1-- Herpes viruses are old. They are ooooooold. Like, hundreds of millions of years old. Specifically, about 400 million years old.
2-- Herpes viruses are everywhere. Fish, reptiles, birds, cows, humans, everywhere. And there are lots of different kinds that humans have to deal with-- CMV, EBV, HHV-8, VZV, HSV...
3-- And, though herpes viruses should not be inserted into the genome of their host cell, generally, some herpes viruses can. Its called 'strategic somatic genome integration', and some herpes viruses (and only a small percentage of cells infected with that virus) do insert.
So considering 1), 2), and 3) above, its kinda odd we havent found an *endogenous* herpes virus yet, right? I mean chance + 400 million years = its gotta happen sometime!
A couple things have complicated the hunt for endogenous herpes-- the fact many host organisms 'complete genome' is not really 'complete' and only 'first drafts', and the nature of the herpes genomes. They are complicated. So even people specifically hunting for endogenous non-retroviruses, shy away from herpes. It can be an exercise in futility.
One of my favorite labs dug in and finally found some!
In the genome of this ridiculously cute creature:
They found a herpes virus that 'looks' like Human Herpes Virus-6 (HHV-6). And not only did they find the virus, they determined the tarsier genome around the virus (as in, it is not a contaminant/mistake, the virus is *in* the tarsier DNA). And, they confirmed the herpes virus was really there themselves, in a different tarsier.
And, like many
specially designed viruses inserted into genomes by our creator viral footprints of evolution in our genome, the endogenous tarsier herpes virus is non functional. Frame-shifts, stop codons, it is no longer the infectious virus it once was. Its just a fossil. In fact some of the characteristics of a HHV-6-like virus were 'mutated beyond recognition'.
Not only did this lab find the first genuine endogenous herpes virus, they did it with 'publicly accessible data and open source software'. They needed a good strategy (looking for HHV-6 like elements) and the will to dig through a lot of garbage. That hard work payed off in them getting exactly what they wanted! Herpes!
Corals. You forgot corals. LOTS of herpesviruses!!
I still don't understand why our genomes accommodate so much damn dead weight. I mean, sure, we don't have to replicate our genomes as much as bacteria, but you'd think there's be *some* selective pressure to ditch the cruft.
Ed - that sounds really interesting, I knew of the oyster herpesvirus, but not corals! Can you recommend a paper?
This can't be right. It violates the principle of homologous recombinaltion tiniker.
Heh. What a great effort, searching through the data. I love the implied (well, to me, at least) image of species as little islands of waxing / ebbing "stability" in a swirling ocean of mobile, transferable genetic elements.
In my old age, I now have biology envy :\ YOU BASTARDS.
Soooo ... you're sayin' God has herpes?
Think of all that "junk" as a backup plan. Kind of like the spare tire you lug around, even though it technically wastes fuel, because you might need it. One day. Or not...
Of course, the other side of that is that a lot of what we used to call junk is stuff we now realize is incredibly important! Who knows what we will learn about the rest of that excess DNA sequence and how it helps us....
Let me first say that i looked up the integration site for the endogenous herpes in these primates. However, the herpesvirus genome is full of enhancers, insulators, transcription factor binding sites and other transcriptional regulatory elements. While the protein coding sequence has degraded over evolutionary time, these regulatory regions may still serve a purpose. There are examples of this for endogenous retroviruses and their LTRs. Other endogenous retroviruses create regulatory long non-coding RNAs that are important for the maintenance of a stem cell phenotype. I believe we are nearing a paradigm shift in biology where we respect these endogenized viruses and stop calling them "junk"
Oops "have not looked up"
@ both Kevins
I think that while some EVEs probably do offer some kind of function, there's probably a lot more that doesn't do anything, which I think is what first Kevin is wondering about. my take on this is that as long as its not *too* harmful, then there won't be enough of a selective pressure to purge something from a genome. This is why much of it just drifts at the neutral rate. However, there is evidence to show that even currently non-functional viral fossils appear to have degraded less than would be expected given the neutral rate and time since integration, therefore suggesting they were once useful to the host. Maybe with more data, we'll be able to answer some of these questions - it would be cool to find out if a host selective advantage was the reason many viruses integrated in the first place!