Info

D.m.

Tntl

Plant

Ty1

LTR Retrotransposons (Invertebrate)

Retroviruses

LTR Retrotransposons (Invertebrate)

Human

Ec67 Mx65

Human

Neurospora

Pararetroviruses

LTR Retrotransposons (Invertebrate)

Retroviruses

LTR Retrotransposons (Invertebrate)

Telomerases

Poly A transposons

Yeast Retrointrons

Neurospora Retroplasmids Bacteria Retrons RNA dependent RNA polymerases

FIGURE 5.23 Phylogenetic tree of the retroelements, based on the sequences of the reverse transcriptases. The blue boxes enclose the retroviruses and pararetroviruses. (Gypsy and Ty3 are known to be infectious viruses and are provisionally classified in a new family, Metaviridae.) The hosts are shown; plant hosts are shown in green. The vertical distances are arbitrary; the length of the horizontal branches is proportional to the number of changes. The tree has been rooted with the RNA-dependent RNA polymerase sequences. Abbreviations of retrovirus names were given in Table 5.1; abbreviations of vertebrate pararetrovirus (Hepadnavirus) names are found in Table 5.9. CoYMV commelina yellow mottle (Badnavirus); CAMV cauliflower mosaic (Caulimovirus); d.m., Drosophila melanogaster (fruit fly). [Redrawn from Coffin et al. (1997, Fig. 17, p. 411).]

which they reside. Otherwise their host would be selected against during evolution.

The number of retroelements in eukaryotic genomes is often very large. In mammals, 5-10% of the genome appears to consist of elements that were introduced by reverse transcription. Of these, approximately one-tenth are provirus-like, containing LTRs and primer binding sites flanking regions with detectable relationships to gag and pol. Some of these are active endogenous viruses that have inserted into the genome recently, whereas others are inert. The time at which any element entered the germline can often be estimated from comparative studies of these elements in different animals, and these proviruses or other retroelements constitute a kind of fossil record for these elements. As one example, chickens have one to four endogenous proviruses closely related to the ALVs, but there are no endogenous viruses in turkey or quail. Thus, insertion into the chicken genome occurred after chicken and turkey separated.

Below, four classes of eukaryotic elements, the endogenous retroviruses, the LTR-containing retrotransposons, the poly(A)-containing retrotransposons, and the group II retrointrons, are described in more detail. The relationships among these elements and their relationships to the infectious retroviruses described above, and to the pararetro-viruses described below, are illustrated by the phylogenetic

Viruses That Use Reverse Transcriptase

FIGURE 5.24 Comparative genome organizations of retroviruses, retrotransposons, and retrons. In each case the integrated form of the element is shown, flanked with dark blue bars representing the host DNA. ORFs for each element are shown below the DNA, and boxes on different lines represent different reading frames. Note that Gypsy has been variously categorized as a retrotransposon and as a true endogenous Errantivirus, family Metaviridae. Various motifs related to retroviruses are indicated with different colors and shadings, as shown in the key. At the 3' end of many non-LTR retro-transposons there are a variable number of TAA repeats (I factor) or adenylate residues (R2). [Adapted from Eickbush (1994).]

A. Retroviruses

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