reducing conditions, indicating that CRL is a disulfide-linked homodimer of 15 kDa subunit. CRL specifically recognized beta-galactosides such as thiodigalactoside followed by N-acetylgalactosamine when examined with their inhibitory effects on CRL-induced hemagglutination. A CRL subunit was composed of 135 residues containing nine Cys residues and showed a high similarity to other C-type galactoside-binding lectins from snake venoms. C. atrox lectin (CAL) showed almost the same sequence except for eight amino acid residues. Neither CRL nor CAL induced platelet aggregation by itself or inhibited platelet aggregation mediated by von Willebrand factor or fibrinogen with agonists. CRL showed a similar oligomeric form and the sugar specificity as CAL, but it showed different divalent cation sensitivity such as Mn(2+) and Ni(2+). Homology modeling suggested that the amino acid substitution found in CRL does not affect sugar recognition of the lectin but might alter the conformation and influence the sugar binding pocket induced by the metal-ion binding.     

Identification of sialoadhesin as a dominant lymph node counter-receptor for mouse macrophage galactose-type C-type lectin 1

In the sensitization phase of contact hypersensitivity in mice, dermal macrophages (MOs) expressing MO galactose-type C-type lectin1 (MGL1) are known to migrate from the dermis to lymph nodes (LNs) where they accumulate in the subcapsular sinus, interfollicular regions, and areas surrounding high endothelial venules. We hypothesize that the interactions between MGL1 and its ligands determine the localizations of MGL1-positive cells within the LNs. In the present study, our major aim was to isolate MGL1 counter-receptor(s) from lysates of LNs using affinity chromatography with immobilized recombinant MGL1. Fractions bound and eluted with EDTA were analyzed by SDS-PAGE and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. One of the predominant components was sialoadhesin (Sn, Siglec-1). Sn from lysates of LNs was immobilized on microtiter plates precoated with anti-Sn monoclonal antibody, and binding of recombinant MGL1 and adhesion of cells expressing MGL1 were tested. The binding of recombinant MGL1 to Sn was shown to be dependent on Ca2+ and N-glycans on Sn. MGL1-transfected Chinese hamster ovary cells adhered to the Sn-coated plates, whereas mock transfectants did not. Immunohistochemical localization of anti-Sn monoclonal antibody in LN coincided with the subcapsular sinus area to which recombinant MGL1 was bound. Furthermore, the distribution of MGL1+ cells after sensitization with FITC was demonstrated to overlap with that of Sn within the subcapsular sinus of draining LNs. These results suggest that Sn acts as an endogenous counter-receptor for MGL1.     

The corpus callosum as an evolutionary innovation

The corpus callosum (CC) is the major interhemispheric fibre bundle in the eutherian brain and has been described as a true evolutionary innovation. This paper reviews the current literature with regard to functional, developmental and genetic concepts that may help elucidate the evolutionary origin of this structure. It has been suggested that the CC arose in the eutherian brain as a more direct and, therefore, more effective system for the interhemispheric integration of topographically organized sensory cortices than the anterior commissure (AC) and hippocampal commissure (HC) already present in nonplacental mammals. It can also be argued, however, that the ability of the CC to integrate the newly evolving motor cortices of placental mammals may have played a role in the evolutionary fixation of this structure. Investigations into the developmental mechanism involved in the formation of the CC and their underlying patterns of gene expression make it possible to formulate a tentative hypothesis about the evolutionary origin of this commissure. This paper suggests that changes in the developmental patterns of the expression of certain regulatory genes may have allowed a first group of callosal pioneering axons to cross the cortical midline. These pioneering fibres may have used the axons of the HC to find their way across the midline. Additional callosal fibres may then have fasciculated with these pioneers. Once the CC had formed in this way, more complex systems of axonal guidance may have evolved over time, thus enabling a gradual increase in the size and complexity of the CC.     

The ligand-binding loops in the tunicate C-type lectin TC14 are rigid

C-type lectin-like domains are very common components of extracellular proteins in animals. They bind to a variety of ligands, including carbohydrates, proteins, ice, and CaCO3 crystals. Their structure is characterized by long surface loops in the area of the protein usually involved in ligand binding. The C-type lectin TC14 from Polyandrocarpa misakiensis specifically binds to D-galactose by coordination of the sugar to a bound calcium atom. We have studied the dynamic properties of TC14 by measuring 15N longitudinal and transverse relaxation rates as well as [1H-15N] heteronuclear NOEs. Relaxation rates and heteronuclear NOE data for holo-TC14 show minimal variations, indicating that there is no substantial difference in rigidity between the elements of regular secondary structure and the extended surface loops. Anisotropic tumbling of the elongated TC14 dimer can account for the main fluctuations in relaxation rates. Loss of the bound calcium does not significantly alter the internal dynamics, suggesting that the stability of the loop region is intrinsic and not dependent on the coordination of the calcium ion. Chemical shift differences between the holo and apo form show that main structural changes occur in the calcium-binding site, but smaller structural changes are propagated throughout the molecule without affecting the overall fold. The disappearance of two resonances for residues following the conserved cis-proline 87 (which is located in the calcium-binding site) in the apo form indicates conformational change on an NMR time scale between the cis and trans configurations of this peptide bond in the absence of calcium. Possible implications of these findings for the ligand binding in C-type lectin-like domains are discussed.     

The carbohydrate-recognition domain of Dectin-2 is a C-type lectin with specificity for high mannose

We examined the carbohydrate-binding potential of the C-type lectin-like receptor Dectin-2 (Clecf4n). The carbohydrate-recognition domain (CRD) of Dectin-2 exhibited cation-dependent mannose/fucose-like lectin activity, with an IC(50) for mannose of approximately 20 mM compared to an IC(50) of 1.5 mM for the macrophage mannose receptor when assayed by similar methodology. The extracellular domain of Dectin-2 exhibited binding to live Candida albicans and the Saccharomyces-derived particle zymosan. This binding was completely abrogated by cation chelation and was competed by yeast mannans. We compared the lectin activity of Dectin-2 with that of two other C-type lectin receptors (mannose receptor and SIGNR1) known to bind fungal mannans. Both mannose receptor and SIGNR1 were able to bind bacterial capsular polysaccharides derived from Streptococcus pneumoniae, but interestingly they exhibited distinct binding profiles. The Dectin-2 CRD exhibited only weak interactions to some of these capsular polysaccharides, indicative of different structural or affinity requirements for binding, when compared with the other two lectins. Glycan array analysis of the carbohydrate recognition by Dectin-2 indicated specific recognition of high-mannose structures (Man(9)GlcNAc(2)). The differences in the specificity of these three mannose-specific lectins indicate that mannose recognition is mediated by distinct receptors, with unique specificity, that are expressed by discrete subpopulations of cells, and this further highlights the complex nature of carbohydrate recognition by immune cells.     

Targeted sequence capture as a powerful tool for evolutionary analysis1

Next-generation sequencing technologies (NGS) have revolutionized biological research by significantly increasing data generation while simultaneously decreasing the time to data output. For many ecologists and evolutionary biologists, the research opportunities afforded by NGS are substantial; even for taxa lacking genomic resources, large-scale genome-level questions can now be addressed, opening up many new avenues of research. While rapid and massive sequencing afforded by NGS increases the scope and scale of many research objectives, whole genome sequencing is often unwarranted and unnecessarily complex for specific research questions. Recently developed targeted sequence enrichment, coupled with NGS, represents a beneficial strategy for enhancing data generation to answer questions in ecology and evolutionary biology. This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. These strategies can be applied to questions at both the infra- and interspecific levels, including those involving parentage, gene flow, divergence, phylogenetics, reticulate evolution, and many more. Here we provide a brief overview of targeted sequence enrichment, and emphasize the power of this technology to increase our ability to address a wide range of questions of interest to ecologists and evolutionary biologists, particularly for those working with taxa for which few genomic resources are available.     

Human macrophage C-type lectin specific for galactose and N-acetylgalactosamine promotes filovirus entry

Filoviruses cause lethal hemorrhagic disease in humans and nonhuman primates. An initial target of filovirus infection is the mononuclear phagocytic cell. Calcium-dependent (C-type) lectins such as dendritic cell- or liver/lymph node-specific ICAM-3 grabbing nonintegrin (DC-SIGN or L-SIGN, respectively), as well as the hepatic asialoglycoprotein receptor, bind to Ebola or Marburg virus glycoprotein (GP) and enhance the infectivity of these viruses in vitro. Here, we demonstrate that a recently identified human macrophage galactose- and N-acetylgalactosamine-specific C-type lectin (hMGL), whose ligand specificity differs from DC-SIGN and L-SIGN, also enhances the infectivity of filoviruses. This enhancement was substantially weaker for the Reston and Marburg viruses than for the highly pathogenic Zaire virus. We also show that the heavily glycosylated, mucin-like domain on the filovirus GP is required for efficient interaction with this lectin. Furthermore, hMGL, like DC-SIGN and L-SIGN, is present on cells known to be major targets of filoviruses (i.e., macrophages and dendritic cells), suggesting a role for these C-type lectins in viral replication in vivo. We propose that filoviruses use different C-type lectins to gain cellular entry, depending on the cell type, and promote efficient viral replication.     

The uncertainty principle as an evolutionary engine.

Heisenberg's uncertainty principle in quantum mechanics underlies the genesis of evolutionary variability. When the uncertainty principle is coupled with the incontrovertible principle of the conservation of energy and material resources, there appears an uncertainty relationship between local fluctuations in the quantities to be conserved on a global scale and the rate of their local variation. Since the local fluctuations are accompanied by the non-vanishing rate of variation because of the uncertainty relationship, they generate subsequent fluctuations. Generativity latent in the uncertainty relationship is non-random and ubiquitous all through various evolutionary stages from abiotic synthesis of monomers and polymers up to the emergence of behavior-induced variability of organisms.     

The robustness of altruism as an evolutionary strategy

Kin selection, reciprocity and group selection are widely regarded as evolutionary mechanisms capable of sustaining altruism among humans andother cooperative species. Our research indicates, however, that these mechanisms are only particular examples of a broader set of evolutionary possibilities.In this paper we present the results of a series of simple replicator simulations, run on variations of the 2–player prisoner's dilemma, designed to illustrate the wide range of scenarios under which altruism proves to be robust under evolutionary pressures. The set of mechanisms we explore is divided into four categories:correlation, group selection, imitation, and punishment. We argue that correlation is the core phenomenon at work in all four categories.     

The beta-beta-alpha fold: explorations in sequence space

The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a betabetaalpha fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized. The experimental stabilities of five of these peptides are strongly correlated with the energies calculated by ORBIT. However, when a peptide with a mutation in the beta-turn is examined, the calculated stability does not accurately predict the experimentally determined stability. The NMR solution structure of a peptide incorporating this mutation (FSD-EY) reveals that the register between the beta-strands is different from the model structure used to select and score the sequences. FSD-EY has a type I' turn instead of the target EbaaagbE turn (rubredoxin knuckle). Two additional peptides that have improved side-chain to backbone hydrogen bonding and turn propensity for the target turn were characterized. Both are of stability comparable to that of FSD-1. These results demonstrate the robustness of the ORBIT protein design methods and underscore the need for continued improvements in negative design.     

Oligomerisation and carbohydrate binding in an Atlantic salmon serum C-type lectin consistent with non-self recognition

A C-type lectin was previously isolated from the blood of healthy Atlantic salmon (Salmo salar) and this salmon serum lectin (SSL) was found to opsonise bacteria. Selective binding to bacteria in vivo requires that the lectin be able to recognise a carbohydrate pattern on the bacterial surface distinguishable from that of the host. In order to investigate this selectivity in the lectin, a phage-display antibody was prepared and then used for detection of lectin by Western blotting. A carbohydrate binding-inhibition assay with Western blot detection of the lectin showed mannose to be the primary ligand and related sugars including glucose, N-acetylglucosamine and methyl alpha-D-mannopyranoside to be additional ligands of this lectin. The SSL in serum detected by Western blotting was shown to form a complex oligomer. These results show that the salmon serum lectin is oligomeric in blood and that it recognizes a broad spectrum of carbohydrates with optimal binding to mannose. The lectin might therefore be an ideal opsonin for multiple salmon pathogens with carbohydrate arrays on their surfaces. No similar lectins were identified in the sera of other fish by Western blotting using the phage-display antibody. Molecular analysis will be required in order to determine whether homologous lectins are expressed in related fish species. It is anticipated that similar lectins might have related pathogen recognition roles in divergent fish species.     

Exacerbation of experimental autoimmune encephalomyelitis in mice deficient for DCIR,an inhibitory C-type lectin receptor

Dendritic cell immunoreceptor (DCIR) is a C-type lectin receptor containing a carbohydrate recognition domain in its extracellular portion and an immunoreceptor tyrosine–based inhibitory motif, which transduces negative signals into cells, in its cytoplasmic portion. Previously, we showed that Dcir^–/– mice spontaneously develop autoimmune diseases such as enthesitis and sialadenitis due to excess expansion of dendritic cells (DCs), suggesting that DCIR is critically important for the homeostasis of the immune system. In this report, we analyzed the role of DCIR in the development of experimental autoimmune encephalomyelitis (EAE), an autoimmune disease model for multiple sclerosis. We found that EAE was exacerbated in Dcir^–/– mice associated with severe demyelination of the spinal cords. The number of infiltrated CD11c⁺ DCs and CD4⁺ T cells into spinal cords was increased in Dcir^–/– mice. Recall proliferative response of lymph node cells was higher in Dcir^–/– mice compared with wild-type mice. These observations suggest that DCIR is an important negative regulator of the immune system, and Dcir^–/– mice should be useful for analyzing the roles of DCIR in an array of autoimmune diseases.     

Identification of a chicken CLEC-2 homologue, an activating C-type lectin expressed by thrombocytes

Receptors on natural killer (NK) cells are classified as C-type lectins or as Ig-like molecules, and many of them are encoded by two genomic clusters designated natural killer gene complex (NKC) and leukocyte receptor complex, respectively. Here, we describe the analysis of an NKC-encoded chicken C-type lectin, previously annotated as homologue to CD94 and NKG2 and thus designated chicken CD94/NKG2. To further elucidate its potential function on NK cells, we produced a specific mab by immunizing with stably transfected HEK293 cells expressing this lectin. Staining of various chicken tissues revealed minimal reactivity with bursal, or thymus cells. In peripheral blood mononuclear cell and spleen, however, the mab reacted with virtually all thrombocytes, whereas most NK cells in organs such as embryonic spleen, lung and intestine were found to be negative. These findings indicate that the gene may not resemble CD94/NKG2, but rather a CLEC-2 homologue, a claim further supported by sequence features such as an additional extracellular cysteine residue and the presence of a cytoplasmic motif known as a hem immunoreceptor tyrosine-based activation motif, found in C-type lectins such as Dectin-1, CLEC-2, but not CD94/NKG2. The biochemical analyses demonstrated that CLEC-2 is present on the cell surface as heavily glycosylated homodimer, which upon mab crosslinking induced thrombocyte activation, as measured by CD107 expression. These analyses reveal that the chicken NKC may not encode NK cell receptor genes, in particular not CD94 or NKG2 genes, and identifies a chicken CLEC-2 homologue.