scholarly journals Genome Structure and Thymic Expression of an Endogenous Retrovirus in Zebrafish

2004 ◽  
Vol 78 (2) ◽  
pp. 899-911 ◽  
Author(s):  
Ching-Hung Shen ◽  
Lisa A. Steiner
Keyword(s):  
Leukemia Virus ◽  
Genome Structure ◽  
Endogenous Retrovirus ◽  
Northern Blotting ◽  
Open Reading Frames ◽  
Genomic Locus ◽  
Dna Libraries ◽  
Adult Thymus ◽  
Reading Frames

ABSTRACT In a search for previously unknown genes that are required for lymphocyte development in zebrafish, a retroviral sequence was identified in a subtracted thymus cDNA library and in genomic DNA libraries. The provirus is 11.2 kb and contains intact open reading frames for the gag, pol, and env genes, as well as nearly identical flanking long terminal repeat sequences. As determined by in situ hybridization, the thymus appears to be a major tissue for retroviral expression in both larval and adult fish. Several viral transcripts were found by Northern blotting in the adult thymus. The provirus was found at the same genomic locus in sperm from four fish, suggesting that it is an endogenous retrovirus. Phylogenetic analysis indicates that it is closest to, yet distinct from, the cluster of murine leukemia virus-related retroviruses, suggesting that this virus represents a new group of retroviruses.

scholarly journals The Nucleotide Sequence of Shiga Toxin (Stx) 2e-Encoding Phage φP27 Is Not Related to Other Stx Phage Genomes, but the Modular Genetic Structure Is Conserved

2002 ◽  
Vol 70 (4) ◽  
pp. 1896-1908 ◽  
Author(s):  
Jürgen Recktenwald ◽  
Herbert Schmidt
Keyword(s):  
Nucleotide Sequence ◽  
Shiga Toxin ◽  
Phage Genome ◽  
Genetic Recombination ◽  
Genome Structure ◽  
Open Reading Frames ◽  
Functional Modules ◽  
Phage Propagation ◽  
Reading Frames ◽  
Lambdoid Phages

ABSTRACT In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage φP27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. φP27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The φP27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the φP27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of φP27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

scholarly journals Characterization of Endogenous Retroviruses in Sheep

2003 ◽  
Vol 77 (20) ◽  
pp. 11268-11273 ◽  
Author(s):  
Nikolai Klymiuk ◽  
Mathias Müller ◽  
Gottfried Brem ◽  
Bernhard Aigner
Keyword(s):  
Endogenous Retrovirus ◽  
Ovis Aries ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
In Vivo Experiments ◽  
Pregnant Sheep ◽  
Reading Frames

ABSTRACT Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV β families and nine OERV γ families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV β family and two OERV γ families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.

scholarly journals Attenuation of bovine leukemia virus by deletion of R3 and G4 open reading frames.

1994 ◽  
Vol 91 (24) ◽  
pp. 11532-11536 ◽  
Author(s):  
L. Willems ◽  
P. Kerkhofs ◽  
F. Dequiedt ◽  
D. Portetelle ◽  
M. Mammerickx ◽  
...  
Keyword(s):  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Reading Frames

scholarly journals An endogenous retrovirus presumed to have been endogenized or relocated recently in a marsupial, the red-necked wallaby

Genome ◽  
2022 ◽  
Author(s):  
Sakura Hayashi ◽  
Konami Shimizu ◽  
Yusuke Honda ◽  
Yukako Katsura ◽  
Akihiko Koga
Keyword(s):  
Endogenous Retrovirus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Length Variation ◽  
Wild Type ◽  
Long Terminal Repeats ◽  
Recent Event ◽  
Melanin Biosynthesis ◽  
Dna Fragment ◽  
Reading Frames

An albino infant wallaby was born to a mother with the wild-type body color. PCR and sequencing analyses of <i>TYR</i> (encoding tyrosinase, which is essential for melanin biosynthesis) of this albino wallaby revealed a 7.1-kb-long DNA fragment inserted in the first exon. Because the fragment carried long terminal repeats, we assumed it to be a copy of an endogenous retrovirus, which we named <i>walb</i>. We cloned other <i>walb</i> copies residing in the genomes of this species and another wallaby species. The copies exhibited length variation, and the longest copy (>8.0 kb) contained open reading frames whose deduced amino acid sequences were well aligned with those of <i>gag</i>, <i>pol</i>, and <i>env</i> of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into <i>TYR</i>: endogenization (infection of a germline cell by an exogenous virus), reinfection (infection by a virus produced from a previously endogenized provirus), or retrotransposition (intracellular relocation of a provirus). In any case, the insertion into <i>TYR</i> is considered to have been a recent event on an evolutionary timescale because albino mutant alleles generally do not persist for long because of their deleterious effects in wild circumstances. 

scholarly journals Transcriptional Organization of the czcHeavy-Metal Homeostasis Determinant from Alcaligenes eutrophus

1999 ◽  
Vol 181 (8) ◽  
pp. 2385-2393 ◽  
Author(s):  
Cornelia Große ◽  
Gregor Grass ◽  
Andreas Anton ◽  
Sylvia Franke ◽  
Alexander Navarrete Santos ◽  
...  
Keyword(s):  
Response Regulator ◽  
Regulatory System ◽  
Alcaligenes Eutrophus ◽  
Northern Blotting ◽  
Open Reading Frames ◽  
Mrna Synthesis ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Reporter Strains ◽  
Reading Frames

ABSTRACT The Czc system of Alcaligenes eutrophus mediates resistance to cobalt, zinc, and cadmium through ion efflux catalyzed by the CzcCB2A cation-proton antiporter. DNA sequencing of the region upstream of the czcNICBADRS determinant located on megaplasmid pMOL30 revealed the 5′ end of czcN and a gene for a MgtC-like protein which is transcribed in the orientation opposite that of czc. Additional open reading frames upstream of czc had no homologs in the current databases. Using oligonucleotide-probed Northern blotting experiments, a 500-nucleotide czcN message and a 400-nucleotideczcI message were found, and the presence of 6,200-nucleotide czcCBA message (D. Van der Lelie et al., Mol. Microbiol. 23:493–503, 1997) was confirmed. Induction ofczcN, czcI, czcCBA, andczcDRS followed a similar pattern: transcription was induced best by 300 μM zinc, less by 300 μM cobalt, and only slightly by 300 μM cadmium. Reverse transcription-PCR gave evidence for additional continuous transcription from czcN toczcC and from czcD to czcS, but not between czcA and czcD nor betweenczcS and a 131-amino-acid open reading frame followingczcS. The CzcR putative response regulator was purified and shown to bind in the 5′ region of czcN. A reporter strain carrying a czcNIC-lacZ-czcBADRS determinant on plasmid pMOL30 was constructed, as were ΔczcR and ΔczcS mutants of this strain and of AE128(pMOL30) wild type. Experiments on (i) growth of these strains in liquid culture containing 5 mM Zn2+, (ii) induction of the β-galactosidase in the reporter strains by zinc, cobalt, and cadmium, and (iii) cDNA analysis of czcCBA mRNA synthesis under inducing and noninducing conditions showed that the CzcRS two-component regulatory system is involved in Czc regulation.

scholarly journals Molecular Characterization and Placental Expression of HERV-W, a New Human Endogenous Retrovirus Family

1999 ◽  
Vol 73 (2) ◽  
pp. 1175-1185 ◽  
Author(s):  
Jean-Luc Blond ◽  
Frédéric Besème ◽  
Laurent Duret ◽  
Olivier Bouton ◽  
Frédéric Bedin ◽  
...  
Keyword(s):  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
Primer Binding Site ◽  
Human Endogenous Retrovirus ◽  
Cdna Clones ◽  
Human Endogenous Retroviruses ◽  
Herv Family ◽  
Flanking Sequences ◽  
Reading Frames

ABSTRACT The multiple sclerosis-associated retrovirus (MSRV) isolated from plasma of MS patients was found to be phylogenetically and experimentally related to human endogenous retroviruses (HERVs). To characterize the MSRV-related HERV family and to test the hypothesis of a replication-competent HERV, we have investigated the expression of MSRV-related sequences in healthy tissues. The expression of MSRV-related transcripts restricted to the placenta led to the isolation of overlapping cDNA clones from a cDNA library. These cDNAs spanned a 7.6-kb region containing gag, pol, and env genes; RU5 and U3R flanking sequences; a polypurine tract; and a primer binding site (PBS). As this PBS showed similarity to avian retrovirus PBSs used by tRNATrp, this new HERV family was named HERV-W. Several genomic elements were identified, one of them containing a complete HERV-W unit, spanning all cDNA clones. Elements of this multicopy family were not replication competent, asgag and pol open reading frames (ORFs) were interrupted by frameshifts and stop codons. A complete ORF putatively coding for an envelope protein was found both on the HERV-W DNA prototype and within an RU5-env-U3R polyadenylated cDNA clone. Placental expression of 8-, 3.1-, and 1.3-kb transcripts was observed, and a putative splicing strategy was described. The apparently tissue-restricted HERV-W long terminal repeat expression is discussed with respect to physiological and pathological contexts.

scholarly journals Complete nucleotide sequence of a mouse VL30 retro-element.

1988 ◽  
Vol 8 (8) ◽  
pp. 2989-2998 ◽  
Author(s):  
S E Adams ◽  
P D Rathjen ◽  
C A Stanway ◽  
S M Fulton ◽  
M H Malim ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Leukemia Virus ◽  
Open Reading Frames ◽  
Long Terminal Repeats ◽  
Base Pairs ◽  
Viral Packaging ◽  
Protein Functions ◽  
Active Promoter ◽  
Reading Frames

The complete nucleotide sequence of a mouse retro-element is presented. The cloned element is composed of 4,834 base pairs (bp) with long terminal repeats of 568 bp separated by an internal region of 3,698 bp. The element did not appear to have any open reading frames that would be capable of encoding the functional proteins that are normally produced by retro-elements. However, some regions of the genome showed some homology to retroviral gag and pol open reading frames. There was no region in VL30 corresponding to a retroviral env gene. This implies that VL30 is related to retrotransposons rather than to retroviruses. The sequence also contained regions that were homologous to known reverse transcriptase priming sites and viral packaging sites. These observations, combined with the known transcriptional capacity of the VL30 promoter, suggest that VL30 relies on protein functions of other retro-elements, such as murine leukemia virus, while maintaining highly conserved cis-active promoter, packaging, and priming sites necessary for its replication and cell-to-cell transmission.

scholarly journals Comparison of novel GH 68 levansucrases of levan-overproducing Gluconobacter species

2012 ◽  
Vol 1 (1) ◽  
pp. 2 ◽  
Author(s):  
Frank Jakob ◽  
Daniel Meißner ◽  
Rudi F. Vogel
Keyword(s):  
Open Reading Frames ◽  
Ex Situ ◽  
Inverse Pcr ◽  
E Coli ◽  
Food Biotechnology ◽  
Food Applications ◽  
Pcr Techniques ◽  
Single Primer ◽  
Reading Frames

<em>Gluconobacter</em> species are capable of incomplete oxidations which are exploited in food biotechnology. Levans isolated from exopolysaccharide (EPS)-overproducing <em>Gluconobacter</em> species are promising functional compounds for food applications. Fructan production strongly depends on the corresponding fructosyltransferases (Ftfs), which catalyze the formation of these polymers from sucrose. Therefore, we characterized novel Ftfs from three EPS-overproducing food-grade strains, i.e. <em>Gluconobacter</em> sp. TMW 2.767 and <em>Gluconobacter</em> sp. TMW 2.1191 isolated from water kefir, and <em>Gluconobacter cerinus</em> DSM 9533T isolated from cherries. Several PCR techniques, including degenerate gradient temperature PCR, modified and standard inverse PCR, modified site-finding PCR and modified single primer PCR, were used to finally detect complete open reading frames coding for Ftfs. The prospective ftf-gene sequences were heterologously expressed in <em>Escherichia coli</em> Top 10. <em>E. coli</em> transformants harboring one of the three different ftf-genes produced polysaccharides from sucrose in contrast to the <em>E. coli</em> wildtype. Each of the heterologously expressed proteins encoded a levansucrase, catalyzing the formation of b-(2&rarr;6)-linked fructose polymers, which corresponded to our previous analyses about the chemical nature of the isolated polymers formed by these <em>Gluconobacter</em> strains. Structurally, these enzymes belong to the glycoside hydrolase 68 family (GH 68), sharing the typical modular topology of levansucrases from gram-negative bacteria. In conclusion, we could identify novel active levansucrases, which can be used for <em>ex situ</em> (enzymatic catalyses) or <em>in situ</em> (fermentation) production of functional fructan polymers by <em>Gluconobacter</em> strains in food and other applications.

scholarly journals Structural analysis of TRAS1, a novel family of telomeric repeat-associated retrotransposons in the silkworm, Bombyx mori.

1995 ◽  
Vol 15 (8) ◽  
pp. 4545-4552 ◽  
Author(s):  
S Okazaki ◽  
H Ishikawa ◽  
H Fujiwara
Keyword(s):  
Bombyx Mori ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Ltr Retrotransposons ◽  
Reading Frames ◽  
28S Ribosomal Dna ◽  
Silkworm Bombyx Mori

We characterized TRAS1, a retrotransposable element which was inserted into the telomeric repetitive sequence (CCTAA)n of the silkworm, Bombyx mori. The complete sequence of TRAS1, a stretch of 7.8 kb with a poly(A) tract at the 3' end, was determined. No long terminal repeat (LTR) was found at the termini of the element. TRAS1 contains gag- and pol-like open reading frames (ORFs) which are similar to those of non-LTR retrotransposons. The two ORFs overlap but are one nucleotide out of frame (+1 frameshift). Most of the approximately 250 copies of TRAS1 elements in the genome were highly conserved in the structure. Chromosomal in situ hybridization showed that TRAS1 elements are clustered at the telomeres of Bombyx chromosomes. A phylogenetic analysis using the amino acid sequence of the reverse transcriptase domain within the pol-like ORF revealed that TRAS1 falls into one lineage with R1, which is a family of non-LTR retrotransposons inserted into the same site within the 28S ribosomal DNA unit in most insects. TRAS1 may have been derived from R1 and changed the target specificity so that TRAS1 inserts into the telomeric repetitive sequence (CCTAA)n. Southern hybridization and Bal 31 exonuclease analyses showed that TRAS1 elements are clustered proximal to the terminal long tract of (CCTAA)n. TRAS1 is a novel family of non-LTR retrotransposons which are inserted into the telomeric repetitive sequences as target sites.

scholarly journals Cloning of Gonadotropin-Releasing Hormone I Complementary DNAs in Songbirds Facilitates Dissection of Mechanisms Mediating Seasonal Changes in Reproduction

Endocrinology ◽  
2009 ◽  
Vol 150 (4) ◽  
pp. 1826-1833 ◽  
Author(s):  
T. J. Stevenson ◽  
K. S. Lynch ◽  
P. Lamba ◽  
G. F. Ball ◽  
D. J. Bernard
Keyword(s):  
Gene Expression ◽  
Seasonal Changes ◽  
Gene Sequence ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Mrna Levels ◽  
European Starlings ◽  
Important Exception ◽  
Reading Frames

Temperate zone animals exhibit seasonal variation in reproductive physiology. In most cases, seasonal changes in reproductive states are regulated by changes in GnRH1 secretion, rather than synthesis, from the preoptic area (POA)/anterior hypothalamus. An important exception occurs in some songbirds that become photorefractory to the stimulatory effects of long days and show profound decreases in brain GnRH1 protein content. Whether this decline reflects changes in gene expression is unknown because of past failures to measure GNRH1 mRNA levels, due in large part to the absence of available GNRH1 gene sequence in this taxon. Here, we report the first cloning of GNRH1 cDNAs in two songbirds: European starlings and zebra finches. Consistent with the size of the prepro-hormone in other avian and non-avian species, the open-reading frames predict proteins of 91 and 92 amino acids, respectively. Whereas the decapeptide in both species is perfectly conserved with chicken GnRH1, the amino acid identity in the signal peptide and GNRH associated peptide subdomains are significantly less well conserved. At the nucleotide level, the starling and zebra finch coding sequences are approximately 88% identical to each other but only approximately 70% identical to chicken GNRH1. In situ hybridization using radiolabeled cRNA probes demonstrated GNRH1 mRNA expression primarily in the POA, consistent with previous studies on the distribution of the GnRH1-immunoreactive cell bodies. Furthermore, we provide evidence for photoperiod-dependent regulation of GNRH1 mRNA in male starlings. Declines in GNRH1 mRNA levels occur in parallel with testicular involution. Thus, photorefractoriness is associated with decreases in GNRH1 gene expression in the medial POA.

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