Viral Fossil Brought Back To Life

hey hey hey writes "In a controversial study, researchers have resurrected a retrovirus that infected our ancestors millions of years ago and now sits frozen in the human genome. Published online by Genome Research this week, the study may shed new light on the history of these genomic intruders, as well as their role in tumors. Although this particular virus, dubbed Phoenix, is a wimpy one, some argue that resuscitating any ancient virus is inherently risky and that the study should have undergone stricter reviews."

Comments

Very interesting

[MillionthMonkey]

Only 3% of the genome is genes, the rest is junk DNA which has a lot of interesting stuff like alternate versions of genes, commented out ideas, and coded critters like this one that sit in your DNA like "sunken ships". There are like 200 copies of reverse transcriptase in the human genome, different versions, all in this junk DNA. Reverse transcriptase has absolutely no legitimate purpose in a eukaryote. It can take a segment of RNA (usually viral RNA), convert it into DNA, and stich it into your genome. Only viruses need to do that. The RNA itself has code for reverse transcriptase, and we see it in our chromosomes all over the place, this gene that is useful to viruses and no one else. It's the most common gene in your body.

Viruses have a lytic cycle where they express nasty genes and build capsids inside you, and a lysogenic cycle, where they adopt a different strategy- they get into your DNA, become part of the junk DNA, and they replicate during normal cell division along with all the rest of your DNA.

Junk DNA has all sorts of nasty critters in it. One trick your body uses is to carpet especially infectious regions with methyl groups via cytosine methylation. Basically the idea is that the methyl groups jam up the machinery that comes along to express proteins, so if the proteins are viral, you can "comment them out" that way. When a cell divides, both strands of its DNA have methylated cytosines in the same regions. After the DNA replicates you have two methylated daughter strands, each coupled with a brand new complimentary strand. This complimentary strand has no methyl groups on it. So a clever enzyme comes along, DNA methyltransferase. It has a regulatory domain and a catalytic domain. The regulatory domain runs across the DNA feeling it for methyl groups. If it finds them on one strand, the catalytic domain deposits methyl groups on the other strand. That way, the stretch of DNA can be marked as "bad news" in a way that is heritable, despite the fact that no actual DNA sequence is being "inherited". As far as where the initial methylation signal came from, that can probably be put down to natural selection.

Re:Very interesting

[MillionthMonkey]

"Only 3% of the genome is genes, the rest is junk DNA..."
  Based on what? We only JUST mapped out the 3% that encodes protiens (the genes). Science does not know what the rest of the DNA does or does not do. There is certainly no study that I can find that offers proof that it is unused. It's the furthering of the trend of treating ignorance as if it were knowledge. If they had intellectual honesty, instead of proclaiming DNA 97% junk, they'd proclaim themselves 97% ignorant. Labeling of it as "junk," especially in our infancy, or rather fetushood, of understanding DNA, is the absolute pinnacle of scientific arrogance. Maybe next they'll look up at the sky, and seeing clear proof of life around one star, and none around the others, declare all the rest "junk stars."

Dude, I'll just refer you to the Wikipedia page on Junk DNA (the bold tags are mine):

In molecular biology, "junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 97% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence is probably an evolutionary artifact that serves no present-day purpose, some may function in ways that are not currently understood. In fact, recent studies have suggested functions for certain portions of what has been called junk DNA. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. Some consider the "junk" label as something of a misnomer, but others consider it apposite as junk is stored away for possible new uses, rather than thrown out; others prefer the term "noncoding DNA" (although junk DNA often includes transposons that encode proteins with no clear value to their host genome).

And I didn't even edit that on Wikipedia before replying either.

You can call it something else if you're offended, but the DNA itself won't have its feelings hurt if you call it junk.

Re:Very interesting

[MillionthMonkey]

What about TERT??? Dont we use reverse transcriptase for telomere repair?

Well that's not the same kind of "reverse transcriptase".

TERT has the job of making DNA molecules longer after replication (telomere lengthening). It appends a sequence of 5'-TTAGGG (a telomere) over and over to the 3' end of a chromosome. To do this, it has an RNA template molecule inside itself with a sequence complimentary to TTAGGG, offset and repeated twice: 3'-CAAUCCCAAUC-5'. The left end of the template aligns to the end of the chromosome and hybridizes to the TTAGGG on the end. Then a new TTAGGG hybridizes to the second half of the template, is bound to the chromosome, and TERT disengages to repeat the process with another TTAGGG chunk. It's a pretty clever implementation actually. You could probably have it repeat any six base monomer other than TTAGGG by changing the RNA template molecule that it uses. Some other species use a different six base sequence for their telomeres.

This technically counts as converting RNA to DNA, so the enzyme is called "telomerase reverse transcriptase". But it's not appending any coding DNA, it's just adding TTAGGG over and over again to give structural integrity to the chromosome. Usually "reverse transcriptase" refers to a family of enzymes with a viral origin that share ancestry and work by converting viral coding RNA into DNA with no proofreading mechanism and a high rate of error.

It's most commonly used by retroviruses along with integrase (used by viruses to splice crud into your DNA) but retrotransposons also use it to jump around. These are genetic parasite sequences that can move around in the genome and use reverse transcriptase to make copies of themselves. LINE (long interspersed element) is a retrotransposon about 5000 bases long that inserts copies of itself all over the place. The human genome now has about 900,000 copies of LINE- fully 21% of the genome. Another 11% of the genome is SINE (short interspersed element) elements. SINE is a 500 base or less sequence. LINE has actual coding DNA in it for something that works like integrase and reverse transcriptase. That lets it copy itself along with its adjacent sequence, and insert the copy in some random place in your DNA. SINEs don't have any coding DNA- they hitch a ride along with the LINEs when they get copied, so they're parasitizing the parasites.

Link to the Original Article in Genome Research

[jestill]

The abstract with a link to the full pdf is available online. The pdf is available on campus from many universities. It is interesting that this is already in the news. This is not technically in print form yet, and was just posted to the journal's advance articles web site.

Re:Wonderful

[vadim_t]

Err, no, at the center of the Earth gravitational pull wouldn't be infinite. Rather, there wouldn't be any.

The mistake you're making is trying to do the calculation with Earth's mass and zero radius. But the thing is the gravity doesn't come from a tiny point in the center, that's just a simplification. As you go inside the earth, there's going to be more and more matter over you pulling in the opposite direction. Were you to end up in the center there would be no gravity at all, as the matter around you would pull equally in every direction.

Re:Not very Intelligent design

[frogstar_robot]

My problem with evolution is that it doesn't explain the beginning.

Then you need not have a problem with evolution. Evolution and abiogenesis (life from non-life) are two separate questions and topics. Evolution tells us that descent with modification is the current best explanation for the species and forms we see today. It does not purport to tell us what the first life form(s)? were or how they came to be. That is a separate and far more speculative field of study.

Even Darwin understood this way back when. His first attempt to systemize evolution was NOT called "Origin of Life". It was called "Origin of Species". Evolution operates on extant forms of life. If it operates in the processes that lead to life starting in the first place, the mechanisms involved are likely different from the ones creationists and (reputable) biologists argue all the time. Evolution presupposes entities capable of self-reproduction. You need replicators of some sort to even talk about evolution in the first place. Once the first replicator either spontaneously arrives or is created (and no this need not be dismissed out of hand but if the only case for it is faith-based then we aren't talking science.....) then evolution can take over and eventually bring about forms vastly more varied and different from the starting point.