Retroviral gag and DNA endonuclease coding sequences in IgE-binding factor gene

[Methods for the identification of horizontal gene transfer (HGT) events and progress in related fields]

Horizontal gene transfer is the gene exchange between different organisms or different organelles, which occurs frequently in prokaryotes. Many newly identified horizontal transfer events in eukaryotes indicates that it is a common phenomenon in all organisms. This paper describes the concept of horizontal gene transfer, the standard for judging a horizontal gene transfer events, the character, the mode, the way of horizontal gene transfer, and its impact on gene and genome evolution. The analyses of phylogenetic tree, base composition, selection pressure, intron sequence comparison, inserted special sequence, and biased nucleotide substitution are the most common methods used in previous researches. Evidence accumulated demonstrated that transposable sequences are most likely undergoing horizontal transferring. Transformation, conjugation, and transduction are the main forms of horizontal gene transfer in prokaryotes, but no clear clue was related with the mechanism of horizontal gene transfer in eukaryotes. Horizontal gene transfer plays a special role in genetic, genomic, and the biological evolution.

Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality

By comparing mammalian genomes, we and others have identified actively transcribed Ty3/gypsy retrotransposon-derived genes with highly conserved DNA sequences and insertion sites. To elucidate the functions of evolutionarily conserved retrotransposon-derived genes in mammalian development, we produced mice that lack one of these genes, Peg10 (paternally expressed 10), which is a paternally expressed imprinted gene on mouse proximal chromosome 6. The Peg10 knockout mice showed early embryonic lethality owing to defects in the placenta. This indicates that Peg10 is critical for mouse parthenogenetic development and provides the first direct evidence of an essential role of an evolutionarily conserved retrotransposon-derived gene in mammalian development.

In silico analysis of gene expression profiles in the olfactory mucosae of aging senescence-accelerated mice

We utilized high-density Affymetrix oligonucleotide arrays to investigate gene expression in the olfactory mucosae of near age-matched aging senescence-accelerated mice (SAM). The senescence-prone (SAMP) strain has a significantly shorter lifespan than does the senescence-resistant (SAMR) strain. To analyze our data, we applied biostatistical methods that included a correlation analysis to evaluate sources of methodologic and biological variability; a two-sided t-test to identify a subpopulation of Present genes with a biologically relevant P-value <0.05; and a false discovery rate (FDR) analysis adjusted to a stringent 5% level that yielded 127 genes with a P-value of <0.001 that were differentially regulated in near age-matched SAMPs (SAMP-Os; 13.75 months) compared to SAMRs (SAMR-Os, 12.5 months). Volcano plots related the variability in the mean hybridization signals as determined by the two-sided t-test to fold changes in gene expression. The genes were categorized into the six functional groups used previously in gene profiling experiments to identify candidate genes that may be relevant for senescence at the genomic and cellular levels in the aging mouse brain (Lee et al. [2000] Nat Genet 25:294-297) and in the olfactory mucosa (Getchell et al. [2003] Ageing Res Rev 2:211-243), which serves several functions that include chemosensory detection, immune barrier function, xenobiotic metabolism, and neurogenesis. Because SAMR-Os and SAMP-Os have substantially different median lifespans, we related the rate constant alpha in the Gompertz equation on aging to intrinsic as opposed to environmental mechanisms of senescence based on our analysis of genes modulated during aging in the olfactory mucosa.

Defects in virion production caused by mutations affecting the C-terminal portion of the Moloney murine leukemia virus capsid protein

The capsid (CA) domain of the Moloney murine leukemia virus (Mo-MuLV) Gag protein has a unique carboxy terminus with a highly charged arginine-rich sequence. Mutant viruses harboring arginine-to-alanine mutations affecting this region of CA displayed significant defects in virion release, and the few viral particles produced were noninfectious. The interaction between the mutant Gag precursors was affected, as judged by the yeast two-hybrid assay. The results suggest that the unique carboxy terminus of CA in the Mo-MuLV plays an important role in Gag-Gag association during virion production.

Molecular cloning of a novel murine cell-surface glycoprotein homologous to killer cell inhibitory receptors

We have isolated a cDNA clone encoding a novel murine cell-surface glycoprotein. This polypeptide is predicted to be composed of a signal peptide of 23 amino acids, an extracellular region of 620 amino acids that contains six immunoglobulin-like domains with five potential N-glycosylation sites, a transmembrane sequence of 20 amino acids, and a cytoplasmic tail of 178 amino acids with four sets of sequences similar to the immunoreceptor tyrosine-based inhibition motif. The relative molecular mass of the mature polypeptide is calculated to be 90,520 Da. The polypeptide, designated as p91, shows striking homologies to human killer cell inhibitory receptors, a murine gp49B1 protein, a bovine Fcgamma2 receptor, and a human Fcalpha receptor. The mRNA of p91 was especially abundant in murine macrophages. Western blot analysis using p91-specific anti-peptide sera detected a 130-kDa polypeptide in macrophages. Surface biotinylation and immunoprecipitation analysis verified the surface expression of the translation products on COS-1 cells transfected with the p91 cDNA, but the cells failed to show any Fc binding activity.

Simple human DNA-repeats associated with genomic hypervariability, flanking the genomic retroposons and similar to retroviral sites

Earlier we found a human hypervariable genomic region (GVR). The DNA hybridization probe isolated from this region detects multiple hypervariability of restriction DNA fragments from genomic loci. The sequencing data suggest that the genomic instability and variability are associated with tandem DNA repeats. The DNA hybridization probe contains two families of simple DNA repeats designated as 'apo' and 'tau'. The (TC)n-rich family of DNA 'tau'-repeats bears some similarity to the simple transcribed repeats of Drosophila virilis, simple repetitive motifs of the human proenkephaline gene exon 1, and short sites of retroviral LTR ends. Apo-repeats show an unusual similarity to Rauscher viral env gene site. Besides GVR, apo- and tau-like repeats are localized in other genomic loci and can form separate tandem clusters and terminal repeats flanking certain copies of retroposons (Alu-SINES).

Micropia: a retrotransposon of Drosophila combining structural features of DNA viruses, retroviruses and non-viral transposable elements

The retrotransposon micropia was first described from Y-chromosomal fertility genes of Drosophila hydei. Screening a Drosophila melanogaster genomic library yielded several clones representing micropia elements in D. melanogaster. The DNA sequences of two elements from D. hydei (micropia-DhMiF2 and micropia-DhMiF8) and two elements from D. melanogaster (micropia-Dm2 and micropia-Dm11) permitted a detailed analysis of the spatial organization of micropia constituents. Micropia represents the typical gene organization represented by "core"-protein domains followed by a protease, reverse transcriptase, RNase and integrase domain. New features of the micropia family compared with other retrotransposons are: (1) a region of similarity to class I major histocompatibility complex antigens of mammals; (2) only one main open reading frame of about 4000 bases length; (3) a non-protein-coding region of about 500 base-pairs length between the 3' end of the open reading frame and the 5' start of the 3' long terminal repeat. This region includes 32 base-pair tandem repeats; (4) within the long terminal repeats, 82 base-pair tandem repeats with four potential ecdysteroid receptor binding sites. Because micropia combines many evolutionary features of different viruses, non-viral transposable elements, chromosomal genes and repetitive sequence organizations, this retrotransposon may be seen as a "minigenome" reflecting evolutionary principles of the construction of genomic components.

Nucleotide sequence of a complete mouse intracisternal A-particle genome: relationship to known aspects of particle assembly and function

The 7,095-nucleotide sequence of a mouse genomic intracisternal A-particle (IAP) element, MIA14, is reported. MIA14 is known to be colinear with IAP 35S RNA and to contain functional long terminal repeats. Its internal genetic organization was determined by comparisons with a homologous Syrian hamster element and the related retroviruses simian retrovirus 1 (simian type D) and Rous sarcoma virus (avian type C). MIA14 contains a gag-protease open reading frame of 827 codons and a pol region of 867 codons entered by a frame shift of -1. The env region of 1,100 base pairs has multiple stop codons in all reading frames, consistent with the failure thus far to detect IAP-related glycosylated envelope components. RNA transcribed in vitro from a cDNA clone containing a closely homologous gag-protease open reading frame was translated in a cell-free system. The main product was a 73-kilodalton polypeptide immunoprecipitable with antiserum against the authentic IAP gag-related structural protein p73. Rather than ending at the gag-protease boundary, p73 appears to contain 7 to 8 kilodaltons of peptide encoded by the protease domain, a peculiarity possibly related to the observed impairment of normal protein processing in IAPs. The N-terminal 217 codons of gag are unique to murine IAPs and may have been contributed by recombination with a cellular gene. The mouse-specific region of gag encodes a hydrophobic signal peptide with an atypical cleavage site. Delayed cleavage of this peptide could result in anchoring of newly synthesized p73 to the endoplasmic reticulum membrane and restriction of particle assembly to this site.

Isolation of novel human retrovirus-related sequences by hybridization to synthetic oligonucleotides complementary to the tRNA(Pro) primer-binding site

Synthetic oligonucleotides complementary to putative retroviral primer-binding sites were used as hybridization probes to detect novel retroviruslike sequences. An 8.1-kilobase element with structural features of a retroviral provirus was isolated from a human genomic library by this approach. Nucleotide sequence analysis of its 600-base-pair long terminal repeats revealed characteristic motifs known as regulatory signals for RNA polymerase II transcription: CCAAT, TATA, and ATTAAA. In addition, a putative pol gene displays apparent homologies to conserved regions of retroviral reverse transcriptase. The 5' long terminal repeat is flanked at its 3' end by a putative primer-binding site for reverse transcription with homology to tRNA(Pro). This element is therefore termed HuRRS-P (human retrovirus-related sequence-proline). There are 20 to 40 copies of HuRRS-P homologous sequences in DNAs of human and simian origin.

Sequence relationships of type D retroviruses which cause simian acquired immunodeficiency syndrome

Simian acquired immunodeficiency syndrome (SAIDS) in macaque monkeys is caused by type D retroviruses; three independent virus isolates are identified as SRV-1 (SAIDS retrovirus-serotype 1), SRV-2, and MPMV (Mason-Pfizer monkey virus). Virions from these three isolates have serologically related core antigens, but distinct surface proteins. Also, SRV-2 is unique since it apparently induces retroperitoneal fibromatosis in addition to SAIDS. The complete DNA sequence of molecularly cloned SRV-2 is presented and compared to the sequences of SRV-1 and MPMV and to the sequences of other retroviruses and retroviral-related elements in the genomes of eucaryotic cells. SRV-1 and MPMV show fewer than 6% differences in predicted amino acid sequences encoding gag, prt, pol, and the C-terminal env domain; SRV-2 displays about 15-18% differences in these regions when aligned with SRV-1 or MPMV. Greater variation of predicted amino acid sequences is noted in the externally located N-terminal env domains; SRV-1 and MPMV have 83% homology whereas SRV-2 has 58% homology with either SRV-1 or MPMV. Nucleotide sequences of the LTRs of SRV-1 and MPMV are 88% homologous; SRV-2 shows 70% homology with the LTRs of SRV-1 and MPMV. Comparisons of the predicted pol region amino acid sequences of these simian type D retroviruses with the pol gene of a type B retrovirus, mouse mammary tumor virus (MMTV), reveal about 50% homology. A human endogenous element related to the pol region of MMTV shows about 25% homology of amino acids with the pol sequences of SRV-1 or SRV-2. The prt genes of the simian type D retroviruses are similar in size and predicted amino acid sequence with the prt genes of MMTV and the hamster intracisternal type A particle genome. The C-terminal env domains of the avian type C retrovirus reticuloendotheliosis virus (REV) and the type C baboon endogenous virus (BaEV) have 60 and 85% predicted amino acid homology, respectively, with the C-terminal env domains of SRV-1, SRV-2, and MPMV. Within the gag and pol genes of the simian type D retroviruses there are striking homologies with the rat IgE-binding protein gene. Sequence relatedness of these type D retroviruses with type A, type B, and type C retrovirus genomes and with cellular sequences supports the notion that recombinational events contribute to the genesis and variation of retroviruses.(ABSTRACT TRUNCATED AT 400 WORDS)

Nucleotide sequence and molecular evolution of mouse retrovirus-like IAP elements

We determined the nucleotide (nt) sequences of cDNA and genomic clones for murine intracisternal type A particle (IAP) elements, which are retrovirus-like repetitive sequences in rodent genomes. The nucleotide sequence of the cDNA resembled that of retrovirus RNA genomes in its lack of the U5 sequence within the 3' long terminal repeat. By sequence comparison of our clones with reported rodent IAP elements, we located the probable gag, pol and env gene regions. The sequences for the pol, env and the 3' two-thirds of the gag region were conserved among the IAP elements. In the regions, synonymous substitutions occurred more frequently than non-synonymous ones, which suggested that the regions in question were functionally constrained until fairly recently. The rate of nucleotide substitutions in the regions was estimated to be 6-10 X 10(-9) nt per site per year, and significantly higher than that of the cellular genes. These rates may exemplify a characteristic of the nucleotide substitutions for an endogenous retrovirus. The sequence homology between the IAP element and IgE-binding factor gene is discussed.

Molecular structure of human lymphocyte receptor for immunoglobulin E

We have isolated and sequenced a cDNA clone encoding the human lymphocyte receptor for IgE (Fc epsilon R). The deduced protein sequence reveals that Fc epsilon R consists of 321 amino acids, without any signal sequence, and is oriented with its N-terminus on the cytoplasmic side and its C-terminus on the outside of the cell. This molecule shows striking sequence homology with chicken asialoglycoprotein receptor (hepatic lectin), suggesting a possible role for Fc epsilon R in endocytosis. Fc epsilon R mRNA is expressed in B cells, B cell lines, and macrophage cell lines. It is not expressed in T cells or T cell lines, with the exception of an HTLV-transformed T cell line. mRNAs expressed in a macrophage line and in the latter T cell line differ in size from mRNA expressed in B cells. Human BSF-1 (or IL-4) induces the expression of Fc epsilon R mRNA in B cells, but not in T cells.

cDNA clones encoding murine IgE-binding factors represent multiple structural variants of intracisternal A-particle genes

Previously [Moore, K. W., Jardieu, P., Mietz, J. A., Trounstine, M. L., Kuff, E. L., Ishizaka, K. & Martens, C. L. (1986) J. Immunol. 136, 4283-4290], we examined a T-hybridoma-derived cDNA clone, 8.3, that encodes a biologically active murine IgE-binding factor (IgE-BF), and we showed that it was a variant member of the endogenous retroviral gene family related to mouse intracisternal A particles (IAPs). We have now characterized four more IgE-BF cDNA clones by heteroduplex and restriction enzyme analysis and found that they all represent different structural variants of the full-size IAP genomic element. In clones 8.3 and 10.2, which have been fully sequenced, the open reading frames span deletions 3.4 and 1.9 kilobases (kb) long, respectively, and specify different gag-pol fusion polypeptides. Clone 9.5 contains a 2.1-kb deletion entirely within the pol region. Two other clones (4.2 and 11.7) contain no internal deletion and may represent truncated cDNA copies of full-size (7.2 kb) IAP gene transcripts. Structural variants very similar to clone 10.2 are common in the mouse genome, and clone 9.5 is also probably not a unique gene form. The sequences of clones 8.3 and 10.2 are different in detail, but each is closely homologous to a randomly cloned mouse genomic IAP element throughout the gag-related portions of their open reading frames. Antibodies against two oligopeptides specified by the sequence of clone 8.3 immunoprecipitated IAP-related proteins from mouse neuroblastoma and myeloma cells, confirming that the IgE-BF produced by this clone shares sequence with expressed IAP elements in different cell types. Thus, information related to the IgE-BF is an integral part of the murine IAP retrotransposon gag gene.

The murine Fc receptor for immunoglobulin: purification, partial amino acid sequence, and isolation of cDNA clones

The murine Fc receptor for IgG (Fc gamma R) was purified to homogeneity by immunoaffinity chromatography from detergent lysates of the macrophage cell line J774. Microsequencing of intact protein yielded a single amino-terminal sequence, which was confirmed and extended to 20 residues by the isolation of an overlapping peptide. The isolation of additional proteolytic fragments obtained by using Staphylococcus aureus V8 protease, cyanogen bromide, and lysine C proteinase, facilitated sequence analysis of a total of 119 amino acid residues. Codon usage charts were used to construct oligonucleotide probes based on the amino acid sequences of three nonoverlapping peptides. These probes were used to screen a cDNA library derived from the WEHI-3B myelomonocytic cell line, and a single cDNA clone (pFc24) to which all three probes hybridized was isolated. This clone, containing a 1.02-kilobase cDNA insert, has been characterized by restriction mapping and partial DNA sequencing, and it has been shown to encode the Fc gamma R. The sequence at the 5' end of the clone contained the coding information for the amino-terminal sequence of the Fc gamma R as well as a putative 13-amino acid signal sequence. The 3' end of the clone encoded a peptide identified in purified receptor preparations. Thus, the presence of coding information at the 5' and 3' ends of this clone suggests that full-length Fc receptor cDNA spans greater than 1 kilobase.

Nucleotide sequence of the intracisternal A-particle genome inserted 5' to the interleukin-3 gene of the leukemia cell line WEHI-3B

The nucleotide sequence of the intracisternal A-particle genome IAP-IL3 is presented. This IAP element was found to have inserted upstream of the promoter of the interleukin-3 gene of the leukemia cell line WEHI-3B. IAP-IL3 is 5095 bp in length, with identical long terminal repeats (LTRs) of 337 bp. The LTRs show many of the conserved sequence elements identified in other retroviruses. Comparison with other available sequences of IAP genomes indicates that IAP-IL3 is a deleted type I element. It carries a deletion covering the 3' end of the putative IAP gag gene and extending into the 5' end of the putative IAP pol gene. IAP-IL3 has extensive sequence homology with an IgE-binding factor cDNA and evidence is presented indicating that it was derived from a member of the mouse IAP sequence family. Comparison between the pol region of IAP-IL3 and other retroviruses suggests that IAP-IL3 is most closely related to type B and type D retroviruses.