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The animal gut serves as a primary location for the complex host-microbe interplay that is essential for homeostasis and may also reflect the types of ancient selective pressures that spawned the emergence of immunity in metazoans. In this review, we present a phylogenetic survey of gut host-microbe interactions and suggest that host defense systems arose not only to protect tissue directly from pathogenic attack but also to actively support growth of specific communities of mutualists. This functional dichotomy resulted in the evolution of immune systems much more tuned for harmonious existence with microbes than previously thought, existing as dynamic but primarily cooperative entities in the present day. We further present the protochordate Ciona intestinalis as a promising model for studying gut host-bacterial dialogue. The taxonomic position, gut physiology and experimental tractability of Ciona offer unique advantages in dissecting host-microbe interplay and can complement studies in other model systems.

SummaryNovel immune-type receptors (NITRs) comprise an exceptionally large, diversified family of activating and inhibitory receptors that has been identified in bony fish. Here, we characterized the structure of an activating NITR that is expressed by a cytotoxic natural killer (NK)-like cell line and that specifically binds an allogeneic B cell target. A single amino acid residue within the NITR immunoglobulin variable (V)-type domain accounts for specificity of the interaction. Structures solved by X-ray crystallography revealed that the V-type domains of NITRs form homodimers resembling rearranging antigen-binding receptor heterodimers. CDR1 elements of both subunits of NITR dimers form ligand-binding surfaces that determine specificity for the nonself target. In the evolution of immune function, it appears that a specific NK type of innate recognition may be mediated by a complex germline multigene family of V structures resembling those that are somatically diversified in adaptive immunological responses.

Transmembrane bound receptors comprised of extracellular immunoglobulin (Ig) or lectin domains play integral roles in a large number of immune functions including inhibitory and activating responses. The function of many of the activating receptors requires a physical interaction with an adaptor protein possessing a cytoplasmic regulatory motif. The partnering of an activating receptor with an adaptor protein relies on complementary charged residues in the two transmembrane domains. The mammalian natural killer (NK) and Fc receptors (FcR) represent two of many receptor families, which possess activating receptors that partner with adaptor proteins for signaling. Zebrafish represent a powerful experimental model for understanding developmental regulation at early stages of embryogenesis and for efficiently generating transgenic animals. In an effort to understand developmental aspects of immune receptor function, we have accessed the partially annotated zebrafish genome to identify six different adaptor molecules: Dap10, Dap12, Cd3zeta, Cd3zeta-like, FcRgamma and FcRgamma-like that are homologous to those effecting immune function in mammals. Their genomic organizations have been characterized, cDNA transcripts have been recovered, phylogenetic relationships have been defined and their cell lineage-specific expression patterns have been established.

Our views of both innate and adaptive immunity have been significantly modified by recent studies of immune receptors and immunity in protostomes, invertebrate deuterostomes, and jawless vertebrates. Extraordinary variation in the means whereby organisms recognize pathogens has been revealed by a series of recent findings, including: novel forms of familiar immune receptors, high genetic polymorphism for new receptor types, germline rearrangement for non-Ig domain receptors, somatic variation of germline-encoded receptors, and unusually complex alternative splicing of genes with both immune and non-immune roles. Collectively, these observations underscore heretofore unrecognized pathways in the evolution of immune recognition and suggest universal processes by which immune systems co-opt and integrate existing cellular mechanisms to effect diverse recognition functions.

Two decades of research have established the zebrafish (Danio rerio) as a significant model system for studying vertebrate development and gene structure-function relationships. Recent advances in mutation screening, the creation of genomic resources, including the Zebrafish Genome Project and the development of efficient transgenesis procedures, make this model increasingly attractive for immunological study.

A novel gene, BIVM (for basic, immunoglobulin-like variable motif-containing), has been identified using an electronic search based on the conservation of short sequence motifs within the variable region of immunoglobulin (Ig) genes. BIVM maps to human chromosome 13q32-q33 and is predicted to encode a 503-amino-acid protein with a pI of 9.1. The 5' untranslated region of BIVM is encoded in two exons; the coding portion is encoded in nine exons. BIVM is tightly linked (41 bp) and in the opposite transcriptional orientation to MGC5302 (also known as KDEL1 and EP58) in human. The ubiquitous expression of BIVM in normal tissues and the presence of a 5' CpG island suggest that BIVM is a housekeeping gene. Characterization of BIVM in representative species demonstrates significant conservation throughout deuterostomes; no sequence with significant identity to BIVM has been detected in proteostomes. However, an unusual gene has been identified in the protozoan pathogen Giardia lamblia that is similar to the core sequence of BIVM, suggesting the possibility of a horizontal gene transfer.

Cartilaginous fish represent the most phylogenetically distant species from man in which immunoglobulin and T cell antigen receptor genes have been identified. Immunoglobulin genes in cartilaginous fish are organized in hundreds of clusters, located on different chromosomes and presumably are under independent regulation; large numbers of immunoglobulin gene clusters are germline-joined and thus their expression is not directly dependent on somatic rearrangement. Despite the unusual nature of immunoglobulin gene genetics in these species, preliminary characterization of the transcription products of immunoglobulin loci in single cell isolates is consistent with haplotype exclusion. Certain features of immunoglobulin gene organization and expression in cartilaginous fish are remarkably similar to that of odorant receptors and suggest that at the level of transcriptional regulation, at least two different mechanisms could exist that relate to haplotype exclusion.

In addition to being an excellent model system for studying vertebrate development, the zebrafish has become a great tool for gene discovery by mutational analysis. The recent availability of the zebrafish EST database and radiation hybrid mapping panels has dramatically expanded the framework for genomic research in this species. Developing comparative maps of the zebrafish and human genomes is of particular importance for zebrafish mutagenesis studies in which human orthologs are sought for zebrafish genes. However, only partial cDNA sequences are determined routinely for mapped ESTs, leaving the identity of the EST in question. It previously had been reported that zebrafish linkage group 7 shares conserved synteny with human chromosome 11q13. In an effort to further define this relationship, five full-length zebrafish cDNAs, fth1, slc3a2, prkri, cd81, and pc, as well as one putative human gene, DBX were identified and their map positions ascertained. These six genes, along with men1, fgf3 and cycd1 define two regions of conserved synteny between linkage group 7 and 11q13.

SummaryAllorecognition in Hydractinia, a cnidarian, is governed by two different, highly polymorphic genes encoding transmembrane proteins. Using a fluorescent cell read-out system, a new study now shows that the basis for specificity involves homophilic interactions between extracellular domains.

Background: X-linked agammaglobulinemia is typically a severe life-threatening disease characterized by the failure of B-cell differentiation and antibody production, which manifests in infancy and early childhood. Recently, we reported a novel mutation (Cys 145→STOP ) in Bruton's tyrosine kinase in a 51-year-old man who was referred for evaluation because of chronic nasal congestion, recurrent sinusitis, sporadic pneumonia, and a family history suggestive of an X-linked immunodeficiency disease. He had not been treated with gammaglobulin. Objective: This study was performed to investigate the clinical and immunologic phenotypes of this patient's other affected male family members. Methods: A detailed family history and comprehensive review of medical records was carried out. Genetic mutation analysis of the gene encoding Bruton's tyrosine kinase was carried out in the proband's brother and nephew. Results: Clinically affected male family members exhibit marked phenotypic variation with manifestations ranging from extremely mild to severe recurrent infections. Immunologic evaluation revealed extreme variation in immunoglobulin levels, B-cell numbers, and functional antibody titers. Genetic analysis documented a novel mutation in the gene encoding Bruton's tyrosine kinase in the proband, his brother, and his nephew. Conclusions: Despite their sharing the same genetic abnormality, extreme variation was noted in the immunologic findings and phenotypic expression of affected family members. This family study is extraordinary in that clinically affected male members who did not receive aggressive medical treatment died of the disease in childhood or survived into late adulthood. (J Allergy Clin Immunol 1997;100:702-6.)

A series of products were amplified using a PCR strategy based on short minimally degenerate primers and R. eglanteria (clearnose skate) spleen cDNA as template. These products were used as probes to select corresponding cDNAs from a spleen cDNA library. The cDNA sequences exhibit significant identity with prototypic (alpha, beta, gamma, and delta T cell antigen receptor (TCR) genes. Characterization of cDNAs reveals extensive variable region diversity, putative diversity segments, and varying degrees of junctional diversification. This demonstrates expression of both alpha/beta and gamma/delta TCR genes at an early level of vertebrate phylogeny and indicates that the three major known classes of rearranging antigen receptors were present in the common ancestor of the present-day jawed vertebrates.

A 20.1s02,w monoclonal IgM, κ immunoglobulin (McE) exhibiting reversible, temperaturedependent insolubility is described. The precipitation of the protein upon reduction in solution temperature displays sharp concentration dependence and is optimal between pH 6 and 8. The effect of temperature on the rate of cryoprecipitation suggests the involvement of either a low temperature-induced conformational change or nucleation event in cryoprecipitation. Structural studies have indicated that the masses (under denaturing conditions) of both heavy and light chains derived from the cryoimmunoglobulin and noncryoimmunoglobulin reference proteins are identical, and the protein possesses a characteristic J chain. The cryoimmunoglobulin is converted to (Fc)5μ§ and Fabμ fragments by limited digestion with trypsin at 56° C. The heavy chain of the McE protein is deficient in tyrosine and contains excess tryptophan relative to noncryoglobulin and other cryoglobulin proteins. Calculation of structural parameters from these amino acid compositions suggests that the heavy chains of cryoimmunoglobulins may contain significantly greater (P< 0.01) amounts of polypeptide chain turns than do noncryoglobulin references. With the exception of a Leu → Phe substitution at position 13, the McE light chain is homologous with other immunoglobulins of the VκII subgroup, while the heavy chain is of the less frequently encountered VHV subgroup. (Fc)5μ and Fabμ fragments, as well as reduction-derived monomeric subunits, do not cryoprecipitate. Removal of J chain does not affect cryoprecipitation of the reassembled molecule while partial enzymatic removal of neutral hexoses and glucosamine enhances cryoprecipitation. Cryoprecipitation of McE is interpreted as a general solubility effect as opposed to an antibody-antigen phenomenon.

The distribution of the covalently bound polycyclic aromatic hydrocarbon carcinogen, benzo(a)pyrene, in nuclease digestible and undigestible regions of chromatin was studied. Binding of [3H]benzo(a)pyrene was effected by incubating the carcinogen with calf thymus nuclei in the presence of NADPH and rat liver microsomes. The time-course of digestion of carcinogen-modified nuclei by Staphylococcal nuclease and DNase I was determined. Both enzymes result in preferential digestion of [3H]benzo(a)-pyrene modified DNA, demonstrating that the carcinogen binds more extensively to nuclease accessible regions of DNA in chromatin. Comparison of the kinetics of digestion by the two enzymes suggests that the carcinogen primarily binds to the outermost “spacer” regions of DNA in the nucleosome.

The acrylamide-quenching patterns of the intrinsic tryptophan fluorescence of six cold-soluble monoclonal immunoglobulin M (IgM) and two monoclonal IgM proteins possessing cryoglobulin properties (abnormal cold insolubility) have been compared. Static and dynamic components of quenching have been resolved by a modified form of the Stern-Volmer relationship. The unusual observation of static quenching seen with the multitryptophan containing IgM is determined to be a consequence of essentially homogeneous indole fluorescence arising from conserved tryptophan residues within each homologous immunoglobulin domain. Although the static component of the quenching of the two IgM cryoimmunoglobulins examined is similar to that of the non-cryoimmunoglobulin, IgM, some of the cryoglobulin's tryptophan residues appear to be more kinetically exposed to acrylamide than the tryptophans in the non-cryoglobulin IgM. An unusually large negative entropy of activation observed for the quenching process of both cryoimmunoglobulins suggests some abnormality in the dynamic (flexibility) properties of these proteins.

High resolution segregation of erythrocyte membrane polypeptides achieved by isoelectric focusing in 8 M urea was employed in conjunction with surface-restricted radioiodination to analyze the disposition of polypeptides within the human erythrocyte membrane. Several membrane polypeptides showed significant uptake of radioiodine, with the principal labeled component migrating between pH values of 3.0 and 3.5. Two approaches were taken in examining membrane polypeptide disposition on both faces of the erythrocyte membrane. Saturation labeling of the outer face of the membrane with one iodine isotope followed by cell lysis and re-iodination with a second iodine isotope did not prove feasible and another procedure based on surface iodination with 125I, formation of sealed inside-out vesicles and re-iodination with 131I was adopted. Studies of sialic acid release from the membrane surface and trypsin cleavage of radioiodinated peptides indicated that selectively labeled, sealed inside-out vesicles had been formed. The ratio of 125I to 131I in membrane polypeptides separated by isoelectric focusing confirmed the existence of externally disposed, internally disposed and spanning proteins.

Raman spectra have been obtained on aqueous solutions of the following human immunoglobulins: IgM-kappa McE, IgG-kappa Ger, IgM-kappa WSm and IgG-lambda Gui. The former two species exhibit the property of cryoprecipitation. Comparison of the spectra shows that all immunoglobulins have similar secondary structures, predominantly of the beta-sheet type. Fab mu and (Fc)5 mu fragments of IgM-kappa McE also yield Raman spectra which indicate closely similar secondary structures. Minor differences among the spectra can be explained by differences in amino acid compositions of the respective proteins.

Affinity labeling of MOPC 315 myeloma protein with m-nitro benzene diazonium fluoroborate (MNBDF) resulted in a significant decrease in association constant and number of binding sites expressed for nitrophenol ligands. An absorption spectrum indicative of exclusive formation of diazo tyrosine was observed with over 90% of the affinity label being present on the light chains. Protection of the active site with excess e-DNP-L-lysine-HC1 prevented incorporation of the affinity label. Circular dichroic examination of the labeled protein in the 300nm–600nm spectral region revealed three extrinsic cotton effects to accompany the modification by MNBDF. Denaturation of the modified protein by guanidine-HCl resulted in disappearence of the three CD bands. The usefulness of diazo probes in antibody active site exploration is discussed.

The thermodynamics of both normal and abnormal (disease-associated) protein solubility has been examined. It is shown that the atypical behavior of monoclonal cryoimmunoglobulins can be explained by the formation of one or a few additional electrostatic contacts or, less frequently, a larger number of van der Waals interactions in the protein-rich solid phase relative to normal immunoglobulin. It is hypothesized that cryoimmunoglobulins represent the outer edge of the solubility distribution of total serum immunoglobulin.

The NH2-terminal amino acid sequence of the heavy chain of the IgG monoclonal cryoimmunoglobulin Ger was determined. Evidence for the glycosylation of the first heavy chain hypervariable region of this protein was found. The inability of the deglycosylated Fab fragment of Ger to inhibit cryoprecipitation provides direct evidence that the presence of an additional sialic acid residue in a heavy chain's first hypervariable region can account for the cryo properties of this protein. This is the first convincing description of a molecular defect that explains the atypical low temperature solubility of a monoclonal cryoimmunoglobulin.

Neutralization and hapten inhibition of neutralization of azobenzenearsonate-(ABA) haptenated bacteriophage by antibody has been used to characterize the response of Heterodontus francisci to immunization with a Brucella abortus —azobenzenearsonate conjugate. Heterodontus appear to have little background antibody to ABA. The liter at 6 months postimmunization is significantly less than that of a rabbit (IgM) anti-ABA; however, the effectiveness of the inhibition of neutralization for a series of hapten analogs is the same for Heterodontus and rabbit antibody. For one hapten pair, the estimated discriminating capacity of Heterodontus antibody was approximately one-tenth that of rabbit antibody. The findings are consistent with the production in Heterodontus of a low affinity antibody population which exhibits limited capacity for specific recognition.