The Role of Retroviruses in Human Evolution

mhackarbie writes "The current edition of the New Yorker magazine has up a story about endogenous retroviruses in the genomes of humans and other species. Although researchers have known about such non-functional retroviral 'fossils' in the human genome for some time, the large amount of recent genomic data underscores just how pervasive they are, in a compelling tale that involves humans, their primate cousins, and a variety of viral invaders. Some researchers are even bringing back non-functional viral remnants from the dead by fixing their broken genes."

Bringing back the dead?

[smooth wombat]

Some researchers are even bringing back non-functional viral remnants from the dead by fixing their broken genes."

So what you're saying is we will now have zombie viruses?

Re:Oh no!

[Dr. Eggman]

Obviously if enough individuals survived with cells reproducing its DNA containing the retrovirus for it to become a species-wide "fossil" it was either not very harmful or possibly even beneficial to our ancestors. You might be able to make the case that perhaps we have since lost the ability to combat these retroviruses, but then we must consider the possibility that in some individuals these portions of dormant virus data have been reactivate naturally. If this has occurred and we are indeed now ill equipt to fight it, then it would have been observed as some disease and possibly classified as a genetic disorder. Who knows, by reactivating these, we have discover the cause, and subsequently the cure (as obviously we naturally beat it once) to some terrible genetic malady!

Re:Bringing back the dead?

[Anonymous Coward]

This is no laughing matter. Solanum [wikipedia.org] is serious sh*t!

Hmm

[pclminion]

How do we know the the retrovirus genome didn't originate with the hosts themselves? Did these viruses evolve truly independently, or might they have started out as fragments of genetic code from some larger organism which somehow escaped and became self-sufficient?

In other words, when we look at the human genome and say, "This is riddled with retroviruses!" is it not possible that the retroviruses were actually there all along, and only later became able to leave the parent cell and operate independently?

Are retroviruses actually just chunks of "rebel DNA" from our own genome, or possibly from some other species?

Aaargh, learn to use the preview button

[Daniel Dvorkin]

What you're describing is probably possible, but for any given stretch of DNA encoding the right polymerases, it's a lot more likely that it's a retrovirus that lost the ability to leave the cell than that it's a transposon that gained that ability and then lost it again.

Is what I meant to say.

Re:Hmm

[Harmonious Botch]

That is a damn good question.

A 'rebel DNA leaving home' must have happened at least once, in some species, otherwise how could viruses exist? They seem way too complex to have happened by chance, and they can't evolve until they are complex enough to infect.

Re:Bringing back the dead?

[skeftomai]

Are viruses even alive in the first place?

Re:Hmm

[cpricejones]

To understand this, you can do sequence comparisons between retroviral genes and our own genes. For example, retroviruses have an enzyme called reverse transcriptase. This enzyme is a type of polymerase. We have many polymerases in our body, and if RT developed from one of them, then there would be very substantial sequence similarity. This is one way to figure out what proteins do if you do not know their function. You compare their amino acid sequence to other known proteins and see if they are similar. This is very common, and it is how researchers establish relationships between retroviruses to understand how they evolve. For example, HIV is a member of the subgroup of retroviruses called lentiviruses, and these viruses have many things in common. HIV has a cousin called SIV (simian immunodeficiency virus) that is very similar. A really good reference is Coffin, RETROVIRUSES, from Cold Spring Harbor Press.

Cambrian explosion?

[Tablizer]

Such viruses may be responsible for the Cambrian Explosion. A new kind of virus may have helped "share good ideas" like eyes, nervous systems, enzymes, etc. between different species of early animals. This may have propelled evolution by allowing life to mix and match instead of each branch having to reinvent stuff from scratch.

Re:Hmm

[maxume]

Do they really infect? Or do they do something else?

My impression is that bacteria are in the habit of absorbing random fragments of DNA from their environment. I can see where some accident would cause such a fragment to carry the instruction 'replicate me' and little else, thus making things interesting. So not so much leaving home as taking it over destructively. Throw in billions of years and trillions of organisms and it starts to get a little ridiculous trying to make any guesses at all.

Re:Bringing back the dead?

[GwaihirBW]

Natural selection is a general principle that applies to anything that reproduces -- things that reproduce well will continue to exist and spread, and when variation occurs, those variants that are best equipped to survive and reproduce successfully in a given environment will come to dominate the population. This has even been applied to ideas in the greatly overhyped meme theory [wikipedia.org].

Re:Oh no!

[drunken_boxer777]

I'm giving up mod privileges on this to comment.

If we "fix that part where they're drug resistant", it would make no difference, unless we could eliminate those viruses in the first place. It's like trying to populate the world with only mice that were more likely to get caught in traps. It would only be possible if we could eliminate all the mice in the world, and then introduce these 'dumb' mice into the wild. What's the point of repopulating the world with dumb mice if we didn't want mice in the first place?

Second of all, if you read the article, you would know how the researchers 'fixed' the 'broken' viruses:

The team took ten versions of that virus (we carry more than thirty) and compared the thousands of nucleotides in the genetic sequence of each version. They were almost identical, but where they differed the researchers selected the nucleotides that appeared most frequently. That permitted them to piece together a working replica of the extinct retrovirus. "If you have a person with a lethal defect in the heart,'' Bieniasz explained, "and another with a lethal defect in the kidney, you could make one healthy person by transplanting the respective organs. That is what we did.

Lastly, and not that it will necessarily assuage your fears, but a species that carries an endogenous retrovirus in its genome is far less likely to be infected by that virus. Some developmental biologists employ a well-characterized and naturally occurring chicken retrovirus, engineering it to misexpress a normal chicken gene of their choice. This way, they can see what happens if they express that gene everywhere within a developing organ, as opposed to the normal expression of the gene only within a small population of cells within that organ. (As an example, they are studying gene X, which plays a role in bone development, and is only expressed in cells that will become bone cells. They make a chicken retrovirus that also expresses gene X, and infect the wing of a developing chicken. Now all the cells in the wing express gene X, and not just those that were going to become bone cells.) In order to do this, these researchers must use eggs from chickens that do not carry endogenous copies of this virus in their genome. Eggs from chickens that carry endogenous copies of this naturally-occurring retrovirus in their genome are far less susceptible to infection by the engineered virus, and therefore are not experimentally useful. Such endogenous retrovirus-free chickens were specially bred.

Sure, there are always potential risks from any type of science. But it is important to know how risky something is, and weigh that versus the potential benefits.

Re:Cambrian explosion?

[Tablizer]

Or maybe... The big change at the Cambrian was a mutation which allowed the creation of shells and bones.

I don't see those as a significant trigger mechanism. Early Cambrian fish hardly had any bones, I would note. And there's now plenty of soft-body precambrian fossils such that we know soft bodies existed in relative abundance at that time. They just lacked many features we take for granted, such as eyes, mouths, digestive tracks, and limbs; and don't seem to match up well with Cambrian-and-forward life.
       

Re:Cambrian explosion?

[Tablizer]

Since most retrovirus markers are useless remnants and are just artifacts of past events. They are not a means of propagating "good ideas" since they are largely non-functional.

For one, early life was simpler such that foreign genes may have been easier to integrate. Second, I've read that it appears that the mammilian placentia may have "learned" how to share life-giving fluids between baby and mother without the immune system complaining via a virus that knew how to disable the immune system for its own needs. I'll see if I can find the article. It was fascinating.

This sounds like some wishful thinking do you have any references?

No, its just speculation, as is all C.E. theories at this point.

Re:Cambrian explosion?

[Tablizer]

Do some actual reading. There was no 'explosion', except in the sense of leaving fossils behind because deposition of hard materials evolved. Those forms have precursors from the Ediacaran period.

Most authors seem to disagree, at least for bilatera. The best candidate is Kimberella, a possible mollusk matched largely because of the "teeth" scrape marks found near fossils. The others have very uncertain relationships. Spriggina, for example, could be an arthropod, annelid (of earth-worm fame), or even a chordate ancestor, among other candidates.
     

RNA world? Or are seeing the history backwards?

[Joseph_Daniel_Zukige]

From what I was just reading now, maybe the RNA world which some theorists have speculated (theorized) predated the DNA biological world we presently live in was the place where something like viruses could reproduce themselves.

But I'm probably misunderstanding everything I read today.

My personal opinion?

I remember playing with a 6802 prototyping board with a flaky power-on reset circuit. (I used cheap switches from Radio Shack.) It had a monitor ROM, of course, then later it had BASIC in ROM. If power came up too fast, the ROM would not be ready to put the reset vector on the bus, and the CPU would jump somewhere else. Sometimes, if the reset button worked, I could look at RAM, and I would find bits and pieces of the ROM sitting out there. Until the thing stabilized, sometimes it was not particular interesting, but sometimes it would dump almost intelligible strings, or even clots of error messages or the symbol tables into video RAM.

I had read, at the time, about how computers with disk drives had to have good power-on reset circuits, or had to be booted up with no media in the drives, and media loaded after the operator stabilized the CPU. Otherwise, the disk drives would tend to get told to write random data on the disks, which, of course, kind of ruins the whole purpose of having disks.

I had also read that (some of?) the first computer viruses were inspired by some of the junk that was left in memory by such episodes of uncontrolled execution.

So I have tended to wonder whether it might not be the case that viruses are not some independent remnants of proto-life, but are rather the results of genetic accidents.

I'm not sure we could tell the difference from looking at the archeological record.

But it's interesting that one of the biologists the friendly article quotes made a comment that almost equated viruses with God.