Diversity of the immunoglobulin gene superfamily

Genomic and transcriptional analysis of genes containing fibrinogen and IgSF domains in the schistosome vector Biomphalaria glabrata, with emphasis on the differential responses of snails susceptible or resistant to Schistosoma mansoni

Achieving a deeper understanding of the factors controlling the defense responses of invertebrate vectors to the human-infecting pathogens they transmit will provide needed new leads to pursue for control. Consequently, we provide new genomic and transcriptomic insights regarding FReDs (containing a fibrinogen domain) and FREPs (fibrinogen domain and one or two IgSF domains) from the planorbid snail Biomphalaria glabrata, a Neotropical vector of Schistosoma mansoni, causative agent of human intestinal schistosomiasis. Using new bioinformatics approaches to improve annotation applied to both genome and RNA-Seq data, we identify 73 FReD genes, 39 of which are FREPs. We provide details of domain structure and consider relationships and homologies of B. glabrata FBG and IgSF domains. We note that schistosome-resistant (BS-90) snails mount complex FREP responses following exposure to S. mansoni infection whereas schistosome-susceptible (M line) snails do not. We also identify several coding differences between BS-90 and M line snails in three FREPs (2, 3.1 and 3.2) repeatedly implicated in other studies of anti-schistosome responses. In combination with other results, our study provides a strong impetus to pursue particular FREPs (2, 3.1, 3.2 and 4) as candidate resistance factors to be considered more broadly with respect to schistosome control efforts, including involving other Biomphalaria species vectoring S. mansoni in endemic areas in Africa.

Structural Characterization and Function Prediction of Immunoglobulin-like Fold in Cell Adhesion and Cell Signaling

Domains that belong to an immunoglobulin (Ig) fold are extremely abundant in cell surface receptors, which play significant roles in cell-cell adhesion and signaling. Although the structures of domains in an Ig fold share common topology of β-barrels, functions of receptors in adhesion and signaling are regulated by the very heterogeneous binding between these domains. Additionally, only a small number of domains are directly involved in the binding between two multidomain receptors. It is challenging and time consuming to experimentally detect the binding partners of a given receptor and further determine which specific domains in this receptor are responsible for binding. Therefore, current knowledge in the binding mechanism of Ig-fold domains and their impacts on cell adhesion and signaling is very limited. A bioinformatics study can shed light on this topic from a systematic point of view. However, there is so far no computational analysis on the structural and functional characteristics of the entire Ig fold. We constructed nonredundant structural data sets for all domains in Ig fold, depending on their functions in cell adhesion and signaling. We found that data sets of domains in adhesion receptors show different binding preference from domains in signaling receptors. Using structural alignment, we further built a common structural template for each group of a domain data set. By mapping the protein-protein binding interface of each domain in a group onto the surface of its structural template, we found binding interfaces are highly overlapped within each specific group. These overlapped interfaces, we called consensus binding interfaces, are distinguishable among different data sets of domains. Finally, the residue compositions on the consensus interfaces were used as indicators for multiple machine learning algorithms to predict if they can form homotypic interactions with each other. The overall performance of the cross-validation tests shows that our prediction accuracies ranged between 0.6 and 0.8.

Human cytomegalovirus pUL10 interacts with leukocytes and impairs TCR-mediated T-cell activation

Human cytomegalovirus (HCMV) is known to exert suppressive effects on the host immune system through expression of various viral genes, thus directly and indirectly affecting antiviral immunity of the infected individuals. We report here that HCMV UL10 encodes a protein (pUL10) with immunosuppressive properties. UL10 has been classified as a member of the HCMV RL11 gene family. Although pUL10 is known to be dispensable for viral replication in cultured cells, its amino-acid sequence is well conserved among different HCMV isolates, suggesting that the protein has a crucial role in viral survival in the host environment. We show that pUL10 is cleaved from the cell surface of fibroblasts as well as epithelial cells and interacts with a cellular receptor ubiquitously expressed on the surface of human leukocytes, demonstrated by ex vivo cell-based assays and flow cytometric analyses on both lymphoid cell lines and primary blood cells. Furthermore, preincubation of peripheral blood mononuclear cells with purified pUL10 ectodomain results in significantly impaired proliferation and substantially reduced pro-inflammatory cytokine production, in particular in CD4⁺ T cells upon in vitro T-cell stimulation. The inhibitory effect of pUL10 is also observed on antigen receptor-mediated intracellular tyrosine phosphorylation in a T-cell line. Based on these observations, we suggest that pUL10 is a newly identified immunomodulatory protein encoded by HCMV. Further elucidation of interactions between pUL10 and the host immune system during HCMV may contribute to finding ways towards new therapies for HCMV infection.

Comparative biophysical characterization of chicken β2-microglobulin

β(2)-microglobulin (β(2)m) is the smallest building block of molecules belonging to the immunoglobulin superfamily. By comparing thermodynamic and structural characteristics of chicken β(2)m with those of other species, we seek to elucidate whether it is possible to pinpoint features that set the avian protein apart from other β(2)m. The thermodynamic assays revealed that chicken β(2)m exhibits a lower melting temperature than human β(2)m, and the H/D exchange behavior observed by infrared spectroscopy indicates a more flexible structure of the former protein. To understand these differences at a molecular level, we determined the structure of free chicken β(2)m by X-ray crystallography to a resolution of 2.0 Å. Our comparisons indicate that certain biophysical characteristics of the chicken protein, particularly its conformational flexibility, diverge considerably from those of the other β(2)m analyzed, although basic structural features have been retained through evolution.

Innate and adaptive autoimmunity directed to the central nervous system

The immune system has two major components, an innate arm and an adaptive arm. Certain autoimmune diseases of the brain represent examples of disorders where one of these constituents plays a major role. Some rare autoimmune diseases involve activation of the innate arm and include chronic infantile neurologic, cutaneous, articular (CINCA) syndrome. In contrast, adaptive immunity is prominent in multiple sclerosis, neuromyelitis optica, and the paraneoplastic syndromes where highly specific T cell responses and antibodies mediate these diseases. Studies of autoimmune brain disorders have aided in the elucidation of distinct neuronal roles played by key molecules already well known to immunologists (e.g., complement and components of the major histocompatibility complex). In parallel, molecules known to neurobiology and sensory physiology, including toll-like receptors, gamma amino butyric acid and the lens protein alpha B crystallin, have intriguing and distinct functions in the immune system, where they modulate autoimmunity directed to the brain.

Cytoplasmic Ig-domain proteins: cytoskeletal regulators with a role in human disease

Immunoglobulin domains are found in a wide variety of functionally diverse transmembrane proteins, and also in a smaller number of cytoplasmic proteins. Members of this latter group are usually associated with the actin cytoskeleton, and most of them bind directly to either actin or myosin, or both. Recently, studies of inherited human disorders have identified disease-causing mutations in five cytoplasmic Ig-domain proteins: myosin-binding protein C, titin, myotilin, palladin, and myopalladin. Together with results obtained from cultured cells and mouse models, these clinical studies have yielded novel insights into the unexpected roles of Ig domain proteins in mechanotransduction and signaling to the nucleus. An emerging theme in this field is that cytoskeleton-associated Ig domain proteins are more than structural elements of the cell, and may have evolved to fill different needs in different cellular compartments. Cell Motil. Cytoskeleton 2009. (c) 2009 Wiley-Liss, Inc.

Genomic structure of the whole D-J-C clusters and the upstream region coding V segments of the TRB locus in pig

In the vertebrate immune system, T cells play a central role in host defense against microbial or viral infection. Previous studies suggested that at least two sets of TRBD-J-C clusters are harbored in the porcine genome. In this study, we determined 212,193 bp of a continuous porcine genomic sequence covering the entire TRBC region. EPHB6, TRPV6, TRY, and ten TRBV genes were conserved in the vicinity of the TRBD-J-C clusters. Interestingly, three TRBD-J-C clusters were identified in this sequence; each TRBD-J-C cluster consisted of one TRBD and seven TRBJ segments, with one TRBC region composed of four exons. The distribution of repetitive sequences and phylogenetic analysis indicated that the TRBD-J-C cluster, located at the center of the three clusters identified, had a structure combined with the others. Most of the TRBJ segments were available in public databases, suggesting that all three TRBD-J-C clusters are functional in pigs.

Characterization of arrangement and expression of the T cell receptor gamma locus in the sandbar shark

Ig and T cell receptor (TCR) genes consist of separate genomic elements, which must undergo rearrangement and joining before a functional protein can be expressed. Considerable plasticity in the genomic arrangement of these elements has occurred during the evolution of the immune system. In tetrapods, all Ig and TCR chain elements are arranged as translocons. In teleosts, the Ig heavy and TCR chains are translocons, but light chain genes may occur as clusters. However, in chondrichthyes, all of the Ig light and heavy chain genes are arranged as clusters. These clusters vary in number from <10 to several hundred, depending on isotype and species. Here, we report that the germ-line gene for the TCR gamma chain in a chondrichthyan, the sandbar shark (Carcharhinus plumbeus), is present as a single locus arranged in a classic translocon pattern. Thus, the shark utilizes 2 types of genomic arrangements, the unique cluster organization for Ig genes and the "conventional" translocon organization for TCR genes. The TCR gamma translocon contains at least 5 V region genes, 3 J segment genes, and 1 C segment. As expected, the third hypervariable segment (CDR3), formed by the rearrangement of the Vgamma and Jgamma segments, contributed the major variability in the intact V region structure. Our data also suggest that diversity may be generated by mutation in the V regions.

Porcine IgG: structure, genetics, and evolution

Eleven genomic porcine Cgamma gene sequences are described that represent six putative subclasses that appear to have originated by gene duplication and exon shuffle. The genes previously described as encoding porcine IgG1 and IgG3 were shown to be the IgG1(a) and IgG1(b) allelic variants of the IGHG1 gene, IgG2a and IgG2b are allelic variants of the IGHG2 gene, while "new" IgG3 is monomorphic, has an extended hinge, is structurally unique, and appears to encode the most evolutionarily conserved porcine IgG. IgG5(b) differs most from its putative allele, and its C(H)1 domain shares sequence homology with the C(H)1 of IgG3. Four animals were identified that lacked either IgG4 or IgG6. Alternative splice variants were also recovered, some lacking the C(H)1 domain and potentially encoding heavy chain only antibodies. Potentially, swine can transcribe >20 different Cgamma chains. A comparison of mammalian Cgamma gene sequences revealed that IgG diversified into subclasses after speciation. Thus, the effector functions for the IgG subclasses of each species should not be extrapolated from "same name subclasses" in other species. Sequence analysis identified motifs likely to interact with Fcgamma receptors, FcRn, protein A, protein G, and C1q. These revealed IgG3 to be most likely to activate complement and bind FcgammaRs. All except IgG5(a) and IgG6(a) should bind to FcgammaRs, while all except IgG6(a) and the putative IgG5 subclass proteins should bind well to porcine FcRn, protein A, and protein G.

Expression and characterization of recombinant C-terminal biotinylated extracellular domain of human receptor for advanced glycation end products (hsRAGE) in Escherichia coli

The receptor for advanced glycation end products (RAGE) is a multi-ligand receptor involved in the development of diabetic complications. Using an Escherichia coli expression system, we have successfully expressed and purified the C-terminal biotinylated extracellular domain of human RAGE (hsRAGE), which consists of three immunoglobulin-like domains carrying three putative disulfide bonds. Over 90% of hsRAGE was expressed in soluble form in trxB and gor mutant E. coli strain Origami (DE3). Most hsRAGE was biotinylated with a C-terminal AviTag, and stably immobilized onto matrix via streptavidin without any treatment. Immobilized hsRAGE without glycosylation recognized its ligands, such as AGEs. Biotinylated hsRAGE was also able to apply in the detection of AGEs on microtitre wells like antibodies used in enzyme-linked immunoassay. SPR analysis demonstrated that the dissociation constant (K(d)) of RAGE for AGE-BSA was 23.1 nM with the two-state reaction model, and 13.5 nM with the 1:1 binding model, comparable to those of RAGEs on cell surface. These results indicate that biotinylated hsRAGE must be useful not only in analysing RAGE-ligand interactions but also detect AGEs.

Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus

Although the origins of genes encoding the rearranging binding receptors remain obscure, it is predicted that their ancestral forms were nonrearranging immunoglobulin-type domains. Variable region-containing chitin-binding proteins (VCBPs) are diversified immune-type molecules found in amphioxus (Branchiostoma floridae), an invertebrate that diverged early in deuterostome phylogeny. To study the potential evolutionary relationships between VCBPs and vertebrate adaptive immune receptors, we solved the structures of both a single V-type domain (to 1.15 A) and a pair of V-type domains (to 1.85 A) from VCBP3. The deduced structures show integral features of the ancestral variable-region fold as well as unique features of variable-region pairing in molecules that may reflect characteristics of ancestral forms of diversified immune receptors found in modern-day vertebrates.

Role of physical mechanisms in biological self-organization

Organs form during morphogenesis, the process that gives rise to specialized biological structures of specific shape and function in early embryonic development. Morphogenesis is under strict genetic control, but shape evolution itself is a physical process. Here we report the results of experimental and modeling biophysical studies on in vitro biological structure formation. Experimentally, by controlling the interaction between cells and their embedding matrices, we were able to build living structures of definite geometry. The experimentally observed shape evolution was reproduced by Monte Carlo simulations, which also shed light on the biophysical basis of the process. Our work suggests a novel way to engineer biological structures of controlled shape.

Postnatal expression profile of OBCAM implies its involvement in visual cortex development and plasticity

This study examined the expression of a neuron-specific cell adhesion molecule, OBCAM (opioid-binding cell adhesion molecule), at both the mRNA and protein levels in the cat primary visual cortex at various postnatal ages, using cDNA array analysis and immunocytochemistry. Results obtained using both methods showed that the expression level of OBCAM was high in young and low in older and adult visual cortex. OBCAM-immunoreactivities were associated predominantly with perikarya and dendrites of pyramidal neurons, and OBCAM-immunopositive neurons were present in all cortical layers. Immunostaining of OBCAM in adult visual cortex showed a reduced number of immunopositive neurons and neurites and relatively lower staining intensities as compared with younger animals. In addition, the number of OBCAM-immunopositive neurons was significantly higher in the visual cortex of 4-month-old animals dark-reared from birth than those in age-matched normally reared animals. These results suggest that OBCAM may play an important role in visual cortex development and plasticity.

IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr) provides a common access to expertly annotated data on the genome, proteome, genetics and structure of immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrates. The NUMEROTATION concept of IMGT-ONTOLOGY has allowed to define a unique numbering for the variable domains (V-DOMAINs) and for the V-LIKE-DOMAINs. In this paper, this standardized characterization is extended to the constant domains (C-DOMAINs), and to the C-LIKE-DOMAINs, leading, for the first time, to their standardized description of mutations, allelic polymorphisms, two-dimensional (2D) representations and tridimensional (3D) structures. The IMGT unique numbering is, therefore, highly valuable for the comparative, structural or evolutionary studies of the immunoglobulin superfamily (IgSF) domains, V-DOMAINs and C-DOMAINs of IG and TR in vertebrates, and V-LIKE-DOMAINs and C-LIKE-DOMAINs of proteins other than IG and TR, in any species.

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes

IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ((R)). IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr.

Developmental expression and gene/enzyme identifications in the alpha esterase gene cluster of Drosophila melanogaster

Here we show how the 10 genes of the alpha esterase cluster of Drosophila melanogaster have diverged substantially in their expression profiles. Together with previously described sequence divergence this suggests substantial functional diversification. By peptide mass fingerprinting and in vitro gene expression we have also shown that two of the genes encode the isozymes EST9 (formerly ESTC) and EST23. EST9 is the major 'alpha staining' esterase in zymograms of gut tissues in feeding stages while orthologues of EST23 confer resistance to organophosphorus insecticides in other higher Diptera. The results for EST9 and EST23 concur with previous suggestions that the products of the alpha esterase cluster function in digestion and detoxification of xenobiotic esters. However, many of the other genes in the cluster show developmental or tissue-specific expression that seems inconsistent with such roles. Furthermore, there is generally poor correspondence between the mRNA expression patterns of the remaining eight genes and isozymes previously characterized by standard techniques of electrophoresis and staining, suggesting that the alpha cluster might only account for a small minority of the esterase isozyme profile.

Adaptor signalling proteins Grb2 and Grb7 are recruited by human G6f, a novel member of the immunoglobulin superfamily encoded in the MHC

The human G6f protein, which is encoded by a gene in the MHC, is a putative cell-surface receptor belonging to the immunoglobulin superfamily. The intracellular tail of G6f is 40 amino acids in length and contains one tyrosine residue (Y281), which is phosphorylated after treatment of cells with pervanadate. This tyrosine residue is found in a consensus-binding motif (YXN) for the Src homology 2 domains of Grb2 and Grb7 (where Grb stands for growth-factor-receptor-bound protein). Glutathione S-transferase pull-down assays showed that the interaction of G6f with both Grb2 and Grb7 is mediated through the Src homology 2 domains of these two proteins and is dependent on the phosphorylation of G6f. Immunoprecipitation experiments showed the interaction of full-length phosphorylated G6f with both full-length Grb2 and Grb7. Antibody cross-linking of G6f expressed in K562 cells resulted in a transient phosphorylation of p42/44 MAP kinase (also known as extracellular-signal-regulated protein kinase-1/2; MAP stands for mitogen-activated protein) which could be prevented by MAP kinase kinase (MEK) inhibitors. These results suggest a coupling of G6f with downstream signal transduction pathways involving Grb2 and Grb7, including the Ras-MAP kinase pathway.

1alpha, 25-dihydroxy-vitamin D3 alters Syk activation through FcgammaRII in monocytic THP-1 cells

In monocytes and macrophages, activation of the tyrosine kinase Syk is an essential step in the biochemical cascade linking aggregation of receptors for immunoglobulin G (FcgammaR) to initiation of effector functions. An increase in Syk activation during differentiation of myeloid cells by different agents has been reported. We studied the activation state of Syk in response to FcgammaRII crosslinking in monocytic cells before and after in vitro differentiation with 1alpha, 25-dihydroxy-vitamin D3. We show here that while in undifferentiated THP-1 cells clustering of FcgammaRII induces significant phosphorylation and activation of Syk, in THP-1 cells differentiated in vitro by 1alpha, 25-dihydroxy-vitamin D3, FcgammaRII crosslinking induced a decrease in Syk activity. In vitro differentiation did not induce changes in the expression of FcgammaRII isoforms. The observed effect on Syk activation though FcgammaRII could be mediated by differentiation-induced changes in the expression and basal activation level of Syk, as well as changes in the association of Syk with the tyrosine phosphatase SHP-1. These results suggest that the biochemical signaling pathways induced by FcgammaRII could be dependent on the differentiation state of the cell.

How additives influence the refolding of immunoglobulin-folded proteins in a stepwise dialysis system. Spectroscopic evidence for highly efficient refolding of a single-chain Fv fragment

The gradual removal of the denaturing reagent guanidine HCl (GdnHCl) using stepwise dialysis with the introduction of an oxidizing reagent and l-arginine resulted in the highly efficient refolding of various denatured single-chain Fv fragments (scFvs) from inclusion bodies expressed in Escherichia coli. In this study, the influence of the additives on the intermediates in scFv refolding was carefully analyzed on the basis of the stepwise dialysis, and it was revealed that the additive effect critically changes the pathway of scFv refolding. Circular dichroism and tryptophan fluorescence emission spectroscopies demonstrated that distinct secondary and tertiary structures were formed upon dialysis from 2 m GdnHCl to 1 m GdnHCl, and 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid dipotassium salt binding analysis indicated that the addition of l-arginine to the stepwise dialysis system effectively stabilized the exposed hydrophobic area on the scFv. Quantification of the free thiol groups in the scFv by means of Ellman's assay revealed that there was a particular stage in which most of the free thiol groups were oxidized and that adding an oxidizing reagent (the oxidized form of glutathione, GSSG) at that stage was important for complete refolding of the scFv. The particular stage depended on the nature of the refolding solution, especially on whether l-arginine was present. Spontaneous folding at the 1 m GdnHCl stage resulted in a structure in which a free thiol group accessed to the proper one for correct disulfide linkage; however, the addition of l-arginine resulted in the formation of a partially folded intermediate without disulfide linkages. Mass spectrometry experiments on alkylated scFv were carried out at each stage to determine the effects of l-arginine. The spectroscopic studies revealed two different pathways for scFv refolding in the stepwise dialysis system, pathways that depended on whether l-arginine was present. Controlled coupling of the effects of GSSG and l-arginine led to the complete refolding of scFv in the stepwise dialysis.

Cloning and characterisation of a highly immunoreactive 37 kDa antigen with multi-immunoglobulin domains from the swine roundworm Ascaris suum

Antigens from larval stages of Ascaris suum have been shown to induce protection against challenge infection with infective A. suum eggs. We previously identified several antigens that reacted strongly with serum from pigs inoculated with infective eggs containing L3. In this study, we isolated an antigen with a molecular mass of 37 kDa and a pI of 4.8 (As37) from A. suum infective eggs using two-dimensional electrophoresis, and obtained a full-length cDNA by reverse transcription-polymerase chain reaction using primers designed based on the internal amino acid sequence of As37. The cDNA sequence consisted of 1,540 bp coding for a protein of 321 amino acids with a complex domain organisation. Simple modular architecture research tool (SMART) analysis indicated that As37 contains three immunoglobulin domains, indicating that it is a member of immunoglobulin superfamily (IgSF). A homology search of GenBank showed that As37 has significant similarity to Caenorhabditis elegans DIM-1 protein and has low similarity to part of the multi-repeat Ig domain from nematode twitchin and mammalian skeleton muscle titin, and to members of the IgSF at the amino acid sequence level. Localisation analysis revealed that antibodies to Escherichia coli-expressed recombinant As37 (rAs37) bound to muscle cells and the hypodermis. The antibodies identified a 37 kDa native antigen in human and dog roundworms, suggesting that there are As37 homologues in ascarid nematodes. Sera from mice, rabbits and pigs immunised with A. suum infective eggs reacted with rAs37 in immunoblot analyses. The potential use of rAs37 for protection against A. suum infection is discussed.

Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products

Sequencing of all human immunoglobulin (Ig) germline gene segments has recently been completed. However, our first glimpses of the recombined products of this combinatorial gene system were in the 1970s, in landmark publications, reporting the crystal structures of two human myeloma proteins, the Mcg lambda light chain dimer and the New IgG1(lambda) Fab. Although numerous crystal structures of murine and human antibodies have now been determined, only a relatively small proportion of the human germline genes have had their corresponding protein three-dimensional structures resolved. Therefore, further structural investigations are required before the inherent diversity of the antibody repertoire can be fully appreciated. We discuss the detailed structural information available for human antibodies with regard to their immune functions. Also discussed, is how the structural information is finding application in the 'humanization' of murine antibodies as part of their development as 'biopharmaceuticals' for the treatment of human disease.

Stimulation of erythroleukaemia cell differentiation by extracellular high-mobility group-box protein 1 is independent of the receptor for advanced glycation end-products

In several cell types the binding of extracellular high-mobility group-box protein 1 (HMGB1) with the receptor for advanced glycation end-products (RAGE) induces cytoskeletal reorganization and cell motility. To establish whether RAGE is also involved in murine erythroleukaemia (MEL) cell differentiation stimulated by HMGB1, we have demonstrated that these cells express a 51 kDa protein identified as RAGE, and then we have produced stable transfectants overexpressing wild-type (wt) RAGE or a dominant negative (dn) RAGE mutant lacking the cytoplasmic domain to analyse the differentiation process in these cells. Several experimental findings indicated that RAGE was not involved in the MEL cell differentiation programme. This was also supported by the identical stimulatory effect exerted by HMGB1 on both wt- or dn-RAGE transfectants. We have also observed that HMGB1 binds a 65 kDa protein on the surface of MEL cells, supporting the hypothesis that alternative targets of HMGB1 are expressed on the MEL cell membrane and may be involved as mediators of its signalling.

Sialic acid, intercellular adhesion molecule-1 and rheumatoid arthritis: a study on the erythrocyte membrane

We measured serum levels of soluble intercellular adhesion molecule-1 and erythrocyte membrane sialic acid in patients with rheumatoid arthritis and studied their correlation with the disease activity. Serum soluble intercellular adhesion molecule-1 level was determined with sandwich ELISA and sialic acid level with the method of Shamberger in 42 patients with rheumatoid arthritis and in 30 healthy controls. Significantly lower erythrocyte membrane sialic acid and higher serum levels of soluble intercellular adhesion molecule-1 were found in patients with rheumatoid arthritis compared with healthy controls (p<0.001 for both). Significant negative correlation between soluble intercellular adhesion molecule-1 level and erythrocyte membrane sialic acid concentration (r=-0.49, p<0.001) and positive correlations between soluble intercellular adhesion molecule-1 level and Ritche Articular Index score and C-reactive protein (r=0.32, p<0.05; r=0.44, p<0.01, respectively) were observed. From these data we conclude that decreases in erythrocyte membrane sialic acid concentration and increases in soluble intercellular adhesion molecule-1, erythrocyte sedimentation rate and C-reactive protein levels are present in rheumatoid arthritis, and that the increased soluble intercellular adhesion molecule-1 in rheumatoid arthritis might be due to the decreased erythrocyte membrane sialic acid concentration. The levels of soluble intercellular adhesion molecule-1 may be a novel marker for the disease status and the activity of rheumatoid arthritis.

Chemokine and chemokine receptor dynamics during genital chlamydial infection

Current design strategies for vaccines against certain microbial pathogens, including Chlamydia trachomatis, require the induction and targeting of specific immune effectors to the local sites of infection known as the mucosal effector sites. Chemokines and their receptors are important mediators of leukocyte trafficking and of the controlled recruitment of specific leukocyte clonotypes during host defense against infections and during inflammation. We analyzed the dynamics of chemokine and chemokine receptor expression in genital mucosae during genital chlamydial infection in a murine model to determine how these molecular entities influence the development of immunity and the clearance of infection. A time course study revealed an increase of up to threefold in the levels of expression of RANTES, monocyte chemotactic protein 1 (MCP-1), gamma-interferon-inducible protein 10 (IP-10), macrophage inflammatory protein 1alpha (MIP-1alpha), and intercellular adhesion molecule type 1 (ICAM-1) after genital infection with the C. trachomatis agent of mouse pneumonitis. Peak levels of expression of RANTES, MCP-1, and MIP-1alpha occurred by day 7 after primary infection, while those of IP-10 and ICAM-1 peaked by day 21. Expression levels of these molecules decreased by day 42 after primary infection, by which time all animals had resolved the infection, suggesting an infection-driven regulation of expression. A rapid upregulation of expression of these molecules was observed after secondary infection. The presence of cells bearing the chemokine receptors CCR5 and CXCR3, known to be preferentially expressed on Th1 and dendritic cells, was also synchronous with the kinetics of immune induction in the genital tract and clearance of infection. Results demonstrated that genital chlamydial infection is associated with a significant induction of chemokines and chemokine receptors that are involved in the recruitment of Th1 cells into the site of infection. Future studies will focus on how selective modulation of chemokines and their receptors can be used to optimize long-term immunity against CHLAMYDIA:

Assessment of the developmental totipotency of neural cells in the cerebral cortex of mouse embryo by nuclear transfer

When neural cells were collected from the entire cerebral cortex of developing mouse fetuses (15.5-17.5 days postcoitum) and their nuclei were transferred into enucleated oocytes, 5.5% of the reconstructed oocytes developed into normal offspring. This success rate was the highest among all previous mouse cloning experiments that used somatic cells. Forty-four percent of live embryos at 10.5 days postcoitum were morphologically normal when premature and early-postmitotic neural cells from the ventricular side of the cortex were used. In contrast, the majority (95%) of embryos were morphologically abnormal (including structural abnormalities in the neural tube) when postmitotic-differentiated neurons from the pial side of the cortex were used for cloning. Whereas 4.3% of embryos cloned with ventricular-side cells developed into healthy offspring, only 0.5% of those cloned with differentiated neurons in the pial side did so. These facts seem to suggest that the nuclei of neural cells in advanced stages of differentiation had lost their developmental totipotency. The underlying mechanism for this developmental limitation could be somatic DNA rearrangements in differentiating neural cells.

G6b, a novel immunoglobulin superfamily member encoded in the human major histocompatibility complex, interacts with SHP-1 and SHP-2

The G6b gene, located in the class III region of the human major histocompatibility complex, has been suggested to encode a putative receptor of the immunoglobulin superfamily. Genomic sequence information was used as a starting point to clone the corresponding cDNA. Reverse transcriptase polymerase chain reaction showed that expression of the gene is restricted to certain hematopoietic cell lines including K562, Molt 4, and Jurkat. Several splice variants were detected, varying only in their C-terminal parts. One of the potential membrane-bound isoforms contained two immunoreceptor tyrosine-based inhibitory motifs in its cytoplasmic tail. Four of the isoforms were expressed as epitope-tagged proteins in the cell lines K562 and COS-7. The two splice isoforms lacking the hydrophobic transmembrane segment were secreted from the cell. Glycosidase treatment of the four recombinant proteins provided evidence for N- and O-glycosylation. Immunofluorescence studies indicated that the spliced isoforms having a transmembrane segment were directed to the cell membrane. The G6b isoform containing two immunoreceptor tyrosine-based inhibitory motifs in its cytoplasmic tail was found to be phosphorylated on tyrosine residues after pervanadate treatment of cells and, subsequently, interacts with the SH2-containing protein-tyrosine phosphatases SHP-1 and SHP-2. Mutagenesis studies showed that phosphorylation of tyrosine 211 is critical for the interaction of G6b with SHP-1 and SHP-2.

Cloning and characterization of a novel mouse immunoglobulin superfamily gene expressed in early spermatogenic cells

We cloned and characterized a novel immunoglobulin superfamily gene from the cDNA library of adult mouse testis. This gene was expressed in the spermatogenic cells and hence termed SgIGSF. The predicted SgIGSF protein was composed of 445 amino-acid residues and contained a signal peptide, three extracellular immunoglobulin (Ig)-like domains, a transmembranous domain, and a cytoplasmic domain. SgIGSF mRNA consisted of two size species, 2.1- and 4.5-kb in length. Besides testis, SgIGSF mRNA was also expressed in a variety of organs, including the cerebrum, liver, kidney, and epididymis. The testis and liver expressed both the 2.1- and 4.5-kb transcripts, whereas the cerebrum and epididymis predominantly expressed the 4.5-kb one. In situ hybridization analysis in testis revealed that SgIGSF mRNA signal was localized to the spermatogenic cells from spermatogonia to zygotene spermatocytes. These results suggested that SgIGSF occurs in the plasma membrane of spermatogenic cells during the earlier stages of spermatogenesis.

DIgR1, a novel membrane receptor of the immunoglobulin gene superfamily, is preferentially expressed by antigen-presenting cells

A novel membrane receptor of immunoglobulin gene superfamily (IgSF) has been identified from mouse dendritic cells (DC) and designated as DC-derived Ig-like receptor 1 (DIgR1). It encodes a 228-amino-acid (aa) residue polypeptide with a 21-aa signal peptide, a 20-aa transmembrane region, a 189-aa extracellular region, and a 19 aa intracellular region. Its extracellular region contains a single V domain of Ig. So it is a novel type I transmembrane glycoprotein of IgSF. DIgR1 shows significant homologies to human CMRF-35 antigens and polymeric immunoglobulin receptors (pIgR). The mRNA expression of DIgR1 was highly abundant in mouse spleen. The preferential expression of DIgR1 mRNA is observed in the known antigen-presenting cells (APC) including DC, monocytes/macrophages, and B lymphocytes. A 40 kDa of protein in NIH/3T3 cells transfected with the DIgR1 cDNA was detected by Western blot analysis using anti-DIgR1 polyclonal antibodies. The expression of DIgR1 protein on DC is not regulated by LPS stimulation. Further study should be conducted to investigate what were biological functions of DIgR1 in the immunobiology of APC.

Upregulation of the Netrin Receptor (DCC) Gene during Activation of B Lymphocytes and Modulation by Interleukins

The DCC (deleted in colon cancer) gene has a brain restricted high expression pattern. It encodes a transmembrane protein of the immunoglobulin superfamily identified as the netrin-1 receptor. It might be a member of the so called "brain-lymphoid" molecules, which control key cell surface events. To test this hypothesis we have assessed the DCC mRNA level in human normal and malignant myeloid and lymphoid cells. A high mRNA content has been observed only in mature B cells at the secreting or presecreting stage. Expression of DCC was also assessed in the anti-CD40 model of immunopoiesis. Activation of purified tonsillar B cells by anti-CD 40 antibody strongly increased the DCC mRNA level and this effect was dramatically enhanced by the association of IL-2 + IL-10, which is a potent and selective in vitro inducer of the B cell memory phenotype. In contrast no effect has been detected after activation of T cells by anti-CD3. These data suggest that the DCC encoded netrin receptor is involved in B cell immunopoiesis.

Longitudinal analysis of T cells responding to tetanus toxoid in healthy subjects as well as in pediatric patients after bone marrow transplantation: the identification of identical TCR-CDR3 regions in time suggests long-term stability of at least part of the antigen-specific TCR repertoire

To understand the nature of long-term Th immune responses, we investigated in the present study the TCRBV gene repertoire of CD4(+) T cells specific for the recall antigen tetanus toxoid (TT) in recipients of an allogeneic bone marrow transplantation (allo-BMT) at several time points after transplantation and in their BM donors. We observed that the TCR repertoire of TT-specific CD4(+) Th cells was heterogeneous, and differed between allo-BMT recipients and their respective donors. Some individuals, however, used similar TCR-complementarity-determining region (CDR) 3 motifs that could reflect recognition of and selection by similar promiscuous epitopes of TT. Longitudinal analysis of this TT-specific T cell response revealed that T cells with completely identical TCR were present at several time points after the first analysis in allo-BMT recipients, most probably reflecting long-term stability of at least part of the antigen-specific TCR repertoire. Similar stability of the TT-specific TCR repertoire in time was also noted in the allo-BMT donors. These observations reveal that within a given individual the dominant antigen-specific T cell clones persist in time in an otherwise diverse TT-specific CD4(+) T cell immune response.

Expression of the IgLON cell adhesion molecules Kilon and OBCAM in hypothalamic magnocellular neurons

The vasopressin (AVP) and oxytocin (OXT) magnocellular neurons in the hypothalamic supraoptic (SON) and paraventricular nuclei (PVN) display reversible structural plasticity of neurons and glial cells under different conditions of neuropeptide secretion. In the present study, we investigated the expression of two immunoglobulin superfamily (IgSF) proteins, Kilon and OBCAM, in the magnocellular neurons by using monoclonal antibodies. Anti-Kilon antibody reacted specifically with the bacterially expressed recombinant Kilon but not with the recombinant OBCAM, and similarly anti-OBCAM antibody specifically recognized the recombinant OBCAM. Western blotting analysis revealed the specific expression of Kilon and OBCAM in the SON homogenates. Although Kilon and OBCAM of the SON homogenates were present as the insoluble form, most Kilon was present in the Triton-insoluble fraction, and OBCAM was localized mainly in the Triton-soluble fraction. Immunocytochemistry revealed Kilon and OBCAM immunoreactivity in the magnocellular neurons of the SON and PVN of the rat hypothalamus compared with outside of the SON and PVN in the hypothalamus. The double-labeling study with confocal microscopy further demonstrated that Kilon immunoreactivity was observed mainly in the dendrites of AVP-secreting neurons and also occasionally OXT-secreting neurons. However, OBCAM immunoreactivity was exclusively seen in the dendrites of AVP-secreting magnocellular neurons. Chronic physiological stimulation by 2% NaCl had no effect on the expression levels of either IgLON protein in the SON. Our study thus demonstrated specific expression of Kilon and OBCAM in the hypothalamic magnocellular neurons, particularly in dendrites, suggesting that they confer on magnocellular neurons the ability to rearrange dendritic connectivity.

Suppression of endogenous IL-10 gene expression in dendritic cells enhances antigen presentation for specific Th1 induction: potential for cellular vaccine development

A new paradigm for designing vaccines against certain microbial pathogens, including Chlamydia trachomatis, is based on the induction of local mucosal Th1 response. IL-10 is an anti-inflammatory cytokine that exerts negative immunoregulatory influence on Th1 response. This study investigated whether biochemical modulation of endogenous IL-10 expression at the level of APCs is a practical strategy for enhancing the specific Th1 response against pathogens controlled by Th1 immunity. The results revealed that the high resistance of genetically engineered IL-10-/- (IL-10KO) mice to genital chlamydial infection is a function of the predilection of their APCs to rapidly and preferentially activate a high Th1 response. Thus, in microbiological analysis, IL-10KO mice suffered a shorter duration of infection, less microbial burden, and limited ascending infection than immunocompetent wild-type mice. Also, IL-10KO were resistant to reinfection after 8 wk of the primary infection. Cellular and molecular immunologic evaluation indicated that IL-10KO mice induced greater frequency of chlamydial-specific Th1 response following C. trachomatis infection. Moreover, IL-10KO APCs or antisense IL-10 oligonucleotide-treated wild-type APCs were potent activators of Th1 response from naive or immune T cells. Furthermore, both Ag-pulsed dendritic cells from IL-10KO mice and IL-10 antisense-treated dendritic cells from wild-type mice were efficient cellular vaccines in adoptive immunotherapeutic vaccination against genital chlamydial infection. These findings may furnish a novel immunotherapeutic strategy for boosting the Th1 response against T cell-controlled pathogens and tumors, using IL-10-deficient APCs as vaccine delivery agents.

The evolution of vertebrate antigen receptors: a phylogenetic approach

Classical T cells, those with alpha beta T-cell receptors (TCRs), are an important component of the dominant paradigm for self-nonself immune recognition in vertebrates. alpha beta T cells recognize foreign peptide antigens when they are bound to MHC molecules on the surfaces of antigen-presenting cells. gamma delta T cells bear a similar receptor, and it is often assumed that these T cells also require specialized antigen-presenting molecules for immune recognition, which we term "indirect antigen recognition." B-cell receptors, or immunoglobulins, bind directly to antigens without the help of a specialized antigen-presenting molecule. Phylogenetically, it has been assumed that T-cell receptors and the genes that encode them are a monophyletic group, and that "indirect" antigen recognition evolved before the split into two types of TCR. Recently, however, it has been proposed that gamma delta-TCRs bind directly to antigens, as do immunoglobulins (Ig's). This calls into question the null hypothesis that indirect antigen recognition is a common characteristic of TCRs and, by extension, the hypothesis that all TCR gene sequences form a monophyletic group. To determine whether alternative explanations for antigen recognition and other historical relationships among TCR genes might be possible, we performed phylogenetic analyses on amino acid sequences of the constant and variable regions which encode the basic subunits of TCR and Ig molecules. We used both maximum-parsimony and genetic distance-based methods and could find no strong support for the hypothesis of TCR monophyly. Analyses of the constant region suggest that TCR gamma or delta sequences are the most ancient, implying that the ancestral immune cell was like a modern gamma delta T cell. From this gamma delta-like ancestor arose alpha beta T cells and B cells, implying that indirect antigen recognition is indeed a derived property of alpha beta-TCRs. Analyses of the variable regions are complicated by strong selection on antigen-binding sequences, but imply that direct antigen binding is the ancestral condition.

FXY2/MID2, a gene related to the X-linked Opitz syndrome gene FXY/MID1, maps to Xq22 and encodes a FNIII domain-containing protein that associates with microtubules

Opitz G/BBB syndrome (OS) is a genetically heterogeneous disorder with an X-linked locus and an autosomal locus linked to 22q11.2. OS affects multiple organ systems with often variable severity even between siblings. The clinical features, which include hypertelorism, cleft lip and palate, defects of cardiac septation, hypospadias, and anorectal anomalies, indicate an underlying disturbance of the developing ventral midline of the embryo. The gene responsible for X-linked OS, FXY/MID1, is located on the short arm of the human X chromosome within Xp22.3 and encodes a protein with both an RBCC (RING finger, B-box, coiled coil) and a B30.2 domain. The Fxy gene in mice is also located on the X chromosome but spans the pseudoautosomal boundary in this species. Here we describe a gene closely related to FXY/MID1, called FXY2, which also maps to the X chromosome within Xq22. The mouse Fxy2 gene is located on the distal part of the mouse X chromosome within a region syntenic to Xq22. Analysis of genes flanking both FXY/MID1 and FXY2 (as well as their counterparts in mouse) suggests that these regions may have arisen as a result of an intrachromosomal duplication on an ancestral X chromosome. We have also identified in both FXY2 and FXY/MID1 proteins a conserved fibronectin type III domain located between the RBCC and B30.2 domains that has implications for understanding protein function. The FXY/MID1 protein has previously been shown to colocalize with microtubules, and here we show that the FXY2 protein similarly associates with microtubules in a manner that is dependent on the carboxy-terminal B30.2 domain.

T-Cell Immune Reconstitution in Pediatric Leukemia Patients After Allogeneic Bone Marrow Transplantation With T-Cell–Depleted or Unmanipulated Grafts: Evaluation of Overall and Antigen-Specific T-Cell Repertoires

To evaluate the role of T-cell selection in the thymus and/or periphery in T-cell immune reconstitution after allogeneic bone marrow transplantation (allo-BMT), we have analyzed the overall and antigen-specific T-cell repertoires in pediatric allo-BMT recipients treated for leukemia. We observed a lack of overall T-cell receptor (TCR) diversity in the repopulating T cells at 3 months after allo-BMT, as was deduced from complementarity determining region 3 (CDR3) size distribution patterns displaying reduced complexity. This was noted particularly in recipients of a T-cell–depleted (TCD) graft and, to a lesser extent, also in recipients of unmanipulated grafts. At 1 year after allo-BMT, normalization was observed of TCR CDR3 size complexity in almost all recipients. Analysis of the antigen-specific T-cell repertoire at 1 year after BMT showed that the T cells responding to tetanus toxoid (TT) differed in TCR gene segment usage and in amino acid composition of the CDR3 region when comparing the recipient with the donor. Moreover, the TT-specific TCR repertoire was found to be stable within a given allo-BMT recipient, because TT-specific T cells with completely identical TCRs were found at 3 consecutive years after transplantation. These observations suggest an important role for T-cell selection processes in the complete restoration of the T-cell immune repertoire in children after allo-BMT.

T-Cell Immune Reconstitution in Pediatric Leukemia Patients After Allogeneic Bone Marrow Transplantation With T-Cell–Depleted or Unmanipulated Grafts: Evaluation of Overall and Antigen-Specific T-Cell Repertoires

To evaluate the role of T-cell selection in the thymus and/or periphery in T-cell immune reconstitution after allogeneic bone marrow transplantation (allo-BMT), we have analyzed the overall and antigen-specific T-cell repertoires in pediatric allo-BMT recipients treated for leukemia. We observed a lack of overall T-cell receptor (TCR) diversity in the repopulating T cells at 3 months after allo-BMT, as was deduced from complementarity determining region 3 (CDR3) size distribution patterns displaying reduced complexity. This was noted particularly in recipients of a T-cell–depleted (TCD) graft and, to a lesser extent, also in recipients of unmanipulated grafts. At 1 year after allo-BMT, normalization was observed of TCR CDR3 size complexity in almost all recipients. Analysis of the antigen-specific T-cell repertoire at 1 year after BMT showed that the T cells responding to tetanus toxoid (TT) differed in TCR gene segment usage and in amino acid composition of the CDR3 region when comparing the recipient with the donor. Moreover, the TT-specific TCR repertoire was found to be stable within a given allo-BMT recipient, because TT-specific T cells with completely identical TCRs were found at 3 consecutive years after transplantation. These observations suggest an important role for T-cell selection processes in the complete restoration of the T-cell immune repertoire in children after allo-BMT.

The intercellular adhesion molecule type-1 is required for rapid activation of T helper type 1 lymphocytes that control early acute phase of genital chlamydial infection in mice

Recent studies in animal models of genital chlamydial disease revealed that early recruitment of dendritic cells and specific T helper type-1 (Th1) cells into the genital mucosae is crucial for reducing the severity of the acute phase of a cervico-vaginal infection and arresting ascending disease. These immune effectors are therefore important for preventing major complications of genital chlamydial infection. Other in vitro studies showed that intercellular adhesion molecule-1 (ICAM-1) plays a role in the antichlamydial action of specific CD4+ and CD8+ T cells. In the present study, we investigated the clinicopathological consequences of ICAM-1 deficiency during chlamydial genital infection in ICAM-1 knockout (ICAM-1KO) mice, and analysed the cellular and molecular immunological bases for any observed pathology or complication. Following a primary genital infection of female ICAM-l-/- and ICAM-1+/+ mice, the intensity of the disease during the first 3 weeks (as assessed by shedding of chlamydiae in the genital tract) was significantly greater in ICAM-1KO mice than in ICAM-1+/+ mice (P < 0.0001), although both ICAM-l-/- and ICAM-1+/+ mice subsequently cleared the primary infection. There was greater ascending disease during the initial stage of the infection, and a higher incidence of tubal disease (hydrosalpinx formation) after multiple infections in ICAM-l-/- mice. Analysis of the cellular and molecular bases for the increased acute and ascending disease in ICAM-l-/- mice revealed that the high affinity of ICAM-1 for leucocyte function antigen type-1 is a property that promotes rapid activation of specific Th1 cells, as well as their early recruitment into the genital mucosa. Moreover, ICAM-1 was more important for naive T-cell activation than primed Th1 cells, although its absence delayed or suppressed immune T-cell activation by at least 50%. Taken together, these results indicated that ICAM-1 is crucial for rapid T-cell activation, early recruitment and control of genitally acquired Chlamydia trachomatis.

Class-defining characteristics in the mouse heavy chains of variable domains

Analysis of residue correlation in over 2700 mouse heavy chains of the V(H) domains was carried out on three hierarchical levels. At the 'position' level, statistical analysis revealed 45 positions that conserve similar residues in almost all chains. At the 'fragment' level, the focus of investigation shifted to the study of combinations of amino acids in strands and loops. It was found that no more than 10 patterns were sufficient for describing strands and loops in the chains. At the 'sequence' level, we determined all possible combinations of these patterns and classified the mouse heavy chains. Comparison of the sequences in the eight classes revealed residues at the class-determining positions that were unique to each class. Because a strong correlation of residues was found, one only needs several residues to classify a sequence. It follows that no all residue alignment procedure is necessary to divide sequences into classes. An important corollary of our approach is the possibility of predicting residues in an incomplete sequence from a small sequence fragment. On the basis of our analysis of mouse heavy chains we hypothesize about the presently unknown mouse V(H) germline repertoire.

Secretory immunoglobulin A: from mucosal protection to vaccine development

Immune responses taking place in mucosal tissues are typified by secretory immunoglobulin A (S-IgA) molecules, which are assembled from proteins expressed in two cell lineages. The heavy and light chains as well as the J chain are produced in plasma cells, whereas the secretory component (SC) is associated to the immunoglobulin complex during transcytosis across the epithelial layer. S-IgA antibodies represent the predominant immunoglobulin class in external secretions, and the best defined entity providing specific immune protection for mucosal surfaces by blocking attachment of bacteria and viruses. S-IgA constitutes greater than 80% of all antibodies produced in mucosa-associated lymphoid tissues in humans. The existence of a common mucosal immune system permits immunization on one mucosal surface to induce secretion of antigen-specific S-IgA at distant sites. In addition, S-IgA antibodies not only function in external secretions, but also exert their antimicrobial properties within the epithelial cell during transport across the epithelium. Passive mucosal delivery of monoclonal IgA molecules neutralizes pathogens responsible for gastrointestinal and respiratory infections. Mucosal and systemic immunity can be achieved by orally administered recombinant S-IgA molecules carrying a protective bacterial epitope within the SC polypeptide primary sequence.

Cryptic intron activation within the large exon of the mouse polymeric immunoglobulin receptor gene: cryptic splice sites correspond to protein domain boundaries

The fourth exon of the mouse polymeric immuno-globulin receptor (pIgR) is 654 nt long and, despite being surrounded by large introns, is constitutively spliced into the mRNA. Deletion of an 84 nt sequence from this exon strongly activated both cryptic 5' and 3' splice sites surrounding a 78 nt cryptic intron. The 84 nt deletion is just upstream of the cryptic 3' splice site; the cryptic 3' splice site was likely activated because the deletion created a better 3' splice site. However, the cryptic 5' splice site was also required to activate the cryptic splice reaction; point mutations in either of the cryptic splice sites that decreased their match to the consensus splice site sequence inactivated the cryptic splice reaction. The activation and inactivation of these cryptic splice sites as a pair suggests that they are being co-recognized by the splicing machinery. Interestingly, the large fourth exon of the pIgR gene encodes two immunoglobulin-like extracellular protein domains; the cryptic 3' splice site coincides with the junction between these protein domains. The cryptic 5' splice site is located between protein subdomains where an intron is found in another gene of the immunoglobulin superfamily.

The immunoglobulin fold family: sequence analysis and 3D structure comparisons

Fifty-two 3D structures of Ig-like domains covering the immunoglobulin fold family (IgFF) were compared and classified according to the conservation of their secondary structures. Members of the IgFF are distantly related proteins or evolutionarily unrelated proteins with a similar fold, the Ig fold. In this paper, a multiple structural alignment of the conserved common core is described and the correlation between corresponding sequences is discussed. While the members of the IgFF exhibit wide heterogeneity in terms of tissue and species distribution or functional implications, the 3D structures of these domains are far more conserved than their sequences. We define topologically equivalent residues in the Ig-like domains, describe the hydrophobic common cores and discuss the presence of additional strands. The disulfide bridges, not necessary for the stability of the Ig fold, may have an effect on the compactness of the domains. Based upon sequence and structure analysis, we propose the introduction of two new subtypes (C3 and C4) to the previous classifications, in addition to a new global structural classification. The very low mean sequence identity between subgroups of the IgFF suggests the occurrence of both divergent and convergent evolutionary processes, explaining the wide diversity of the superfamily. Finally, this review suggest that hydrophobic residues constituting the common hydrophobic cores are important clues to explain how highly divergent sequences can adopt a similar fold.

Molecular evolution of immunoglobulin and fibronectin domains in titin and related muscle proteins

The family of regulatory and structural muscle proteins, which includes the giant kinases titin, twitchin and projectin, has sequences composed predominantly of serially linked immunoglobulin I set (Ig) and fibronectin type III (FN3) domains. This paper explores the evolutionary relationships between 16 members of this family. In titin, groups of Ig and FN3 domains are arranged in a regularly repeating pattern of seven and 11 domains. The 11-domain super-repeat has its origins in the seven-domain super-repeat and a model for the duplications which gave rise to this super-repeat is proposed. A super-repeat composed solely of immunoglobulin domains is found in the skeletal muscle isoform of titin. Twitchin and projectin, which are presumed to be orthologs, have undergone significant insertion/deletion of domains since their divergence. The common ancestry of myomesin, skelemin and M-protein is shown. The relationship between myosin binding proteins (MyBPs) C and H is confirmed, and MyBP-H is proposed to have given rise to MyBP-C by the acquisition of some titin domains.