C-ski cDNAs are encoded by eight exons, six of which are closely linked within the chicken genome.

The c-ski locus extends a minimum of 65 kb in the chicken genome and is expressed as multiple mRNAs resulting from alternative exon usage. Four exons comprising approximately 1.5 kb of cDNA sequence have been mapped within the chicken c-ski locus. However, c-ski cDNAs include almost 3 kb of sequence for which the exon structure was not defined. From our studies using the polymerase chain reaction and templates of RNA and genomic DNA, it is clear that c-ski cDNAs are encoded by a minimum of eight exons. A long 3' untranslated region is contiguous in the genome with the distal portion of the ski open reading frame such that exon 8 is composed of both coding and noncoding sequences. Exons 2 and 3 are separated by more than 25 kb of genomic sequence. In contrast, exons 3 through 8, representing more than half the length of c-ski cDNA sequences, are closely linked within 10 kb in the chicken genome.     

Diverse endogenous antigens for mouse NKT cells: self-antigens that are not glycosphingolipids

NKT cells with an invariant Ag receptor (iNKT cells) represent a highly conserved and unique subset of T lymphocytes having properties of innate and adaptive immune cells. They have been reported to regulate a variety of immune responses, including the response to cancers and the development of autoimmunity. The development and activation of iNKT cells is dependent on self-Ags presented by the CD1d Ag-presenting molecule. It is widely believed that these self-Ags are glycosphingolipids (GSLs), molecules that contain ceramide as the lipid backbone. In this study, we used a variety of methods to show that mammalian Ags for mouse iNKT cells need not be GSLs, including the use of cell lines deficient in GSL biosynthesis and an inhibitor of GSL biosynthesis. Presentation of these Ags required the expression of CD1d molecules that could traffic to late endosomes, the site where self-Ag is acquired. Extracts of APCs contain a self-Ag that could stimulate iNKT cells when added to plates coated with soluble, rCD1d molecules. The Ag(s) in these extracts are resistant to sphingolipid-specific hydrolase digestion, consistent with the results using live APCs. Lyosphosphatidylcholine, a potential self-Ag that activated human iNKT cell lines, did not activate mouse iNKT cell hybridomas. Our data indicate that there may be more than one type of self-Ag for iNKT cells, that the self-Ags comparing mouse and human may not be conserved, and that the search to identify these molecules should not be confined to GSLs.     

Structure of the mouse nucleolin gene. The complete sequence reveals that each RNA binding domain is encoded by two independent exons

Nucleolin is a multifunctional nucleolar protein involved in the synthesis, packaging and maturation of pre-rRNA in eukaryotic cells. We describe the molecular organization and complete sequence of the mouse nucleolin gene, the first higher eukaryotic gene encoding a protein that is both an RNA binding protein involved in rRNA processing and a specific nucleolar protein. The nucleolin gene extends over 9000 base-pairs and is split into 14 exons that encode the 706 amino acid residues of the protein. The promoter sequence is G + C-rich (67% G + C) with four G/C boxes, it lacks bona fide TATA and CAAT boxes and shows capping site heterogeneity. The existence of pyrimidine-rich motifs, similar to those found in the promoter of ribosomal protein genes, could be relevant to the co-regulation of genes whose products are involved in ribosome biogenesis. Nucleolin contains four RNA binding domains, each about 80 amino acid residues long, which include the 11-residue core ribonucleoprotein consensus motif. Each domain is encoded by two exons, with an intervening sequence interrupting the conserved core motif at roughly the same amino acid position. This latter result suggests that the RNA binding domains are composed of two independent subdomains, whose functions remain to be determined.     

Heparin-binding growth-associated molecule contains two heparin-binding beta -sheet domains that are homologous to the thrombospondin type I repeat

Heparin-binding growth-associated molecule (HB-GAM) is an extracellular matrix-associated protein implicated in the development and plasticity of neuronal connections of brain. Binding to cell surface heparan sulfate is indispensable for the biological activity of HB-GAM. In the present paper we have studied the structure of recombinant HB-GAM using heteronuclear NMR. These studies show that HB-GAM contains two beta-sheet domains connected by a flexible linker. Both of these domains contain three antiparallel beta-strands. In addition to this domain structure, HB-GAM contains the N- and C-terminal lysine-rich sequences that lack a detectable structure and appear to form random coils. Studies using CD and NMR spectroscopy suggest that HB-GAM undergoes a conformational change upon binding to heparin, and that the binding occurs primarily to the beta-sheet domains of the protein. Search of sequence data bases shows that the beta-sheet domains of HB-GAM are homologous to the thrombospondin type I repeat (TSR). Sequence comparisions show that the beta-sheet structures found previously in midkine, a protein homologous with HB-GAM, also correspond to the TSR motif. We suggest that the TSR sequence motif found in various extracellular proteins defines a beta-sheet structure similar to that found in HB-GAM and midkine. In addition to the apparent structural similarity, a similarity in biological functions is suggested by the occurrence of the TSR sequence motif in a wide variety of proteins that mediate cell-to-extracellular matrix and cell-to-cell interactions, in which the TSR domain mediates specific cell surface binding.     

Selection of antibody probes to correlate protein sequence domains with their structural distribution

We propose a new approach that permits correlation of specific domains defined by their primary sequence with their location in the structure of complex macromolecular aggregates. It is based on the combination of well-established structural analysis methods that incorporate the use of overlapping peptides on cellulose membranes for the isolation and purification of specific antibodies from a polyclonal antiserum. Monospecific antibodies to the connector protein of bacteriophage phi29 were isolated from polyclonal antisera using a new development of the spotscan method. These antibodies can be purified in quantities that allow antigenicity testing in enzyme-linked immunosorbent assays, Western blotting and immunoprecipitations, demonstrating the specificity of this isolation procedure. This approach has allowed us to generate direct antibody probes for immunoelectron microscopy mapping of different connector protein domains in a low resolution three-dimensional epitope map.     

The triple-helical domain of alpha 2(VI) collagen is encoded by 19 short exons that are multiples of 9 base pairs

We have analyzed the structure of the gene coding for the alpha 2(VI) subunit of chicken type VI collagen. The triple-helical domain of this polypeptide is encoded by 19 short exons distributed over 10 kilobase pairs of genomic DNA. These exons begin with the codon for glycine and end with the codon for the Y amino acid of the collagenous triplet Gly-X-Y. The sizes of the exons are integral multiples of 9 base pairs (bp) (27, 36, 45, 54, 63, and 90 bp), the predominant one being 63 bp. The organization of this type VI collagen gene is therefore quite different from that of the fibrillar collagen genes which have evolved by duplication of a primordial 54-bp unit. It also differs from that of the basement membrane collagen genes whose exon/intron boundaries often split the codons for amino acids.     

A protein encoded by a new family of mobile elements from Euryarchaea exhibits three domains with novel folds

We present here the 2.6Å resolution crystal structure of the pT26‐6p protein, which is encoded by an ORF of the plasmid pT26‐2, recently isolated from the hyperthermophilic archaeon, Thermococcus sp. 26,2. This large protein is present in all members of a new family of mobile elements that, beside pT26‐2 include several virus‐like elements integrated in the genomes of several Thermococcales and Methanococcales (phylum Euryarchaeota). Phylogenetic analysis suggested that this protein, together with its nearest neighbor (organized as an operon) have coevolved for a long time with the cellular hosts of the encoding mobile element. As the sequences of the N and C‐terminal regions suggested a possible membrane association, a deletion construct (739 amino acids) was used for structural analysis. The structure consists of two very similar β‐sheet domains with a new topology and a five helical bundle C‐terminal domain. Each of these domains corresponds to a unique fold that has presently not been found in cellular proteins. This result supports the idea that proteins encoded by plasmid and viruses that have no cellular homologues could be a reservoir of new folds for structural genomic studies.     

Non-H-2 histocompatibility antigens encoded by Moloney-murine leukemia virus in Mov mouse strains are detectable by skin grafting and cytolytic T lymphocytes

The integration and expression of Moloney-murine leukemia virus (M-MuLV) into the germ line of Mov mouse strains on the C57BL/6 background results in the expression of a cell-surface Ag with characteristics expected from non-H-2 histocompatibility Ag: the ability to stimulate graft rejection and generation of CTL. However, both the previously studied Mov-3 and Mov-14 strains differ from the coisogenic C57BL/6 strain by different length segments of chromosome derived from the ICR strain in addition to the integrated M-MuLV genome. To conclusively demonstrate that an Ag encoded by M-MuLV is solely responsible for rejection of Mov skin grafts by coisogenic recipients, we have studied additional Mov strains that differ from coisogenic 129 or BALB/c backgrounds only by integration of an M-MuLV genome. A total of 129 strain recipients reject skin grafts from two viremic Mov strains, Mov-17 and Mov-18. A total of 129 strain hosts primed with either 1) multiple sets of Mov-17 and Mov-18 skin grafts or 2) single injections of Mov-17 and Mov-18 spleen cells produce M-MuLV-specific CTL that could be boosted in primary mixed lymphocyte culture. Generated CTL were reactive with Con A-stimulated lymphoblasts from all tested viremic Mov strains on the B6 and 129 backgrounds as well as B6 lymphomas. Further, we have observed that 129 strain mice reject Mov-9 skin grafts if these skin grafts are transplanted to virgin 129 recipients which have not received prior skin grafts from non-viremic Mov donors. In addition, skin grafts were transplanted from two viremic Mov strains, Mov-15 and Mov-16, to coisogenic BALB/c recipients; rejection of both sets of grafts was observed. However, BALB/c responders did not generate specific CTL after priming in vivo, with either multiple sets of allogeneic grafts or spleen cell injections, and boosting in vitro. These observations confirm the ability of integrated and expressed M-MuLV genomes to encode what is operationally defined as a non-H-2 histocompatibility Ag.     

Three cDNA clones encoding mouse transplantation antigens: Homology to immunoglobulin genes

We constructed cDNA libraries from poly(A)⁺ RNA isolated from cell lines of two different inbred strains of mice, and screened the libraries with a cDNA clone encoding a human transplantation antigen. Three cDNA clones were identified, sequenced and found to encode amino acid sequences highly homologous to portions of a known mouse transplantation antigen. Comparison of the cDNA sequences of mouse transplantation antigens with the constant region domains of the mouse immunoglobulin μ gene reveals a striking homology, which suggests that the two genes share a common ancestor. Antibody genes undergo DNA rearrangements during B cell differentiation that are correlated with their expression. In contrast, DNA blots with these cDNA probes suggest that the genes for the transplantation antigens are not rearranged in the genomes of liver or embryo cells, which express these antigens, as compared with sperm cells, which do not express these antigens. In Bam HI-digested liver DNAs from different inbred strains of mice, 10–15 bands of hybridization were found. Accordingly, the genes encoding the transplantation antigens appear to constitute a multigene family with similar gene numbers in different mice.     

The PreA4(695) precursor protein of Alzheimer''s disease A4 amyloid is encoded by 16 exons.

Alzheimer's disease (AD) is characterized by the cerebral deposition of fibrillar aggregates of the amyloid A4 protein. Complementary DNA's coding for the precursor of the amyloid A4 protein have been described. In order to identify the structure of the precursor gene relevant clones from several human genomic libraries were isolated. Sequence analysis of the various clones revealed 16 exons to encode the 695 residue precursor protein (PreA4(695] of Alzheimer's disease amyloid A4 protein. The DNA sequence coding for the amyloid A4 protein is interrupted by an intron. This finding supports the idea that amyloid A4 protein arises by incomplete proteolysis of a larger precursor, and not by aberrant splicing.     

Identification and characterization of the Escherichia coli RecT protein, a protein encoded by the recE region that promotes renaturation of homologous single-stranded DNA.

Recombination of plasmid DNAs and recombination of bacteriophage lambda red mutants in recB recC sbcA Escherichia coli mutants, in which the recE region is expressed, do not require recA. The recE gene is known to encode exonuclease VIII (exoVIII), which is an ATP-independent exonuclease involved in the RecE pathway of recombination. A 33,000-molecular-weight (MW) protein was observed to be coexpressed with both exoVIII and a truncated version of exoVIII, pRac3 exo, when they were overproduced under the control of strong promoters. We have purified this 33,000-MW protein (p33) and demonstrated by protein sequence analysis that it is encoded by the same coding sequence that encodes the C-terminal 33,000-MW portion of exoVIII. p33 is expressed independently of exoVIII but is probably translated from the same mRNA. p33 was found to bind to single-stranded DNA and also to promote the renaturation of complementary single-stranded DNA. It appears that p33 is functionally analogous to the bacteriophage lambda beta protein, which may explain why RecE pathway recombination does not require recA.     

A probabilistic method to correlate ion pairs with protein thermostability

Recent developments in research on the stability of proteins - specifically, comparisons of the ion pairs of homologous structures - show that ion pairs potentially contribute to the thermostability of proteins. This study proposes a probabilistic Bayesian statistical method to efficiently predict the thermostability of proteins based on the properties of ion pairs. The experimental results suggest that the numbers, types and bond lengths of ion pairs can be used to predict with high accuracy (up to 80%) the thermostability of functionally similar proteins. The predictions have high precision (99%), especially for hyperthermophilic proteins. Results for proteins with differing functions also indicate that the number of ion pairs is related to the thermostability of proteins, and that predictions of thermostability can also be made for proteins with different functions.     

Identification of 51 novel exons of the Usher syndrome type 2A (USH2A) gene that encode multiple conserved functional domains and that are mutated in patients with Usher syndrome type II

The USH2A gene is mutated in patients with Usher syndrome type IIa, which is the most common subtype of Usher syndrome and is characterized by hearing loss and retinitis pigmentosa. Since mutation analysis by DNA sequencing of exons 1-21 revealed only ~63% of the expected USH2A mutations, we searched for so-far-uncharacterized exons of the gene. We identified 51 novel exons at the 3' end of the gene, and we obtained indications for alternative splicing. The putative protein encoded by the longest open reading frame harbors, in addition to the known functional domains, two laminin G and 28 fibronectin type III repeats, as well as a transmembrane region followed by an intracellular domain with a PDZ-binding domain at its C-terminal end. Semiquantitative expression profile analysis suggested a low level of expression for both the long and the short isoform(s) and partial overlap in spatial and temporal expression patterns. Mutation analysis in 12 unrelated patients with Usher syndrome, each with one mutation in exons 1-21, revealed three different truncating mutations in four patients and two missense mutations in one patient. The presence of pathogenic mutations in the novel exons indicates that at least one of the putative long isoforms of the USH2A protein plays a role in both hearing and vision.     

Characterization of the targeting, binding, and phosphorylation site domains of an A kinase anchor protein and a myristoylated alanine-rich C kinase substrate-like analog that are encoded by a single gene.

A novel Drosophila A kinase anchor protein, Drosophila A kinase anchor protein 200 (DAKAP200), is predicted to be involved in routing, mediating, and integrating signals carried by cAMP, Ca(2+), and diacylglycerol (Li, Z., Rossi, E. A., Hoheisel, J. D., Kalderon, D., and Rubin, C. S. (1999) J. Biol. Chem. 274, 27191-27200). Experiments designed to assess this hypothesis now (a) establish the function, boundaries and identity of critical amino acids of the protein kinase AII (PKAII) tethering site of DAKAP200; (b) demonstrate that residues 119-148 mediate binding with Ca(2+)-calmodulin and F-actin; (c) show that a polybasic region of DAKAP200 is a substrate for protein kinase C; (d) reveal that phosphorylation of the polybasic domain regulates affinity for F-actin and Ca(2+)-calmodulin; and (e) indicate that DAKAP200 is myristoylated and that this modification promotes targeting of DAKAP200 to plasma membrane. DeltaDAKAP200, a second product of the DAKAP200 gene, cannot tether PKAII. However, DeltaDAKAP200 is myristoylated and contains a phosphorylation site domain that binds Ca(2+)-calmodulin and F-actin. An atypical amino acid composition, a high level of negative charge, exceptional thermostability, unusual hydrodynamic properties, properties of the phosphorylation site domain, and a calculated M(r) of 38,000 suggest that DeltaDAKAP200 is a new member of the myristoylated alanine-rich C kinase substrate protein family. DAKAP200 is a potentially mobile, chimeric A kinase anchor protein-myristoylated alanine-rich C kinase substrate protein that may facilitate localized reception and targeted transmission of signals carried by cAMP, Ca(2+), and diacylglycerol.     

Responses against antigens encoded by theH-3 histocompatibility locus: Antigens stimulating class I MHC- and class II MHC-restricted T cells are encoded by separate genes

The purpose of this work was to study the genetic basis of histocompatibility antigens encoded by the mouse minor histocompatibility (H) locusH-3. Both class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) and class II MHC-restricted helper T cells (TH) specific for antigens encoded by genes within theH-3 locus were isolated and analyzed. Typing a number of mouse strains for expression of antigens recognized by these TH and CTL suggested that there was a different strain distribution pattern of expression of the antigens recognized by TH compared with those recognized by CTL. Separation of the genes whose products stimulate TH from those whose products stimulate CTL was suggested by: (1) analysis of the strain B10.FS(92NX)/Grf that has undergone recombination within theH-3 region; (2) genetic segregation studies of (B10.UW-H-3 ^b/Sn×C57BL/10Sn)F₂ mice; and (3) F₁ complementation studies in which CTL specific for products of the TH-defined gene(s) could not be detected, even in the absence of immune responses to products of the CTL-defined genes. Taken together, these data suggest that in addition to two genes (B2m andCd-1) within theH-3 region whose products typically stimulate class I MHC-restricted CTL, there is at least one additional gene whose product selectively stimulates class II MHC-restricted TH. This new gene is located telomeric from the CTL-defined genes and between the lociwe andun on chromosome 2. These data demonstrate a novel degree of complexity of theH-3 “locus” and suggest selective presentation of minor H gene products in the context of class I or class II MHC proteins.     

A lymphoma protein with an in vitro site of tyrosine phosphorylation homologous to that in pp60src

The major in vitro substrate for a tyrosine protein kinase in the particulate fraction of the lymphoma cell line LSTRA is a protein of molecular weight of 58,000 (pp58) (Casnellie, J. E. Harrison, M. L., Pike, L. J., Hellstrom, K. E., and Krebs, E. G. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 282-286). In order to determine if this protein was related to pp60src, the transformation-specific protein from Rous sarcoma virus, partial proteolysis maps of in vitro 32P-labeled pp58 and pp60src were prepared using Staphylococcus aureus V8 protease and papain. The maps were clearly different, indicating the pp58 is distinct from pp60src. However characterization of the tryptic fragment containing the single site of in vitro tyrosine phosphorylation in pp58 has revealed that the amino acid sequence around this site is extremely homologous to, if not identical with the sequence around the site of tyrosine phosphorylation in pp60src.     

Evolution of aspartyl proteases by gene duplication: the mouse renin gene is organized in two homologous clusters of four exons.

Overlapping recombinant clones that appear to encompass the entire renin gene, named Ren 1, have been isolated from a library of BALB/c mouse genomic DNA fragments. Based on restriction endonuclease mapping and DNA sequence analysis, Ren 1 spans 9.6 kb and contains nine exons interrupted by eight intervening sequences of highly variable size. The first exon, encoding the signal peptide of preprorenin, is separated from the eight following exons by a 3-kb intron. These eight exons are organized into two clusters of four separated by a 2-kb intron. DNA stretches encoding the aspartyl residues, which are part of the active site of renin, are located at homologous positions in both clusters. Our results show that aspartyl protease genes have arisen by duplication and fusion of an ancestral gene containing five exons. The estimated date of the duplication event of the mouse renin genes Ren 1 and Ren 2 is discussed.     

A Drosophila melanogaster gene encodes a protein homologous to the mouse t complex polypeptide 1

We have isolated and sequenced a cDNA from Drosophila melanogaster that is homologous to the mouse Tcp-1 gene encoding the t complex polypeptide 1, TCP-1. The Drosophila gene maps by in situ hybridization to bands 94B1-2 of the polytene chromosomes. It shares 66% nucleotide sequence identity with the mouse gene. The predicted Drosophila protein consists of 557 amino acids and shares 72% identity with the mouse polypeptide. The TCP-1 polypeptide appears to be highly conserved in evolution from mammals to simple eukaryotes because the Drosophila gene probe also detects related sequences in DNA from the yeast, Saccharomyces cerevisiae. The presence of TCP-1-related polypeptides in organisms such as Drosophila and yeast should facilitate biochemical and genetic analysis of its function.