1. sa smith
  2. Lentiviruses: Me, and you, and Zaboomafoo

Lentiviruses: Me, and you, and Zaboomafoo

By sa smith on December 17, 2008.

Ive been *patiently* waiting two damn weeks for this paper to come out:

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution.

Gifford and Katzourakis are the same folks who found RELIK a while back-- a lentiviral ERV in a species of European rabbit.

This time, after screening the available sequences of 21 primates (including humans and chimpanzees) they found two in the genome of gray mouse lemurs (Zaboomafoos cousin :P). The gray mouse lemurs genome isnt totally sequenced yet, so they think there might be up to six lentiviral ERVs in these guys!

Why is this cool?

Well, first of all, we didnt know that lentiviruses could even turn into ERVs in primates. Scientists have run a fine-toothed comb through our (and chimpanzees) genome, and we hadnt found any. So we thought maybe lentiviruses physically couldnt endogenize for some reason, or maybe they were just 'too young', evolutionarily speaking.

Now we know that it is biologically possible for primates to endogenize lentiviruses, and lentiviruses could be older than we thought. Gifford et al proposed three models for the age of lentiviruses: 85 million years old (with relatively little genetic drift? eeeh...), 14 million years (okay...), or less than 10 million years (what i find most plausible).

Cooool!

But this isnt just 'Oh cool!' science. There are real world applications for finding endogenous lentiviruses in primates: we can study what happened in these gray mouse lemurs, and try to figure out how they controlled their uninvited genomic guests.

Because the lemur lentiviral ERVs?

They look like HIV-1.

They are proviral simian immunodeficiency virus.

But these lemurs have 'domesticated' the viruses.

These little lemurs could play a part in helping us figure out how to control HIV-1.

Oh, and as a fun side note, just for the lulz-- Grimm et al included a figure connecting HIV-1, SIVs, BIV, EIAV, etc, where they identify when new genes with new functions evolved (or were lost).

Photobucket

heh.

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[sawa]

But the REAL important thing here is the epigenetic factors and their implications for quasi-lateral plasmoidal transfer rates and quantum-phased arrays of neutrinos interfering with graviton particle beams bounced off the main deflector dish after being routed through the starboard power coupling. Those are the REAL driving forces behind evolution!

[/sawa]

The full paper is available to everyone free "open access" at the PNAS webpages:

http://www.pnas.org/content/early/2008/12/15/0807873105.full.pdf+html

There is also a commentary available (subscribers only):

Welkin E. Johnson
A proviral puzzle with a prosimian twist
PNAS published online before print December 17, 2008, doi:10.1073/pnas.0811419106

I was anticipating that you would have something to say about it.

Oh come now, does erv do ANYTHING patiently?

The figure shows vpu evolving twice. I was going to ask if two distinct versions evolved or if it was some kind of lateral transfer, but thanks to TomS giving a link (yeah we don't have dish out lots of money) the answer is given in:

Fig. 2. Phylogenetic relationships among lentiviruses. The inferred timing of accessory gene acquisition and loss events, based on the principle of parsimony,
and assuming no recombination between groups, is indicated. Geneacquisition/loss events that are uncertain with regard to timing or directionality are indicated
by question marks. Bootstrap scores and Bayesian posterior probabilities are indicated to the left and right of the forward slash respectively, while nodes with
only 100 indicated showed maximal support under both measures. See Methods for taxa definitions and sequence accession numbers. *Subsequent to its origin
in the SIVsyk/SIVmon/SIVgsn lineage, the vpu gene was acquired in the HIV-1/SIVcpz lineage via recombination (33). Some primate lentiviruses have an additional
gene, vpx (data not shown).

"Subsequent to its origin in the SIVsyk/SIVmon/SIVgsn lineage, the vpu gene was acquired in the HIV-1/SIVcpz lineage via recombination"

I'm just a chemist, can somebody explain what that means? I've heard of Syk before... but it's probably not the same Syk?

Those are different kinds of SIV-- syk is Sykes monkey 'HIV', mon is sun-tailed monkeys (I think), gsn is greater spot-nosed monkeys, and cpz is chimpanzees :)

So chimpanzees version of SIV stole its Vpu from one of those other SIVs.