Characterization of a full-length endogenous beta-retrovirus, EqERV-beta1, in the genome of the horse (Equus caballus).
Abstract: Information on endogenous retroviruses fixed in the horse (Equus caballus) genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus), was 10434 nucleotide (nt) in length with the usual retroviral genome structure of 5'LTR-gag-pro-pol-env-3'LTR. The LTRs were 1361 nt long, and differed approximately 1% from each other, suggestive of a relatively recent integration. Coding sequences for gag, pro and pol were present in three different reading-frames, as common for beta-retroviruses, and the reading frames were completely open, except that the env gene was interrupted by a single stopcodon. No reading frame was apparent downstream of the env gene, suggesting that EqERV-beta1 does not encode a superantigen like mouse mammary tumor virus (MMTV). A second proviral genome of EqERV-beta1, with no stopcodon in env, is additionally integrated on chromosome 5 downstream of the first virus. Single EqERV-beta1 LTRs were abundantly present on all chromosomes except chromosome 24. Phylogenetically, EqERV-beta1 most closely resembles an unclassified retroviral sequence from cattle (Bos taurus), and the murine beta-retrovirus MMTV.
Publication Date: 2011-06-01 PubMed ID: 21994749PubMed Central: PMC3185775DOI: 10.3390/v3060620Google Scholar: Lookup
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- Journal Article
Summary
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The research paper discusses the detection and characterization of a full-length endogenous retrovirus, EqERV-beta1, integrated in the horse (Equus caballus) genome.
Background and Objective
- The study aims to provide valuable information on endogenous retroviruses present in the horse genome, which at the time of the research was relatively less explored.
- The recent availability of the horse genome’s draft sequence allowed researchers to detect integrated viruses in the genome by using a similarity search method.
Methodology
- Researchers employed translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for the initial searches.
- A full-length beta-retrovirus genome was identified and retrieved from a horse chromosome 5 contig.
The Retrovirus: EqERV-beta1
- The identified provirus was named EqERV-beta1, which stands for the first equine endogenous beta-retrovirus, and its length was found to be 10434 nucleotides.
- Interestingly, it displayed the standard retroviral genome structure of 5’LTR-gag-pro-pol-env-3’LTR.
- The LTRs (Long Terminal Repeats), vital for integration of the virus into the host genome, were discovered to be 1361 nt long, differing by approximately 1% from each other, suggesting a relatively recent integration.
- The virus displayed the common characteristic of beta-retroviruses: the coding sequences for genes gag, pro, and pol were present in three different reading frames.
- However, the env gene was found to be interrupted by a single stop codon, showing that the reading frames were not completely open.
Additional Observations and Phylogenetic Relationship
- No reading frame was found downstream of the env gene, indicating that EqERV-beta1 does not encode a superantigen, unlike the mouse mammary tumor virus (MMTV).
- A second proviral genome of EqERV-beta1, with no stop codon in env, was also identified to be present on chromosome 5, downstream of the first virus.
- Single EqERV-beta1 LTRs were found to be plentiful on all chromosomes except chromosome 24.
- Upon conducting a phylogenetic analysis, EqERV-beta1 was found to be most closely related to an unclassified retroviral sequence from cattle (Bos taurus) and the mouse’s beta-retrovirus, MMTV.
Cite This Article
APA
van der Kuyl AC.
(2011).
Characterization of a full-length endogenous beta-retrovirus, EqERV-beta1, in the genome of the horse (Equus caballus).
Viruses, 3(6), 620-628.
https://doi.org/10.3390/v3060620 Publication
Researcher Affiliations
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Centre of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. a.c.vanderkuyl@amc.uva.nl
MeSH Terms
- Amino Acid Sequence
- Animals
- Base Sequence
- Betaretrovirus / classification
- Betaretrovirus / genetics
- Betaretrovirus / isolation & purification
- Betaretrovirus / physiology
- Cattle
- Chromosomes, Mammalian / genetics
- Chromosomes, Mammalian / virology
- Endogenous Retroviruses / classification
- Endogenous Retroviruses / genetics
- Endogenous Retroviruses / isolation & purification
- Endogenous Retroviruses / physiology
- Genes, pol
- Genome
- Horses / genetics
- Horses / virology
- Mice
- Molecular Sequence Data
- Open Reading Frames
- Phylogeny
- Proviruses / classification
- Proviruses / genetics
- Proviruses / isolation & purification
- Sequence Alignment
- Terminal Repeat Sequences
- Virus Integration
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Citations
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