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PubMed1992

Genomic organization and nucleotide sequence of a long mosaic repetitive DNA in the mouse genome.

A long mosaic repetitive sequence (LMRS) was isolated from a mouse liver genome library using a mouse repetitive DNA as a probe. LMRS exhibits the following features: (1) it is almost 15 kb in length; (2) it is partly organized in tandem array and frequently interrupted by other repeated sequences; and (3) it is located predominantly on the A3 band of the mouse X Chromosome (Chr). One fragment of LMRS (B6) shows restriction fragment length polymorphism (RFLP) between different mouse strains, and is thus potentially useful for mapping studies. The nucleotide sequence confirms a mosaic organization of LMRS which includes three repeats in the 5' part, showing similarity with the 5' end of L1Md-A2, and seven long A + T rich segments in the central part of the element. Our findings suggest that this sequence may have arisen from the duplication of an ancestral motif and has expanded by successive waves of amplification and invasion by foreign sequences.

Animals↗
PubMed1996

Pig genome analysis: differential distribution of SINE and LINE sequences is less pronounced than in the human and mouse genomes.

The distribution of SINE and LINE sequences in the pig genome was examined by fluorescence in situ hybridization (FISH), interspersed repeat PCR, and restriction analysis of high molecular weight DNA. FISH revealed a largely uniform hybridization to the euchromatic chromosome regions with both interspersed repeats, although a bias toward the G-bands was observed for the LINE probe. Southern blots of inter-SINE and inter-LINE PCR products showed strong hybridization to LINE and SINE probes, respectively. High molecular weight DNA derived from a pig x hamster hybrid cell line was cut with a panel of G + C and A + T rich rare cutter restriction enzymes, then run on a pulsed field gel and Southern blotted. Sequential hybridization with SINE and LINE probes showed that SINE hybridization was to relatively low molecular weight fragments with the G + C rich enzymes, whereas the LINE probe gave hybridization to significantly larger fragments produced by these enzymes. DNA samples digested with A + T rich enzymes gave essentially similar patterns with SINE and LINE probes. We conclude that the pattern of differential distribution of SINEs and LINEs, which has been described in man and mouse, does exist in the pig but is much less pronounced.

Animals↗
PubMed1993

Sequence analysis of the Ebola virus genome: organization, genetic elements, and comparison with the genome of Marburg virus.

Sequence analysis of the second through the sixth genes of the Ebola virus (EBO) genome indicates that it is organized similarly to rhabdoviruses and paramyxoviruses and is virtually the same as Marburg virus (MBG). In vitro translation experiments and predicted amino acid sequence comparisons showed that the order of the EBO genes is: 3'-NP-VP35-VP40-GP-VP30-VP24-L. The transcriptional start and stop (polyadenylation) signals are conserved and all contain the sequence 3'-UAAUU. Three base intergenic sequences are present between the NP and VP35 genes (3'-GAU) and VP40 and GP genes (3'-AGC), and a large intergenic sequence of 142 bases separates the VP30 and VP24 genes. Novel gene overlaps were found between the VP35 and VP40, the GP and VP30, and the VP24 and L genes. Overlaps are 20 or 18 bases in length and are limited to the conserved sequences determined for the transcriptional signals. Stem-and-loop structures were identified in the putative (+) leader RNA and at the 5' end of each mRNA. Hybridization studies showed that a small second mRNA is transcribed from the glycoprotein gene, and is produced by termination of transcription at an atypical polyadenylation signal located in the middle of the coding region. The predicted amino acid sequence of the glycoprotein contains an N-terminal signal peptide sequence, a hydrophobic anchor sequence, and 17 potential N-linked glycosylation sites. Alignment of predicted amino acid sequences showed that the structural proteins of EBO and MBG contain large regions of homology despite the absence of serologic cross-reactivity.

Amino Acid Sequence↗
PubMed1994

Identification of the primary structure and the coding capacity of the genome of insect iridescent virus type 6 between the genome coordinates 0.310 and 0.347 (7990 bp).

The primary structure and the coding capacity of the insect iridescent virus type 6--Chilo iridescent virus (CIV)--were determined between the genome coordinates 0.310 (EcoRI site) and 0.347 (ClaI site). The EcoRI CIV DNA fragment M (7.1 kb; 0.310-0.345 map units) harbors one out of at least six loci of DNA replication origins which is located at nucleotide position 485-513. The identification of the structural properties and the coding capacity of the EcoRI CIV DNA fragment M was carried out by DNA nucleotide sequencing, computer-aided sequence analysis and DNA/RNA hybridization. The EcoRI CIV DNA fragment M (7,099 bp; 71.14% A+T and 28.86% G+C) possesses two clusters of five tandemly organized repetitive DNA elements with complex structural arrangements (R1-R5) which are located between nucleotide positions 3272-3350 and 3403-3414. The analysis of the DNA sequences of the EcoRI CIV DNA fragment M revealed the presence of six open reading frames (ORFs 1-6). Two out of six detected putative proteins are of particular interest. ORF-2 was found to be terminated at nucleotide position 366 (TAA) within the DNA sequence of the EcoRI CIV DNA fragment L (0.345-0.381 map units; 7.4 kb). The analysis of ORF-2 (1,051 amino acids; 120 kD) revealed homologies to several DNA-directed RNA polymerases. ORF-6 encodes a protein (606 amino acids; 69 kD) which is related to a group of yeast, Drosophila and mammalian proteins of a distinct family of putative DNA and/or RNA helicases belonging to the 'DEAD/H' superfamily. The transcriptional activity of the EcoRI CIV DNA fragment M was determined by DNA/RNA hybridization experiments. These analyses revealed the existence of three RNA transcripts of about 3.4 kb (t1), 1.8 kb (t2) and 1.2 kb (t3) which agree with the predicted size of the expected RNA transcripts from ORF-2 (1,051 amino acids; 3.1 kb) and ORF-6 (606 amino acids; 1.8 kb).

Amino Acid Sequence↗
PubMed1994

Lymphoepithelial-like carcinoma of the uterine cervix. Study of a case with in situ hybridization of the Epstein-Barr virus genome and the human papillomavirus genome.

Lymphoepithelial-like carcinoma of the uterine cervix is very rare in Caucasian women. We present a new case in a 74 year-old European. Morphologically the undifferentiated carcinoma was accompanied by intense lymphocytic infiltration. Immunohistochemically the tumor expressed epithelial markers such as cytokeratin CAM 5.2, and a large proportion of cells expressed the proliferating cell nuclear antigen. The accompanying lymphocytic reaction was composed predominantly of T-lymphocytes which express the UCHL1 antigen. The in situ hybridization of the Epstein-Barr virus genome and the human papillomavirus proved negative.

Aged↗
PubMed1995

The genomic sequence of a virulent bovine viral diarrhea virus (BVDV) from the type 2 genotype: detection of a large genomic insertion in a noncytopathic BVDV.

A second genotype of bovine viral diarrhea virus, BVDV genotype 2 or BVDV 2, has been identified based on phylogenic analysis of sequences from the 5' untranslated region of the viral RNA. In this study, we derived the complete nucleic acid sequence of a virulent BVDV 2 virus, BVDV2-890, isolated from an animal that died of an acute uncomplicated BVDV infection. BVDV2-890 is noncytopathic in cell culture and does not produce a p80 viral polypeptide. The ORF of BVDV2-890 is 11,922 nucleotide bases long and codes for 3973 amino acids. In comparison, the ORFs of other noncytopathic pestiviruses are shorter by about 250 nucleotides. The sequence identity at the amino acid level, between BVDV2-890 and published sequences for other pestiviruses, is 74% or less. The most conserved nucleotide and amino acid sequences between BVDV2-890 and other pestiviruses are located in the region coding for the nonstructural protein p80. The least conserved are in the regions coding for the structural polypeptide gp53 and nonstructural polypeptides p54 and p58. The larger size of the BVDV2-890 ORF is due to a 228-nucleotide insertion in the portion of the genome coding for the viral polypeptide p54. The location of this insertion was upstream from those reported in cytopathic pestiviruses. This insertion was not characteristic of all of the BVDV 2 viruses or all of the virulent BVDV 2 viruses.

Amino Acid Sequence↗
PubMed1991

The mitochondrial genome of fission yeast: inability of all introns to splice autocatalytically, and construction and characterization of an intronless genome.

In this paper we report the inability of four group I introns in the gene encoding subunit I of cytochrome c oxidase (cox1) and the group II intron in the apocytochrome b gene (cob) to splice autocatalytically. Furthermore we present the characterization of the first cox1 intron in the mutator strain anar-14 and the construction and characterization of strains with intronless mitochondrial genomes. We provide evidence that removal of introns at the DNA level (termed DNA splicing) is dependent on an active RNA maturase. Finally we demonstrate that the absence of introns does not abolish homologous mitochondrial recombination.

Amino Acid Sequence↗
PubMed1984

Virus genome integration as a function of the host cell genome replicative cycle.

Mouse 3T3 cells were grown and synchronized in monolayer with the double thymidine block. Their infection with SV40 took place continuously during the cellular cycle. However, integration of viral DNA into host cell DNA occurred preferentially during the S phase. Phase G1 appeared to be necessary for virus-cell DNA recombination in S phase. Phase G2 did not alter the stability of the integrated viral genome.

Animals↗
PubMed1990

The cyanelle genome of Cyanophora paradoxa encodes ribosomal proteins not encoded by the chloroplasts genomes of higher plants.

The rpl35, rpl20, rpl5, rps8, and a portion of the rpl6 genes of the cyanelle genome of Cyanophora paradoxa have been cloned, mapped and sequenced. Homologs of the rpl35, rpl5, and rpl6 genes are not found in the chloroplasts of higher plants. The rpl35 genes most likely form a dicistronic operon which is located upstream from the apcE-apcA-apcB locus of the cyanelle and which is divergently transcribed from this locus. The rpl5, rpl8, and rpl6 genes probably form a part of a larger cluster of genes encoding components of the cyanellar ribosomes. These genes are organized in a fashion similar to that observed in all procaryotes examined to date, with the exception that the rps14 gene is not found between the rpl5 and rps8 coding sequences. Hypotheses concerning the origins of cyanelles and chloroplasts are discussed.

Amino Acid Sequence↗
PubMed1994

Genomic and non-genomic effects of steroidal drugs on smooth muscle contraction in vitro.

The effect of steroidal drugs on KCl (60 mM)-induced tonic contraction in in vitro rat uterus has been assayed. Ouabain had no effect and aldosterone only relaxed the KCl contraction up to 27 +/- 7.3%. However, estradiol, testosterone, progesterone, cortisol and alphaxalone relaxed the contraction in a dose-dependent way, and CaCl2 (0.1 to 6 mM) counteracted this effect. Cycloheximide (1 and 10 micrograms/ml) did not modify the effect of progesterone, testosterone or alphaxalone. Cycloheximide, but not actinomycin D (5 micrograms/ml), reduced the effect of cortisol. Both cycloheximide and actinomycin D shifted righward the relaxing effect of estradiol. This suggests that the steroidal relaxing effect in smooth muscle is preferably non-genomic and at plasma membrane level. However, cortisol and estradiol also act at intracellular levels and induce transcriptional (estradiol) or non-transcriptional (cortisol) effects.

Animals↗
PubMed1991

Rescue of a Sendai virus DI genome by other parainfluenza viruses: implications for genome replication.

Using a defective interfering Sendai virus stock (DIH4) freed of nondefective helper virus, we found that the closely related parainfluenza viruses 1 and 3 could substitute for the Sendai virus helper in replicating DIH4, creating chimeric nucleocapsids. The morbillivirus measles and the rhabdovirus VSV could not substitute. When DIH4 is incubated intracellularly for 5 days in the absence of help, the ability of PIV3 to rescue DIH4 at this time depended on fresh Sendai virus polymerase. The PIV3 polymerase apparently can only copy the chimeric template, but not that wrapped in the homologous Sendai NP protein. These results suggest that the cis-acting RNA sequences important for genome replication, e.g., the promoter and the encapsidation site, have been conserved among these viruses, but that the interactions between the polymerase and the template protein NP are unique for each virus.

Animals↗
PubMed1990

Primer extension dideoxy chain termination nucleotide sequencing of partially purified RNA virus genomes: a technique for investigating low titre viruses with extensive genome secondary structure.

A modified version of the primer extension dideoxy chain termination nucleotide sequencing technique (Sanger et al., 1977) is described. This method has advantages over existing molecular cloning and primer extension techniques in that it allows the genome of RNA viruses to be directly sequenced from partially purified RNA preparations. Thus, viruses growing at unacceptably low titres in tissue culture can now be partially purified from infected mouse brain and sequenced. The technique also incorporates steps for the denaturation of secondary structure which has previously provided difficulties for primer extension sequencing.

Animals↗
PubMed1993

Zidovudine-resistant human immunodeficiency virus type 1 genomes detected in plasma distinct from viral genomes in peripheral blood mononuclear cells.

The emergence of zidovudine (3'-azido-2',3'-deoxythymidine)-resistant strains of human immunodeficiency virus type 1 (HIV-1) from AIDS patients treated with zidovudine has been linked to six amino acid substitutions localized within the viral polymerase gene. Here, in 2 patients, three resistance mutations were detected by polymerase chain reaction amplification of HIV-1 polymerase (reverse transcriptase) sequences from cultures of patient plasma only and not from the same patients' uncultured leukocytes. The differences in distribution of the mutant genotypes from the two sources were highly significant. Both plasma- and peripheral blood mononuclear cell (PBMC)-derived virus (and/or RNA genomes) should be studied in additional subjects to confirm the hypothesis raised by these data that zidovudine-resistant virus may be more frequent in plasma than in uncultured PBMC.

Acquired Immunodeficiency Syndrome↗
PubMed1984

Complete sequences of the intergenic and mRNA start signals in the Sendai virus genome: homologies with the genome of vesicular stomatitis virus.

All of the consensus intergenic and transcription initiation sequences of the genome of Sendai virus, a paramyxovirus, have been determined. The boundary between the intergenic sequence, 3'-GAA, and the mRNA start signal, 3'- UCCCANUUUC , was identified by sequencing the 5' termini of specific viral mRNA molecules. One of the five intergenic trinucleotides differed from the rest, consisting of 3'- GGG , and single base substitutions were observed in two of the mRNA start signals. The Sendai virus intergenic sequence was similar to the analogous sequence (3'-GA) of vesicular stomatitis virus (VSV), a member of another family of negative-strand RNA viruses, the rhabdoviruses , but there was no sequence homology between the mRNA start signals of the two viruses. Nevertheless, these mRNA start signals were organized in the same way, being ten bases long and possessing two consensus regions, divided by one (Sendai virus) or two (VSV) variable internal nucleotides. These findings extend the evidence that both families of negative-strand RNA viruses descended from a common ancestor and that an archetypal mechanism of transcriptional regulation has been conserved in their evolution.

Allantois↗
PubMed1990

The cyanelle genome of Cyanophora paradoxa, unlike the chloroplast genome, codes for the ribosomal L3 protein.

We describe a 1132 bp sequence of the cyanelle genome of Cyanophora paradoxa containing the rpl3 gene. This gene, which is not chloroplast encoded in plants, is the first of a long cyanelle ribosomal operon whose organization resembles that of the S10 operon of E. coli. We have shown that the rpl3 gene is transcribed in cyanelles as a 7500 nucleotide precursor and that the 5'-end of the mRNA starts approximately 90 nucleotides upstream from the initiation codon. However, no typical procaryotic promoter could be found for this gene. We have detected, using anti E. coli L3 antibodies, the cyanelle L3 protein in cyanelle extracts and in E. coli cells transformed with the cyanelle rpl3 gene.

Amino Acid Sequence↗
PubMed1984

Homology of genome of AIDS-associated virus with genomes of human T-cell leukemia viruses.

A T lymphotropic virus found in patients with the acquired immune deficiency syndrome (AIDS) or lymphadenopathy syndrome has been postulated to be the cause of AIDS. Immunological analysis of this retrovirus and its biological properties suggest that it is a member of the family of human T-lymphotropic retroviruses known as HTLV. Accordingly, it has been named HTLV-III. In the present report it is shown by nucleic acid hybridization that sequences of the genome of HTLV-III are homologous to the structural genes (gag, pol, and env) of both HTLV-I and HTLV-II and to a potential coding region called pX located between the env gene and the long terminal repeating sequence that is unique to the HTLV family of retroviruses.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Genetic instability and associated genome plasticity in Streptomyces ambofaciens: pulsed-field gel electrophoresis evidence for large DNA alterations in a limited genomic region.

Using pulsed-field gel electrophoresis (PFGE) analysis, the amplifiable units of DNA (AUD) loci AUD6 and AUD90 of Streptomyces ambofaciens DSM40697 could be mapped in the wild-type genome within two adjacent AseI restriction fragments estimated to be about 75 and 850 kb. In addition, the genetic instability and formation of very large deletions were strictly correlated. Their sizes were estimated to range from 250 to more than 2,000 kb. These deletions affected the DNA region overlapping both amplifiable loci. PFGE also allowed us to localize the amplified DNA sequences and to establish their structure: amplification takes place at the AUD locus as a tandem array of the wild-type AUD sequence.

DNA, Bacterial↗