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Endogenous retroviruses

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Endogenous retroviruses (ERVs) are vestiges of ancestral viral infection that have been incorporated into a host's germline DNA. ERVs are identifiable due to the presence of sequences that code (or once coded) for viral proteins, including gag (structural proteins), pol (viral enzymes), and env (surface proteins), as well as telltale long terminal repeats.

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How a retrovirus works

Retroviruses, unlike some other viruses, are RNA-based. In addition to two single strands of RNA that constitute its genome, a retroviral particle also carries several copies of reverse transcriptase. After invading a host cell, the reverse transcriptase is used in a process called reverse transcription to decode its RNA into DNA, which it then inserts into the host cell's chromosome. With the newly created viral DNA in place, the host cell's RNA polymerase is used to make more virus RNA, a template for both the RNA new particles will carry into other cells and for mRNA, which produces the viral proteins. The new copies of viral RNA and proteins are collected together into a new virus particle, and set free to infect other cells.

For more see the retrovirus article.

ERVs and Evolution

(to be completed)

Creationist Replies

Although creationists have been, for the most part, conspicuously silent on ERVs as strong evidence for evolution (a notable exception was AIG's Carl Wieland, who wrote a response to Edward Max's Plagiarized Errors and Molecular Genetics; Max's reply, pointing out the piece's serious and misleading errors, convinced him to remove it from their webpage) a common theme of dissenters is to deny, implicitly or explicitly, the randomness of proviral integration into the host genome. If integration is non-random, they argue, the extreme improbability of ERVs showing up at the same loci across different species (a problem circumvented by acknowledging they represent ancestry, and not different, convergent instances of infection) effectively goes out the window. To buttress this claim, creationists cite mainstream literature on specific aspects of integration specificity. For example, Zhu et al (1999) knocked out Sir3p and Sir4p, two components of silent chromatin, in the yeast Saccharomyces cerevisiae. This was followed by a more than nine-fold decrease in Ty5 (one of the families of S. cerevisiae ERV) integration specificity, which normally (more than 90%) occur near the silent chromatin bounded telomeres and HM loci.

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References

  1. Johnson, W.E. & Coffin, J.M. 1999. Constructing primate phylogenies from ancient retrovirus sequences. Proceedings of the National Academy of Sciences, 96: 10254-10260. ([1])
    Abstract:The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers. Endogenous retroviruses (ERVs) provide phylogenetic information in two ways: (i) by comparison of integration site polymorphism and (ii) by orthologous comparison of evolving, proviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the two LTRs of an ERV are identical at the time of integration but evolve independently, each ERV locus can provide two estimates of species phylogeny based on molecular evolution of the same ancestral sequence. Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. Although other animal species are rich in ERV sequences, the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extension the ERVs of other species, constitute a unique and plentiful resource for studying the evolutionary history of the Retroviridae and their animal hosts.
  2. Griffiths, D.J. 2001. Endogenous retroviruses in the human genome sequence. Genome Biology, 2: 1017.1-1017.5. ([2])
    Abstract:The human genome contains many endogenous retroviral sequences, and these have been suggested to play important roles in a number of physiological and pathological processes. Can the draft human genome sequences help us to define the role of these elements more closely?
  3. Sandmeyer, S.B. et al. 1990. Integration specificity of retrotransposons and retroviruses. Annual Review of Genetics, 24: 491-518. ([3])
    Abstract:Analysis of in vivo integration patterns has provided no data to support the notion that retroelement integration is random. Rather, the diversity of insertion patterns of retroelements suggests numerous ways in which genomic DNA is identified for preferential targeting. These range from specific to general and include sequence content, removal of chromatin proteins, nuclear localization, distinctive topology, and association with particular trans-acting factors. Many are similar to mechanisms already demonstrated to affect activities of previously described recombinases. Moreover, such proposed targeting mechanisms could act directly or indirectly to influence integration site selection. A variety of observations are consistent with the preferential use of open chromatin for retroelement insertion.


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