Recently started to read some literature but getting very confused:
1. As far as I understand, "endogenous retrovirus" (ERV) and "LTR-retrotransposon" are both LTR-retroelements, as opposed to non-LTR retroelements (SINE and LINE). ERV and LTR-retrotransposon are different in that the former contains a env gene, while the latter does not. However I've seen so many paper just mix up these terms. There are 3 major types of LTR-retrotransposons (Ty1-copia, Ty3-gypsy and BEL-Pao) but none of which seems to exist in human genome. Is it safe to say that all the so-called "LTR-retrotransposons" in human genome are actually ERVs?
2. I've seen many papers suggest that since LTR-retrotransposons have sequence similarity with Pseudoviridae, Metaviridae etc, they may have been the origin of these viruses. In other words LTR-retrotransposons acquired an env gene to become a retrovirus. But doesn't it make more sense for the other way around (these viruses affect cells and become LTR-retrotransposons by losing the env gene)? I understand there are some cases where this is true, namely Drosophila gypsy LTR has gained an env-like protein and become a retrovirus, but I could imagine this should not be a common phenomenon, given that retroviruses have existed for billions of years. When we talk about ERVs, it is clear that these were retroviruses that infected primate cells millions of years ago, became degenerate and mutated and became ERV today. Why is it retrotransposon --> virus when discussing LTR-retrotransposons (Ty1-copia, Ty3-gypsy and BEL-Pao)?
Thank you very much
Hi Ching-Pin,
1. Yes, it is safe to say so. Vertebrate retroviruses (Retroviridae) form a distinct branch in the phylogeny of reverse transcriptases that is separate from gypsy/Ty3 (Metaviridae), copia/Ty1 (Pseudoviridae) and BEL/Pao/Cer (Belpaoviridae). In some hosts they can co-exist (for example, in fishes you can find both retroviruses and LTR retrotransposons). A brief taxonomic guide is found here: https://pubmed.ncbi.nlm.nih.gov/29618642/
2. Acquisition of the env gene by any group of LTR retrotransposons from an enveloped virus (either DNA or RNA) may occur sporadically, and its retention or loss would depend on the combination of selective advantages and disadvantages of the extracellular vs. intracellular replication cycle for both retrotransposon and the host.
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