Genomically Intact Endogenous Feline Leukemia Viruses of Recent Origin

ABSTRACT We isolated and sequenced two complete endogenous feline leukemia viruses (enFeLVs), designated enFeLV-AGTT and enFeLV-GGAG. In enFeLV-AGTT, the open reading frames are reminiscent of a functioning FeLV genome, and the 5′ and 3′ long terminal repeat sequences are identical. Neither endogenous provirus is genetically fixed in cats but polymorphic, with 8.9 and 15.2% prevalence for enFeLV-AGTT and enFeLV-GGAG, respectively, among a survey of domestic cats. Neither provirus was found in the genomes of related species of the Felis genus, previously shown to harbor enFeLVs. The absence of mutational divergence, polymorphic incidence in cats, and absence in related species suggest that these enFeLVs may have entered the germ line more recently than previously believed, perhaps coincident with domestication, and reopens the question of whether some enFeLVs might be replication competent.

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Insertional Polymorphisms of Endogenous Feline Leukemia Viruses

Journal of Virology ◽

10.1128/jvi.79.7.3979-3986.2005 ◽

2005 ◽

Vol 79 (7) ◽

pp. 3979-3986 ◽

Cited By ~ 26

Author(s):

Alfred L. Roca ◽

William G. Nash ◽

Joan C. Menninger ◽

William J. Murphy ◽

Stephen J. O'Brien

Keyword(s):

X Chromosome ◽

Fluorescent In Situ Hybridization ◽

Genomic Variation ◽

Domestic Cats ◽

Hybrid Mapping ◽

Chromosomal Distribution ◽

Ectopic Recombination ◽

Leukemia Viruses ◽

Feline Leukemia Viruses

ABSTRACT The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one autosomal locus, B4q15, was enFeLV present in both homologues of all four cats. A single enFeLV occurred in the X chromosome of the Burmese cat, while three to five enFeLV proviruses occurred in each Y chromosome. The X chromosome and nine autosomal enFeLV loci were telomeric, suggesting that ectopic recombination between nonhomologous subtelomeres may contribute to enFeLV distribution. Since endogenous FeLVs may affect the infectiousness or pathogenicity of exogenous FeLVs, genomic variation in enFeLVs represents a candidate for genetic influences on FeLV leukemogenesis in cats.

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Genetic Structures at the Origin of Acquisition of the β-Lactamase blaKPC Gene

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01451-07 ◽

2008 ◽

Vol 52 (4) ◽

pp. 1257-1263 ◽

Cited By ~ 308

Author(s):

Thierry Naas ◽

Gaelle Cuzon ◽

Maria-Virginia Villegas ◽

Marie-Frédérique Lartigue ◽

John P. Quinn ◽

...

Keyword(s):

United States ◽

Pseudomonas Aeruginosa ◽

The United States ◽

Open Reading Frames ◽

Insertion Sequences ◽

Transposase Gene ◽

Repeat Sequences ◽

Class A ◽

Genetic Structures ◽

Reading Frames

ABSTRACT Genetic structures surrounding the carbapenem-hydrolyzing Ambler class A bla KPC gene were characterized in several KPC-positive Klebsiella pneumoniae and Pseudomonas aeruginosa strains isolated from the United States, Colombia, and Greece. The bla KPC genes were associated in all cases with transposon-related structures. In the K. pneumoniae YC isolate from the United States, the β-lactamase bla KPC-2 gene was located on a novel Tn3-based transposon, Tn4401. Tn4401 was 10 kb in size, was delimited by two 39-bp imperfect inverted repeat sequences, and harbored, in addition to the β-lactamase bla KPC-2 gene, a transposase gene, a resolvase gene, and two novel insertion sequences, ISKpn6 and ISKpn7. Tn4401 has been identified in all isolates. However, two isoforms of this transposon were found: Tn4401a was found in K. pneumoniae YC and K. pneumoniae GR from the United States and Greece, respectively, and differed by a 100-bp deletion, located just upstream of the bla KPC-2 gene, compared to the sequence of Tn4401b, which was found in the Colombian isolates. In all isolates tested, Tn4401 was flanked by a 5-bp target site duplication, the signature of a recent transposition event, and was inserted in different open reading frames located on plasmids that varied in size and nature. Tn4401 is likely at the origin of carbapenem-hydrolyzing β-lactamase KPC mobilization to plasmids and its further insertion into various-sized plasmids identified in nonclonally related K. pneumoniae and P. aeruginosa isolates.

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Evolution of the Xenopus piggyBac Transposon Family TxpB: Domesticated and Untamed Strategies of Transposon Subfamilies

Molecular Biology and Evolution ◽

10.1093/molbev/msm191 ◽

2007 ◽

Vol 24 (12) ◽

pp. 2648-2656 ◽

Cited By ~ 23

Author(s):

Akira Hikosaka ◽

Toshihiro Kobayashi ◽

Yumiko Saito ◽

Akira Kawahara

Keyword(s):

Phylogenetic Analyses ◽

Single Species ◽

Single Copy ◽

Open Reading Frames ◽

Terminal Inverted Repeat ◽

Repeat Sequences ◽

New Family ◽

Molecular Phylogenetic ◽

Multiple Copies ◽

Reading Frames

Abstract A new family, termed TxpB, of DNA transposons belonging to the piggyBac superfamily was found in 3 Xenopus species (Xenopus tropicalis, Xenopus laevis, and Xenopus borealis). Two TxpB subfamilies of Kobuta and Uribo1 were found in all the 3 species, and another subfamily termed Uribo2 was found in X. tropicalis. Molecular phylogenetic analyses of their open reading frames (ORFs) revealed that TxpB transposons have been maintained for over 100 Myr. Both the Uribo1 and the Uribo2 ORFs were present as multiple copies in each genome, and some of them were framed by terminal inverted repeat sequences. In contrast, all the Kobuta ORFs were present as a single copy in each genome and exhibited high evolutionary conservation, suggesting domestication of Kobuta genes by the host. Genomic insertion polymorphisms of the Uribo1 and Uribo2 transposons (nonautonomous type) were observed in a single species of X. tropicalis, indicating recent transposition events. Transfection experiments in cell culture revealed that an expression vector construct for the intact Uribo2 ORF caused precise excision of a nonautonomous Uribo2 element from the target vector construct but that for the Kobuta ORF did not. The present results support our viewpoint that some Uribo2 members are naturally active autonomous transposons, whereas Kobuta members may be domesticated by hosts.

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Long Terminal Repeat Regions from Exogenous but Not Endogenous Feline Leukemia Viruses Transactivate Cellular Gene Expression

Journal of Virology ◽

10.1128/jvi.74.20.9742-9748.2000 ◽

2000 ◽

Vol 74 (20) ◽

pp. 9742-9748 ◽

Cited By ~ 8

Author(s):

Sajal K. Ghosh ◽

Pradip Roy-Burman ◽

Douglas V. Faller

Keyword(s):

Gene Expression ◽

Long Terminal Repeat ◽

Cell Line ◽

Fibroblast Cell ◽

Terminal Repeat ◽

Cellular Gene ◽

Cellular Gene Expression ◽

Leukemia Viruses ◽

Feline Leukemia Viruses ◽

Collagenase Iv

ABSTRACT We have previously reported that the long terminal repeat (LTR) region of feline leukemia viruses (FeLVs) can enhance expression of certain cellular genes such as the collagenase IV gene andMCP-1 in trans (S. K. Ghosh and D. V. Faller, J. Virol. 73:4931–4940, 1999). Genomic DNA of all healthy feline species also contains LTR-like sequences that are related to exogenous FeLV LTRs. In this study, we evaluated the cellular gene transactivational potential of these endogenous FeLV LTR sequences. Unlike their exogenous FeLV counterparts, neither nearly full-length endogenous FeLV molecular clones (CFE-6 and CFE-16) nor their isolated LTRs were able to activate collagenase IV gene or MCP-1expression in transient transfection assays. We had also demonstrated previously that production of an RNA transcript from exogenous FeLV LTRs correlates with their transactivational activity. In the present study, we demonstrate that the endogenous FeLV LTRs do not generate LTR-specific RNA transcripts in the feline embryo fibroblast cell line AH927. Furthermore, infection of AH927 cells by an exogenous FeLV subgroup A virus did not induce production of such LTR-specific transcripts from the endogenous proviral genomes, although the LTR-specific transcripts from the exogenous virus were readily detected. Finally, LTR-specific transcripts were not generated in BALB/3T3 cells transiently transfected with isolated CFE-6 LTR, in contrast to transfections with LTRs from exogenous viruses. Our data thus suggest that the inability of endogenous FeLV LTRs in gene transactivation is not due to cell line specificity or presence of any upstream inhibitory cis-acting element. Endogenous, nonleukemogenic FeLV LTRs, therefore, do not transactivate cellular gene expression, and this property appears to be specific to exogenous, leukemogenic FeLVs.

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Sequence Analysis and Molecular Characterization of the Lactococcus lactis Temperate Bacteriophage BK5-T

Applied and Environmental Microbiology ◽

10.1128/aem.67.8.3564-3576.2001 ◽

2001 ◽

Vol 67 (8) ◽

pp. 3564-3576 ◽

Cited By ~ 28

Author(s):

Chitladda Mahanivong ◽

John D. Boyce ◽

Barrie E. Davidson ◽

Alan J. Hillier

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Lactococcus Lactis ◽

Direct Repeat ◽

Open Reading Frames ◽

Temperate Bacteriophage ◽

Terminal Sequence ◽

Repeat Sequences ◽

Reading Frames

ABSTRACT The Lactococcus lactis temperate bacteriophage BK5-T is one of twelve type phages that define L. lactis phage species. This paper describes the nucleotide sequence and analysis of a 21-kbp region of the BK5-T genome and completes the nucleotide sequence of the genome of this phage. The 40,003-nucleotide linear genome encodes 63 open reading frames. Sequence runoff experiments showed that the cohesive ends of the BK5-T genome contained a 12-bp 3′ single-stranded overhang with the sequence 5′-CACACACATAGG-3′. Two major BK5-T structural proteins, of approximately 30 and 20 kDa, were identified, and N-terminal sequence analysis determined that they were encoded by orf7 and orf12, respectively. A 169-bp fragment containing a 37-bp direct repeat and several smaller repeat sequences conferred resistance to BK5-T infection when introduced in trans to the host cell and is likely a part of the BK5-T origin of replication (ori).

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Complete Genome Sequence of the Naegleria fowleri (Strain LEE) Closed Circular Extrachromosomal Ribosomal DNA Element

Microbiology Resource Announcements ◽

10.1128/mra.01055-20 ◽

2020 ◽

Vol 9 (49) ◽

Author(s):

John C. Mullican ◽

Kristen M. Drescher ◽

Nora M. Chapman ◽

Steven Tracy

Keyword(s):

Ribosomal Dna ◽

Direct Repeat ◽

Repeated Sequence ◽

Single Copy ◽

Open Reading Frames ◽

Naegleria Fowleri ◽

Content Type ◽

Repeat Sequences ◽

Nægleria Fowleri ◽

Reading Frames

ABSTRACT The circular extrachromosomal ribosomal DNA (rDNA) element of Naegleria fowleri strain LEE was molecularly cloned and fully sequenced. The element comprises 15,786 bp and contains a single copy of the organism’s rDNA cistron. The nonribosomal sequence contains five potential open reading frames, two large direct repeat sequences, and numerous smaller repeated-sequence regions.

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A Tn7-Like Transposon Is Present in theglmUS Region of the Obligately Chemoautolithotrophic Bacterium Thiobacillus ferrooxidans

Journal of Bacteriology ◽

10.1128/jb.180.11.3007-3012.1998 ◽

1998 ◽

Vol 180 (11) ◽

pp. 3007-3012 ◽

Cited By ~ 15

Author(s):

Joseph C. Oppon ◽

Robert J. Sarnovsky ◽

Nancy L. Craig ◽

Douglas E. Rawlings

Keyword(s):

Thiobacillus Ferrooxidans ◽

Blot Hybridization ◽

Southern Blot Hybridization ◽

Open Reading Frames ◽

Ecological Niches ◽

E Coli ◽

Repeat Sequences ◽

Genes Encoding ◽

Reading Frames ◽

Different Parts

ABSTRACT The region downstream of the Thiobacillus ferrooxidansATCC 33020 atp operon was examined, and the genes encodingN-acetylglucosamine-1-uridyltransferase (glmU) and glucosamine synthetase (glmS) were found. ThisatpEFHAGDC-glmUS gene order is identical to that ofEscherichia coli. The T. ferrooxidans glmS gene was shown to complement E. coli glmS mutants for growth on minimal medium lacking glucosamine. A Tn7-like transposon, Tn5468, was found inserted into the region immediately downstream of the glmS gene in a manner similar to the site-specific insertion of transposon Tn7 within the termination region of the E. coli glmS gene. Tn5468 was sequenced, and Tn7-like terminal repeat sequences as well as several open reading frames which are related to the Tn7 transposition genes tnsA,tnsB, tnsC, and tnsD were found. Tn5468 is the closest relative of Tn7 to have been characterized to date. Southern blot hybridization indicated that a similar or identical transposon was present in three T. ferrooxidans strains isolated from different parts of the world but not in two Thiobacillus thiooxidans strains or aLeptospirillum ferrooxidans strain. Since T. ferrooxidans is an obligately acidophilic autotroph and E. coli is a heterotroph, ancestors of the Tn7-like transposons must have been active in a variety of physiologically different bacteria so that their descendants are now found in bacteria that occupy very different ecological niches.

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