Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes.

Different Dictyostelium discoideum strains contain between 2 and 200 copies of a retrotransposable element termed DRE (Dictyostelium repetitive element). From the analysis of more than 50 elements, it can be concluded that DRE elements always occur 50 +/- 3 nucleotides upstream of tRNA genes. All analyzed clones contain DRE in a constant orientation relative to the tRNA gene, implying orientation specificity as well as position specificity. DRE contains two open reading frames which are flanked by nonidentical terminal repeats. Long terminal repeats (LTRs) are composed of three distinct modules, called A, B, and C. The tRNA gene-proximal LTR is characterized by one or multiple A modules followed by a single B module (AnB). With respect to the distal LTR, two different subforms of DRE have been isolated. The majority of isolated clones contains a distal LTR composed of a B module followed by a C module (BC), whereas the distal LTR of the other subform contains a consecutive array of a B module, a C module, a slightly altered A module, another B module, and another C module (BC.ABC). Full-length as well as smaller transcripts from DRE elements have been detected, but in comparison with the high copy number in D. discoideum strains derived from the wild-type strain NC4, transcription is rather poor.

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Structure of DRE, a retrotransposable element which integrates with position specificity upstream of Dictyostelium discoideum tRNA genes

Molecular and Cellular Biology ◽

10.1128/mcb.12.1.229-239.1992 ◽

1992 ◽

Vol 12 (1) ◽

pp. 229-239

Author(s):

R Marschalek ◽

J Hofmann ◽

G Schumann ◽

R Gösseringer ◽

T Dingermann

Keyword(s):

Dictyostelium Discoideum ◽

Trna Gene ◽

Open Reading Frames ◽

Trna Genes ◽

Long Terminal Repeats ◽

Retrotransposable Element ◽

Position Specificity ◽

Terminal Repeats ◽

Orientation Specificity ◽

Reading Frames

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The open reading frames in the 3' long terminal repeats of several mouse mammary tumor virus integrants encode V beta 3-specific superantigens.

Journal of Experimental Medicine ◽

10.1084/jem.175.1.41 ◽

1992 ◽

Vol 175 (1) ◽

pp. 41-47 ◽

Cited By ~ 46

Author(s):

A M Pullen ◽

Y Choi ◽

E Kushnir ◽

J Kappler ◽

P Marrack

Keyword(s):

Mammary Tumor ◽

Sequence Data ◽

Cell Receptor ◽

Open Reading Frames ◽

Long Terminal Repeats ◽

Tumor Viruses ◽

Mouse Mammary Tumor ◽

Tumor Virus ◽

Terminal Repeats ◽

Reading Frames

Mice expressing the minor lymphocyte stimulation antigens, Mls-1a, -2a, or -3a, singly on the B10.BR background have been generated. Mls phenotypes correlate with the integration of mouse mammary tumor viruses (MTV) in the mouse genome. The open reading frames within the 3' long terminal repeats of the integrated MTVs 1, 3, 6, and 13 encode V beta 3-specific superantigens. Sequence data for these viral superantigens is presented, indicating that it is the COOH-terminal portion of the viral superantigen that interacts with the T cell receptor V beta element.

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Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium castaneum, is Associated With a Recent Mutation

Genetics ◽

10.1093/genetics/143.1.417 ◽

1996 ◽

Vol 143 (1) ◽

pp. 417-426

Author(s):

Richard W Beeman ◽

M Scott Thomson ◽

John M Clark ◽

Marco A DeCamillis ◽

Susan J Brown ◽

...

Keyword(s):

Sequence Analysis ◽

Tribolium Castaneum ◽

Frameshift Mutation ◽

Open Reading Frames ◽

Red Flour Beetle ◽

Intron Sequence ◽

Coding Region ◽

Long Terminal Repeats ◽

Flour Beetle ◽

Reading Frames

Abstract A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains.

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An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4485 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4485-4492 ◽

Cited By ~ 56

Author(s):

B A Dombroski ◽

Q Feng ◽

S L Mathias ◽

D M Sassaman ◽

A F Scott ◽

...

Keyword(s):

Reverse Transcriptase ◽

Consensus Sequence ◽

Unknown Origin ◽

Open Reading Frames ◽

Long Terminal Repeats ◽

Base Pairs ◽

In Vivo Assay ◽

Reading Frames

L1 elements constitute a highly repetitive human DNA family (50,000 to 100,000 copies) lacking long terminal repeats and ending in a poly(A) tail. Some L1 elements are capable of retrotransposition in the human genome (Kazazian, H. H., Jr., C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips, and S.E. Antonarakis, Nature (London) 332:164-166, 1988). Although most are 5' truncated, a consensus sequence of complete L1 elements is 6 kb long and contains two open reading frames (ORFs) (Scott, A. F., B. J. Schmeckpeper, M. Abdelrazik, C. T. Comey, B. O'Hara, J. P. Rossiter, T. Cooley, P. Health, K. D. Smith, and L. Margolet, Genomics 1:113-125, 1987). The protein encoded by ORF2 has reverse transcriptase (RT) activity in vitro (Mathias, S. L., A. F. Scott, H. H. Kazazian, Jr., J. D. Boeke, and A. Gabriel, Science 254:1808-1810, 1991). Because L1 elements are so numerous, efficient methods for identifying active copies are required. We have developed a simple in vivo assay for the activity of L1 RT based on the system developed by Derr et al. (Derr, L. K., J. N. Strathern, and D. J. Garfinkel, Cell 67:355-364, 1991) for yeast HIS3 pseudogene formation. L1 ORF2 displays an in vivo RT activity similar to that of yeast Ty1 RT in this system and generates pseudogenes with unusual structures. Like the HIS3 pseudogenes whose formation depends on Ty1 RT, the HIS3 pseudogenes generated by L1 RT are joined to Ty1 sequences and often are part of complex arrays of Ty1 elements, multiple HIS3 pseudogenes, and hybrid Ty1/L1 elements. These pseudogenes differ from those previously described in that there are base pairs of unknown origin inserted at several of the junctions. In two of three HIS3 pseudogenes studied, the L1 RT appears to have jumped from the 5' end of a Ty1/L1 transcript to the poly(A) tract of the HIS3 RNA.

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Salmonellagenomic island 3 is an integrative and conjugative element and contributes to copper and arsenic resistance ofSalmonella enterica

10.1101/564534 ◽

2019 ◽

Author(s):

Nobuo Arai ◽

Tsuyoshi Sekizuka ◽

Yukino Tamamura ◽

Masahiro Kusumoto ◽

Atsushi Hinenoya ◽

...

Keyword(s):

Mobile Genetic Element ◽

Open Reading Frames ◽

Trna Genes ◽

Sequencing Analysis ◽

Arsenic Resistance ◽

Filter Mating ◽

Serovar Typhimurium ◽

Resistance Island ◽

Reading Frames ◽

Integrative And Conjugative Element

ABSTRACTSalmonellagenomic island 3 (SGI3) was first described as a chromosomal island inSalmonella4,[5],12:i:-, a monophasic variant ofSalmonella entericasubsp.entericaserovar Typhimurium. The SGI3 DNA sequence detected fromSalmonella4,[5],12:i:-isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic resistance operon in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter mating experiments using theS. entericaserovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3′ end of the tRNA genespheVorpheR. The length of the target site was 52 or 55 bp, and a 55-bpattIsequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4compared with the recipient strains under anaerobic conditions. Resistance was defined by thecusgene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4compared with recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic resistance ofS. enterica.

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

Genome ◽

10.1139/gen-2021-0047 ◽

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 TYR (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 walb. We cloned other walb 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 gag, pol, and env of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into TYR: 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 TYR 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.

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SalmonellaGenomic Island 3 Is an Integrative and Conjugative Element and Contributes to Copper and Arsenic Tolerance ofSalmonella enterica

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00429-19 ◽

2019 ◽

Vol 63 (9) ◽

Cited By ~ 7

Author(s):

Nobuo Arai ◽

Tsuyoshi Sekizuka ◽

Yukino Tamamura ◽

Masahiro Kusumoto ◽

Atsushi Hinenoya ◽

...

Keyword(s):

Open Reading Frames ◽

Trna Genes ◽

Sequencing Analysis ◽

Content Type ◽

Arsenic Tolerance ◽

Filter Mating ◽

Serovar Typhimurium ◽

Resistance Island ◽

Reading Frames ◽

Integrative And Conjugative Element

ABSTRACTSalmonellagenomic island 3 (SGI3) was first described as a chromosomal island inSalmonella4,[5],12:i:–, a monophasic variant ofSalmonella entericasubsp.entericaserovar Typhimurium. The SGI3 DNA sequence detected fromSalmonella4,[5],12:i:– isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic tolerance operon, in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter-mating experiments using theS. entericaserovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3′ end of the tRNA genespheVorpheR. The length of the target site was 52 or 55 bp, and a 55-bpattIsequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4compared to the recipient strains under anaerobic conditions. Tolerance was defined by thecusgene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4compared to recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic tolerance ofS. enterica.

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Protein Interactions Involved in tRNA Gene-Specific Integration of Dictyostelium discoideum Non-Long Terminal Repeat Retrotransposon TRE5-A

Molecular and Cellular Biology ◽

10.1128/mcb.01173-07 ◽

2007 ◽

Vol 27 (24) ◽

pp. 8492-8501 ◽

Cited By ~ 15

Author(s):

Thanh Chung ◽

Oliver Siol ◽

Theodor Dingermann ◽

Thomas Winckler

Keyword(s):

Long Terminal Repeat ◽

Dictyostelium Discoideum ◽

Protein Interactions ◽

Insertional Mutagenesis ◽

Trna Gene ◽

Terminal Repeat ◽

Trna Genes ◽

Preintegration Complex ◽

Integration Sites ◽

A Novel Pathogenicity Island Integrated Adjacent to the thrW tRNA Gene of Avian Pathogenic Escherichia coli Encodes a Vacuolating Autotransporter Toxin

Infection and Immunity ◽

10.1128/iai.71.9.5087-5096.2003 ◽

2003 ◽

Vol 71 (9) ◽

pp. 5087-5096 ◽

Cited By ~ 80

Author(s):

V. R. Parreira ◽

C. L. Gyles

Keyword(s):

Escherichia Coli ◽

Serine Protease ◽

Trna Gene ◽

Signal Sequence ◽

Sequence Similarity ◽

Pathogenicity Island ◽

Open Reading Frames ◽

Integrase Gene ◽

E Coli ◽

Reading Frames

ABSTRACT We report the complete nucleotide sequence and genetic organization of the Vat-encoding pathogenicity island (PAI) of avian pathogenic Escherichia coli strain Ec222. The 22,139-bp PAI is situated adjacent to the 3′ terminus of the thrW tRNA gene, has a G+C content of 41.2%, and includes a bacteriophage SfII integrase gene, mobile genetic elements, two open reading frames with products exhibiting sequence similarity to known proteins, and several other open reading frames of unknown function. The PAI encodes an autotransporter protein, Vat (vacuolating autotransporter toxin), which induces the formation of intracellular vacuoles resulting in cytotoxic effects similar to those caused by the VacA toxin from Helicobacter pylori. The predicted 148.3-kDa protein product possesses the three domains that are typical of serine protease autotransporters of Enterobacteriaceae: an N-terminal signal sequence of 55 amino acids, a 111.8-kDa passenger domain containing a modified serine protease site (ATSGSG), and a C-terminal outer membrane translocator of 30.5 kDa. Vat has 75% protein homology with the hemagglutinin Tsh, an autotransporter of avian pathogenic E. coli. A vat deletion mutant of Ec222 showed no virulence in respiratory and cellulitis infection models of disease in broiler chickens. We conclude that the newly described PAI and Vat may be involved in the pathogenicity of avian septicemic E. coli strain Ec222 and other avian pathogenic E. coli strains.

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Complete nucleotide sequence of a mouse VL30 retro-element.

Molecular and Cellular Biology ◽

10.1128/mcb.8.8.2989 ◽

1988 ◽

Vol 8 (8) ◽

pp. 2989-2998 ◽

Cited By ~ 35

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.

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