Evolutionary comparison of murine and human delta T-cell receptor deleting elements

The gene for the T-cell antigen receptor (TCR) delta chain is a gene within a gene, being located in the TCR alpha chain gene in both mice and humans. The human delta locus is flanked by delta deleting elements that undergo preferential rearrangement in the thymus, resulting in deletion of internal delta coding segments. The mouse has conserved analogous elements, m delta Rec and m phi J alpha, which separate delta from alpha and undergo a m delta Rec/m phi J alpha rearrangement in polyclonal thymus. The 5' element, m delta Rec, which is an isolated heptamer-spacer-nonamer (h-s-n), lies within 200 kb of D delta 1, and displays two areas of nearly 80% homology to human delta Rec. The downstream element, m phi J alpha, lies 12.5 kb 3' to C delta, lacks the consensus amino acids for J alpha, and retains 80% homology to human phi J alpha. Cells from murine neonatal thymus show three prominent m delta Rec rearrangements consisting of the m delta Rec/m phi J alpha recombination, a delta Rec/D delta 1/D delta 2/J delta 1 recombination, and two hybrid recombinations. A consequence of the m delta Rec/M phi J alpha rearrangement is a deletion of internal D delta and J delta coding segments that would prevent their incorporation into alpha TCR products. The conservation of noncoding deleting elements flanking the delta TCR in mice and humans is similar to the evolutionarily preserved kappa deleting element of the B-cell lineage and argues for an important role in receptor utilization.     

Apparent 'sympatric' speciation in ecologically similar herbivorous beetles facilitated by multiple colonizations of an island

Coexistence of recently diverged and ecologically similar sister species in complete sympatry represents a particularly compelling case for sympatric speciation. This study investigates the possible sympatric origin of two coexisting bark beetle taxa that utilize the same host plant on the island of La Palma in the Canary Islands. Aphanarthrum subglabrum and Aphanarthrum glabrum ssp. nudum breed inside dead twigs of Euphorbia lamarckii plants and are closely related to the allopatric A. glabrum ssp. glabrum in Tenerife, El Hierro and La Gomera. We tested the various speciation hypotheses in a genealogical context, using mitochondrial gene fragments from Cytochrome Oxidase I and 16S, and nuclear gene fragments from Enolase, Elongation Factor 1alpha and Histone H3. Phylogenetic analyses of the combined nuclear DNA data strongly supported a sister relationship between two sympatric and reproductively isolated taxa in La Palma. However, network analyses of subdivided nonrecombinant segments of the Enolase locus indicated a closer relationship between the two allopatric A. glabrum subspecies, suggesting multiple colonizations of this island. A bimodal distribution of mtDNA haplotypes in La Palma further documented the independent colonization of this island, with asymmetric introgression of mtDNA between two lineages. Consequently, the sympatric origin of the La Palma species is concluded to have involved allopatric phases before the parallel colonization of this island and subsequent introgression at some loci. The clear genetic and morphological evidence for reproductive isolation between these species suggests that the sympatric completion of divergence was either due to initial genetic incompatibility, morphological character displacement in male genitalia, or a combination of these factors.     

Alpha-chains of IgM and IgD antigen receptor complexes are differentially N-glycosylated MB-1-related molecules

The major B cell Ag receptors, membrane (m) IgM and mIgD, are noncovalently associated with disulfide-linked heterodimers of alpha, beta, and gamma glycoproteins. The beta and gamma chains have apparent molecular masses of 37 and 34 kDa, respectively, and are associated with both mIgM and mIgD. Receptor alpha chains, however, exhibit Ig isotype specificity. IgM-alpha and IgD-alpha have apparent molecular masses of 32 and 33 kDa, respectively. Recently, the alpha chain of the IgM Ag receptor complex was identified as the product of the mb-1 gene, and the beta and gamma chains were characterized as products of the B29 gene. The failure of mb-1 cDNA to hybridize with mRNA from J558 delta m2.6 plasmacytomas expressing surface mIgD in association with IgD-alpha has led to the conclusion that IgM-alpha and IgD-alpha are not closely related. In this report we have used protein biochemical methods to characterize differences in the mIgM- and mIgD-associated alpha chains. In addition to a slightly greater apparent m.w., IgD-alpha was slightly more acidic than IgM-alpha. The alpha chains had nearly identical proteolytic peptide maps, and were also noted to have multiple loci of identity with MB-1 based on amino terminal sequencing and immunoblotting. In an attempt to determine whether the alpha chains differed as a result of differential posttranslational modification, they were compared after deglycosylation with N-glycanase. The results indicate that the apparent m.w. as well as isoelectric point differences are primarily due to differential N-linked glycosylation. These studies indicate that IgM-alpha and IgD-alpha are products of the mb-1 gene or closely related genes.     

Developmentally regulated alternative splicing of Drosophila integrin PS2 alpha transcripts

We report the characterization of a chromosomal integrin gene that encodes the Drosophila PS2 alpha subunit. The gene is composed of 12 exons spanning 31 kb. By employing a novel method for directed cDNA cloning, we have analyzed over 300 independent cDNA clones for the existence of alternate RNA products. Two forms of PS2 alpha mRNA are frequently observed: a canonical (C) form and a form lacking the 75 nucleotide exon 8 (m8). The relative ratio of these two forms varies widely during development. Although region A, derived from exon 8 and the adjacent 25 amino acids, shows weak conservation among the sequences of alpha subunits that bind to different ligands, it is highly conserved in the homologous PS2 alpha gene of the distantly related Mediterranean fruitfly. We suggest that the variable region A may be important in determining the specificity and affinity of integrin receptors for their ligands.     

Cloning a calcium channel alpha2delta-3 subunit gene from a putative tumor suppressor gene region at chromosome 3p21.1 in conventional renal cell carcinoma

We have identified loss of heterozygosity (LOH) of approx. 1 cM region around locus D3S1289 at chromosome 3p21.1 in a conventional renal cell carcinoma (RCC). During construction of a YAC/BAC contig for this region and shotgun sequencing of BACs 277p5, 55m24 and 428i24, we detected four new microsatellites. We narrowed down the target region by analysing these new loci to less than 100 kb within the BAC 55m24 and subsequently cloned a human calcium channel alpha2delta-3 subunit gene. This gene is widely expressed in fetal tissues and different types of adult tumors. The exons of the alpha2delta-3 subunit gene are distributed along approx. 500 kb DNA sequences. As the LOH involved exclusively intronic sequences and sequencing the entire coding region did not reveal any mutation, the alpha2delta-3 subunit gene is probably not a tumor suppressor gene.     

La(3+) stabilizes the hexagonal II (H(II)) phase in phosphatidylethanolamine membranes.

The mechanism of the effects of the lanthanum ion (La(3+)) and the gadolinium ion (Gd(3+)), which are lanthanides, on the function of membrane proteins and the stability of the membrane structure is not well understood. We investigated the effects of La(3+) on the stability of the hexagonal II (H(II)) phase of the phosphatidylethanolamine (PE) membrane at 20 degrees C by small-angle X-ray scattering. As PE membrane we used DPOPE (dipalmitoleoylphosphatidylethanolamine) membrane, which was in the L(alpha) phase in 10 mM PIPES buffer (pH 7.4) at 20 degrees C. An L(alpha) to H(II) phase transition occurred in the DPOPE membrane at 1.4 mM La(3+) in 0 M KCl, and at 0.4 mM La(3+) in 0.5 M KCl and above the critical concentrations the membranes were in the H(II) phase, indicating that La(3+) stabilizes the H(II) phase rather than the L(alpha) phase. The basis vector length, d, of DPOPE and DOPE (dioleoylphosphatidylethanolamine) membranes containing 16 wt% tetradecane in excess water condition did not change with an increase in La(3+) concentration, suggesting that La(3+) did not change the spontaneous curvature of these PE monolayer membranes. The chain-melting transition temperature of the dielaidoylphosphatidylethanolamine membrane increased with an increase in La(3+) concentration, indicating that the lateral compression pressure increased. To elucidate the effects of a small percentage of 'guest' lipids with longer acyl chains than the average length of 'host' lipids on the stability of the H(II) phase, we investigated the effects of the concentration of a guest lipid (DOPE) in a host lipid (DPOPE) membrane on their phase behavior and structure. 12 mol% DOPE induced an L(alpha) to H(II) phase transition in DOPE/DPOPE membrane, without changing the spontaneous curvature of the monolayer membrane. We found that Ca(2+) also induced an L(alpha) to H(II) phase transition in the DPOPE membrane, and compared the effects of Ca(2+) on PE membranes with those of La(3+). Based on these results, we have proposed a new model for the mechanism of the L(alpha) to H(II) phase transition and the stabilization of the H(II) phase by La(3+).     

Activation of calcium mobilization and calcium influx by alpha 1-adrenergic receptors in a smooth muscle cell line

Alpha 1-adrenergic receptor (alpha 1R) mediated increases in the cytosolic levels of free Ca+2 and the inositol phosphates were measured in a smooth muscle cell line, DDT1. Norepinephrine (NE) stimulated a rapid increase in cytosolic Ca+2 by two distinct components: 1) release of Ca+2 from intracellular sites (mobilization), and 2) influx of extracellular Ca+2. The mobilization component was not affected by removal of extracellular Ca+2 or addition of La+3 or Co+2 to the buffer. The influx component was abolished by EGTA, La+3, or Co+2, but was not affected by the voltage-operated Ca+2 channel blockers diltiazem or nifedipine. Depolarization of DDT1 cells with 100 mM KCl or with gramicidin did not induce Ca+2 influx. NE also increased inositol trisphosphate to 78% over basal levels within 1 minute. These results suggest that alpha 1R on DDT1 cells are coupled to both the mobilization of intracellular Ca+2 and to receptor-operated Ca+2 channels in the plasma membrane, and that polyphosphoinositide hydrolysis may play a role in these phenomena.     

The La antigen inhibits the activation of the interferon-inducible protein kinase PKR by sequestering and unwinding double-stranded RNA.

The La (SS-B) autoimmune antigen is an RNA-binding protein that is present in both nucleus and cytoplasm of eukaryotic cells. The spectrum of RNAs that interact with the La antigen includes species which also bind to the interferon-inducible protein kinase PKR. We have investigated whether the La antigen can regulate the activity of PKR and have observed that both the autophosphorylation of the protein kinase that accompanies its activation by dsRNA and the dsRNA-dependent phosphorylation of the alpha subunit of polypeptide chain initiation factor eIF-2 by PKR are inhibited in the presence of recombinant La antigen. This inhibition is partially relieved at higher concentrations of dsRNA. Once activated by dsRNA the protein kinase activity of PKR is insensitive to the La antigen. We have demonstrated by a filter binding assay that La is a dsRNA binding protein. Furthermore, when recombinant La is incubated with a 900 bp synthetic dsRNA or with naturally occurring reovirus dsRNA it converts these substrates to single-stranded forms. We conclude that the La antigen inhibits the dsRNA-dependent activation of PKR by binding and unwinding dsRNA and that it may therefore play a role in the regulation of this protein kinase in interferon-treated or virus-infected cells.     

A novel type of aberrant T cell receptor alpha-chain gene rearrangement. Implications for allelic exclusion and the V-J recombination process

In the process of analyzing the contribution of nonproductive alpha- and beta-chain gene rearrangements to the allelic exclusion of TCR gene expression, we have found a novel type of aberrant alpha-gene rearrangement. In one alpha-allele of the mouse KB5-C20 T cell clone, a J alpha gene segment has been abutted precisely to a sequence that does not display any homology to known V and D gene segment. The appended sequence originates from within the V alpha locus and is located, in the germ-line, 1 kb upstream of a member of the V alpha 2-gene segment subfamily. No recombination signal sequences have been found contiguous to the recombination point. These observations indicate that in normal T lymphocytes, TCR alpha-genes may be affected by aberrant rearrangements similar to those that predominate in human T cell tumors containing chromosome 14 inversion or translocation. Furthermore, compilation of published data and cloning and sequencing of three additional alpha-alleles has allowed us to examine the status of alpha-loci in nine mouse T cell clones expressing functional alpha beta-heterodimers. Interestingly, in contrast to the situation observed at the beta-locus, only 1 of 18 analyzed alpha-alleles has retained a germ-line unrearranged configuration. In addition, in each T cell clone, alpha-rearrangements on homologous chromosomes were unevenly distributed over the J alpha region and shown to generally involve neighboring J alpha gene segments.     

DNA and chromatin structure of the human alpha 1 (I) collagen gene

The human alpha 1 (I) collagen gene and 48 kilobase pairs of flanking DNA have been isolated on two overlapping cosmids. The alpha 1 (I) gene is 18 kilobase pairs long and contains a single repetitive element of the Alu family; at least 15 repetitive elements are present in the flanking DNA. Analysis of chromatin structure in nuclei isolated from cultured fibroblasts demonstrated a single chromatin domain greater than 65 kilobase pairs in length that contained 9 DNase I-hypersensitive sites. The pattern of hypersensitive sites was also determined in nuclei derived from placental tissue. Five of the DNase I-hypersensitive sites were observed in both placental and fibroblast chromatin including one site near the 5' end and another near the 3' end of alpha 1 (I). An additional two sites located near the 3' end of the alpha 1 (I) gene in fibroblast chromatin are associated with the tissue-specific use of different polyadenylation sites. Two DNase I-hypersensitive sites found only in fibroblast chromatin and one site found only in placental chromatin were located more than 10 kilobase pairs away from the alpha 1 (I) gene and may be related to tissue-specific expression of other genes in the domain. However, the only abundant placental mRNAs from the 65-kilobase pair domain were those transcribed from the alpha 1 (I) gene. These findings suggest that physical linkage does not play a predominant role in controlling coordinate expression of collagen genes.     

Recombination and mutation of class II histocompatibility genes in wild mice

We have compared the tryptic peptide fingerprints of the A alpha, A beta, E alpha, and E beta subunits encoded by four wild-derived H-2 complexes expressing A molecules closely related to Ak. The A molecules encoded by these Ak-related mice have A alpha and A beta subunits that differ from A alpha k and A beta k by less than 10% of their tryptic peptides. Comparisons among the four wild-derived A molecules suggested that these contemporary A alpha and A beta alleles arose by sequential mutational events from common ancestor A alpha and A beta alleles. These results suggest that A alpha and A beta may co-evolve as an A beta A alpha gene duplex in wild mice. Tryptic peptide fingerprint comparisons of the E beta gene linked to these Ak-related A beta A alpha gene duplexes indicate that two encode E beta d-like subunits, whereas another encodes an E beta s-like subunit. These results strongly suggest that the A beta A alpha duplex and E beta recombine in wild mouse populations. The significantly different evolutionary patterns exhibited by the class II genes encoding A vs E molecules are discussed.     

Immunochemical detection, physicochemical characterization and levels of pregnancy-associated endometrial alpha 2-globulin (alpha 2-PEG) in seminal plasma of men

Pregnancy-associated endometrial alpha 2-globulin (alpha 2-PEG), the major secretory protein of the human uterine endometrium during the luteal phase of the menstrual cycle and early first trimester of pregnancy, has been detected by immunochemical techniques in seminal plasma. Biochemical analysis and immunoblotting has verified that immunoreactive alpha 2-PEG in seminal plasma exhibits properties identical to those of endometrial alpha 2-PEG, i.e. Concanavalin A-binding dimeric glycoprotein of native Mr 56,000, subunit Mr 28,000, average pI 4.7 and of alpha 2-mobility. Concentration of alpha 2-PEG in seminal plasma was 22.13 +/- 2.82 micrograms/ml (mean +/- s.e.m., n = 110) which compared to 12.02 +/- 1.65 micrograms/ml (mean +/- s.e.m., n = 48) found in amniotic fluid at 11-20 weeks of pregnancy, to 4.29 +/- 1.66 micrograms/ml (mean +/- s.e.m., n = 15) in uterine luminal fluid in women during the luteal phase and to 0.245 +/- 0.025 micrograms/ml (mean +/- s.e.m., n = 10) in sera at 10 weeks of pregnancy. This distribution is very different from that observed for pregnancy-associated placentally-derived serum proteins detected in seminal plasma. The source of alpha 2-PEG in seminal plasma is unknown but is unlikely to be the testis because of the normal levels observed in vasectomized men. In the endometrium alpha 2-PEG synthesis and secretion appears to be related to progesterone-dependent differentiation of the glandular epithelium. Therefore these observations suggest that a different mechanism of regulation of the gene for alpha 2-PEG operates in the male reproductive tract.     

Nucleotide sequence of the goat embryonic alpha globin gene (zeta) and linkage and evolutionary analysis of the complete alpha globin cluster

In previous studies we identified and sequenced clones containing two adult alpha globin genes of the goat. Additional studies have revealed the presence of an embryonic alpha globin gene termed zeta. Sequence analysis of the gene shows that it is the largest mammalian or avian globin gene cloned to date. Its unusual size is mainly due to a 14 base-pair tandem repeat sequence in its first intron. A similar sequence is also found in the first intron of the human zeta gene. The goat zeta coding sequence differs greatly from that of the adult alpha, particularly at amino acid position 38, where it codes for the amino acid replacement of Gln for Thr. This change may confer a higher intrinsic O2 affinity on the zeta globin protein, ensuring a sufficient O2 supply for the developing goat embryo. The cloning and sequencing of this gene completes the alpha globin locus of the goat, composed of three genes in the following order 5'-zeta-I alpha-II alpha-3'. Evolutionary comparisons of the goat alpha locus with other amphibian, avian and mammalian loci reveal several interesting features. Statistical analysis confirms the hypothesis that the embryonic alpha gene is much older (400 million years) than the embryonic beta gene (200 million years), and that it is descended from a primordial gene, whose present-day counterpart is the Xenopus larval alpha globin gene. Our results also suggest that after the divergence of the avian line, the alpha A gene converted the alpha D gene during the evolution of the pre-mammalian line. The alpha D globin gene remains unconverted in the avian line, potentially because of insertion/deletion sequences that may prevent any gene conversion event. The divergence rates of specific globin genes have been analyzed and found to form an essentially straight line, in agreement with the neutralist view of evolution.     

The alternative stimulatory G protein alpha-subunit XLalphas is a critical regulator of energy and glucose metabolism and sympathetic nerve activity in adult mice

The complex imprinted Gnas locus encodes several gene products including G(s)alpha, the ubiquitously expressed G protein alpha-subunit required for receptor-stimulated cAMP generation, and the neuroendocrine-specific G(s)alpha isoform XLalphas. XLalphas is only expressed from the paternal allele, whereas G(s)alpha is biallelically expressed in most tissues. XLalphas knock-out mice (Gnasxl(m+/p-)) have poor suckling and perinatal lethality, implicating XLalphas as critical for postnatal feeding. We have now examined the metabolic phenotype of adult Gnasxl(m+/p-) mice. Gnasxl(m+/p-) mice had reduced fat mass and lipid accumulation in adipose tissue, with increased food intake and metabolic rates. Gene expression profiling was consistent with increased lipid metabolism in adipose tissue. These changes likely result from increased sympathetic nervous system activity rather than adipose cell-autonomous effects, as we found that XLalphas is not normally expressed in adult adipose tissue, and Gnasxl(m+/p-) mice had increased urinary norepinephrine levels but not increased metabolic responsiveness to a beta3-adrenergic agonist. Gnasxl(m+/p-) mice were hypolipidemic and had increased glucose tolerance and insulin sensitivity. The similar metabolic profile observed in some prior paternal Gnas knock-out models results from XLalphas deficiency (or deficiency of the related alternative truncated protein XLN1). XLalphas (or XLN1) is a negative regulator of sympathetic nervous system activity in mice.