One Species' Genome Discovered Inside Another's

slyyy writes "The Universtiy of Rochester has discovered the complete genome of a bacterial parasite inside the genome of the host species. This opens the possibility of exchanging DNA between unrelated species and changing our understanding of the evolutionary process. From the article: 'Before this study, geneticists knew of examples where genes from a parasite had crossed into the host, but such an event was considered a rare anomaly except in very simple organisms. Bacterial DNA is very conspicuous in its structure, so if scientists sequencing a nematode genome, for example, come across bacterial DNA, they would likely discard it, reasonably assuming that it was merely contamination--perhaps a bit of bacteria in the gut of the animal, or on its skin. But those genes may not be contamination. They may very well be in the host's own genome. This is exactly what happened with the original sequencing of the genome of the anannassae fruitfly--the huge Wolbachia insert was discarded from the final assembly, despite the fact that it is part of the fly's genome.'"

There are retroviral genomes in ours genome

There are multiple retroviral genomes in our own genome. So I am not too surprised.

http://genomebiology.com/2001/2/6/reviews/1017 [genomebiology.com]

Re:There are retroviral genomes in ours genome

Yes, but it's part of a virus' nature to insert its DNA into the host. THat's how they work. This is a BACTERIAL genome. Bacteria don't just mix themselves into the hosts.

Re:There are retroviral genomes in ours genome

Wolbachia are kind of funky though. They can live inside of host cells (as an intracellular symbiont) which is a bit uncommon for most bacteria. They do weird things like infect female gametes (eggs) and kill male offspring, that way only infect females will be produced. Still doesn't take away from the fact that you have a bacterial genome integrated into it's host. But they're definitely not a run of the mill bacteria.

Re:There are retroviral genomes in ours genome

Wolbachia are kind of funky though. They can live inside of host cells (as an intracellular symbiont) which is a bit uncommon for most bacteria.

Sounds a bit like the story of the mitochondria [rice.edu]

All your base (pairs) belong to us!

Re:There are retroviral genomes in ours genome

the Bacteria had done precisely that.

Do you think that the retrovirus now could sue for this outstanding patent violation?

Enrico

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Any bets on what this does to ID?

This doesn't do anything to Intelligent Design. No scientific evidence will ever do anything to Intelligent Design, because "God did it" covers a multitude of sins. If Intelligent Design were a scientific theory, then i

mmm... home made mutants!

This might have an interesting impact on the 10 year forecast to creating artificial life [slashdot.org] discussion from earlier today.

i don't care

as long as i don't get the genes from my neighbour

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Get a DNA test. You may have gotten the gene's from your neighbor's father...

Re:i don't care

Agreed. He is a rather attractive fellow in a greasy, bald kind of way.

scifi tag?

What's with the scifi tag? This is real stuff, not fiction. And not entirely surprising sicne mitochondria in humans are (hypothesized?) ancient bacteria that have been incorporated into the human genome

Re:scifi tag?

The mitochondria have not been incorporated into the human genome. Mitochondria contains its own circular DNA structure, which exists and replicates independently of the genomic DNA. There must have been some gene loss/exchange, however, because many proteins necessary for mitochondrial structure and function are found solely in the genomic DNA.

Re:scifi tag?

Not only that, but it seems that geneticists are now thinking that mtDNA directs the expression of the genes encoded in the nuclear DNA. So things are MUCH more complex than we once thought (no surprise there).

Re:scifi tag?

The mitochondria have not been incorporated into the human genome.

funny you mention that, apparently when two species merge into a symbiotic relationship like that not only is there genomic reduction but integration of parts of the endosymbiont's genetic material into the host genome. http://www.pubmedcentral.nih.gov/articlerender.fcg i?artid=166356 [nih.gov]

Re:scifi tag?

You're right, but "some gene loss/exchange" would be an understatement. IIRC, there are about 1600 mitochondrial genes, and only about 20 of them are actually on mtDNA (most of those are tRNA). So the rest have been integrated into the "host" genome. This is actually an ongoing process and gene transfer happens a lot more frequently than you'd think. Mitochondrial genes that get inserted are called NUMTs and have actually been associated with human disease.

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'There must have been some gene loss/exchange, however, because many proteins necessary for mitochondrial structure and function are found solely in the genomic DNA.'

In fact _most_ of the genes that encode mitochondrial proteins are now in the nucleus, pre

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Are there mitochondria in a woman's egg before fertilization? I'm wondering how they get there in the first place if it's not in the DNA of the 2 parents.

Re:scifi tag?

There are mitochondria in both sperm and egg. Offspring generally inherit only the mothers mitochondria, though their have been a few reported cases paternal mitochondria inheritance. I believe the theory is that while they are present in both male and female gametes, the males mitochondria are degraded almost immediately after fertilization.

Re:scifi tag?

There is some info on it at the Wikipedia page for mitochondrion:
http://en.wikipedia.org/wiki/Mitochondrion#Replica tion_and_gene_inheritance [wikipedia.org]
http://en.wikipedia.org/wiki/Mitochondrial_DNA#Mit ochondrial_inheritance [wikipedia.org]

I don't know what kind of access you have to scientific journals but this abstract has a pretty good description of sperm mitochondria and how they are degraded via ubiquitinylation (a common degradation pathway)

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed &Cmd=ShowDetailView&TermToSearch=12672125 [nih.gov]

Hope that helps.

Re:scifi tag?

So the genome of the e. coli in our intestines is part of our genome? I don't think so. Mitochondrial dna, yes, because mitochondria are not considered separate organisms, but e. coli are. Admittedly, the lines can be a bit blurry, but still. One big difference is that mitochondrial dna normally passes from parent (specifically mother) to child and ancestry can be traced with it, but e. coli can move "horizontally" much more readily.

Mitochondria

Hmm, weren't mitochondria, that occur in all our cells, originally symbiotic bacteria?

Round up ready weeds and other horrors.

This discovery is unsetling and I hope that it's an error. There's already evidence that pesticide resistance from GM crops has turned up in weeds. Gene swapping in the wild might happen more often than we would like. Some of the unpleasant possibilities include food you can't eat, cotton you can't wear and weeds you can't get rid of.

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"There's already evidence that pesticide resistance from GM crops has turned up in weeds."
oh?

Oh yeah.

Weeds have already been given pesticide resistance through regular polenation [slashdot.org] and natural selection [indybay.org]. This is bad enough because it defeats the purpose and there are plenty of studies that GM crops are harmful to wildlife [commondreams.org], including mysteriously disappearing honey bees.

Newer concerns are better written and documented here by a Monsanto whistle blower [seedsofdeception.com]. We already know that the industry was sloppy because unapproved GM crops have contaminated the US rice supply [washingtonpost.com]. It may be that the people who worried about GM crops were right and evidence of genes crossing species is just one of the many things they feared. Genetic sequencing is new and bound to bring big surprises.

It's good practice to keep an open mind but be careful until you know things are safe. A couple of historical examples show how caution works and what industry does when it's not careful. People who hear about the use of lead and arsenic in paint and wallpaper often wonder how people could be so stupid as to have that kind of thing in their homes. The answer is that printers and painters overstepped their knowledge and embraced new toys that made them money. At the opposite end of the of caution is Rontgen, the discover of Xrays. He was very careful to shield all of his sources with lead bricks because he did not know what his newly created rays would do to him. Unlike many of his contemporaries, he did not die of cancer. People continued to expose themselves needlessly for half a century before sane practices were finally codified.

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mysteriously disappearing honey bees?
Here's the argument from the highly biased source [commondreams.org] you linked to:

Test 1: Spring-sown oilseed rape, October 2003

Nationwide tests found that biotech oilseed rape sown in the spring could be more harmful to many groups of w

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We've long known about a few genes getting transfered between species but this is talking about a whole genome not little pieces like genes.

Wow

I thought I was into some kinky shit, but I never tried to stick my genome into someone.

-Peter

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I thought I was into some kinky shit, but I never tried to stick my genome into someone.

I recommend you try it some time. It turns out it is pretty fun [wikipedia.org].

It'd be cool if we could spawn our own bacteria

Of course I'm being high, here, and talking out of my ass, but it does lend a whole new perspective on our role as a part of the ecosystem, as opposed to separate from it.

Dawkins

Not so surprising if you've read Dawkins (For the non geneticists among us).

You see, according to him, we are machines whose purpose is to allow genes to replicate. The fact that other genes co-opt this mechanism isn't entirely surprising if you look at it from that perspective.

 

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Yep. Of course, we've always known for a while that it's possible for biological agents to co-opt other organisms ... viruses co-opt cellular functions to reproduce themselves and retroviruses will co-opt the host's DNA itself, often to the detriment of t

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'Jesus said, "Blessed is the lion which becomes man when consumed by man; and cursed is the man whom the lion consumes, and the lion becomes man."

--Gospel of Thomas'

Since Thomas didn't write the Gospel of Thomas (and the same is true of all the books in th

humility, what's that?

But of course we understand genetics and the dynamics of genome development well enough that it's perfectly reasonable for us to manipulate the genes of our primary food crops and release them into the wild. No problem there.

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Yep, no problem. After all, this shows that the species barrier (which is one of the main criticisms against GM crops) is thinner than believed. We get an interesting variety through modern methods. The problem of a not completely described monoculture is

Re:humility, what's that?

Yes, we are really playing with fire.

And we all know that human beings would be much better off without fire.

mitochondria, chloroplasts, viral DNA

I haven't heard of a whole genome being inside another species. Although, the mitochondria (which are small energy producing factories inside most life - including mammals) have their own DNA which is separate from our nuclear DNA. Its DNA sequence resembles the sequence of single-celled organisms, which hints that there was a fusion of two different organisms hundreds of millions of years ago. Additionally, plants have chloroplasts (which do photosynthesis), and these are similar - they appear to have been cyanobacteria (independent organisms) that fused with another organism and became organelles within those cells. There are also bits of viral DNA in our own genome - it apparently fused into our DNA long ago. (In fact, you can trace evolutionary relationships by comparing the sequence and positions of these viral bits of DNA across species. Unsurprisingly, humans and apes share a remarkable number of matching viral DNA chunks.)

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Apes... don't have... tails.

phoenix

roughly 8% of our own species' genome consists of bacterial and viral genetic material. some of the segments are nearly complete with at least one case of a virus being resurected called Phoenix. it seems to be a fairly common process, viruses can lose critical genes while trying to replicate in cells which can leave them unable to reproduce as usual, the genome becomes integrated into our own. there are also cases [herpes for example] which can integrate their genome with ours in certyain cells and effectively become dormant, they start the cycle again when and if certain conditions are met. http://www.nytimes.com/2006/11/07/science/07virus. html?ei=5088&en=492dd1d370217836&ex=1320555600&adx nnl=1&partner=rssnyt&emc=rss&adxnnlx=1163032655-5n RqAOkgWGeKvh/qQcSYCg [nytimes.com]

Effect of retrovirus on Human Evolution

I think it is safe to say that retroviruses (a virus that inserts its DNA into the host genome) has influenced our own evolution.
According to this article "retroviruses (ERVs) comprise roughly 5% of the human genome."
(Note that the HTML translation is unclear - open the PDF to see that it says 5%)
http://www.hindawi.com/GetArticle.aspx?doi=10.1002 /cfg.216&e=cta [hindawi.com]

Hard to imagine that viral DNA is 5% of our genome without having any impact..

Actually, it's very easy to imagine

Hard to imagine that viral DNA is 5% of our genome without having any impact..

Actually, it's very easy to imagine. Transcribing DNA to proteins happens between a START and a STOP marker. If those markers are lost -- heck, even if just the START marker is l

Benefits for the host?

FTA:

Werren and Clark are now looking further into the huge insert found in the fruitfly, and whether it is providing a benefit. "The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host," says Werren. "The question is, are these foreign genes providing new functions for the host? This is something we need to figure out."

I wonder if this has already happened to humans through generations. In fact, I wonder if this is a standard working component of evolution, where bacteria are a catalyst. It seems that nature always gives us nice surprises to keep us in awe and realizing we don't know anything about biology.

(As a side note, I was suddenly reminded of the Metroid Fusion game, where Samus absorbs the X cores' DNA and incorporates them into her system)

Parasites and host behavior

It dosen't stop there. Certain parasites [wikipedia.org] are apparently able to change the behavior of their hosts.

Re:Parasites and host behavior

I just read a superb book called "Survival Of The Sickest" that went on at *length* about parasite control of parasitized animals, from wasps that sting spiders and implant eggs, that during their development cause the spiders to weave cocoons for the hatching wasps, through the effects of toxoplasmosis on altering how mice behave so they get eaten by the toxoplasmosis host, to other things I'd never even considered. Guinea worm is this horrible disease where a worm bores through your skin with acid. It hurts, a lot, so people go find rivers and pools because the water makes it hurt less -- and the guinea worm dumps eggs as soon as it's in water, to get the next person who drinks from that water. Rabies infects brains, making animals aggressive, and also concentrates in saliva, so the aggressive animals are more likely to bite and transfer the disease. The book even went over some guidelines for predicting how lethal a disease would be, based on its mode of transmission: typically, we've thought that diseases get less lethal over time because that increases their ability to spread, but the book says it depends on the transmission path. Malaria wants -- inasmuch as a disease can want anything -- people to be very ill indeed, so that they spend lots of time not moving, giving mosquitoes a better chance of finding the people, while colds do want people to be as mildly sick as possible so they can maximize their distribution. A particularly neat case is cholera, which can be spread by human-human contact, or more usually by contamination of drinking water. In the latter case, the sicker the person, the better, because more bacteria will be voided by the person through diarrhea, while in the former case, milder infections spread more because there's longer-term contact with heath care personnel, meaning more chances to spread. Watching cholera epidemics in South America, that's exactly what they observed: in countries that were poor, where there wasn't really any official health care, the disease became progressively more lethal over time, while in countries where infected people got immediate health care, the disease got less lethal over time. It's not a bad read, although the doctor who wrote it, Sharon Morel (I believe) should've just written it, instead of hiring a ghost writer who turned it into a succession of USAToday-feeling articles.

Doesn't mean two organisms combined

it just means the FSM reused his code. Doesn't everyone?

Mebbe it's just me but

I think it would be interesting to take a person's stem cell and try to remove all the "junk DNA" from the nucleus, then grow the cell thru a few generations (perhaps even to a full clone) and see how different it is from the original person. Very likely a lot of what we think is junk DNA isn't useless after all. Probably the reason we have 46 chromosomes in the first place is that we've been accumulating genetic material from other microbes over the span of millions of years...

Re:Mebbe it's just me but

I think it would be interesting to take a person's stem cell and try to remove all the "junk DNA" from the nucleus

Uh huh, and how exactly do you propose to do that? (also, doing this on a human seems like a pretty bold move)

People tend to throw around "junk DNA" without really specifying what they mean. For humans, we know that about 1.5% is coding, about 4% is highly conserved (so, probably very important) and we suspect that a fair amount more is involved in transcription regulation (there's been a lot of activity in that particular area recently), but we have a very faint idea of how much that would be. I saw a talk a few weeks ago where they claimed that nearly all non-coding DNA is involved in this function; that's not a widely held view, though.

It seems likely that since there are so few actual genes and they are so sensitive to mutation, then a highly redundant and more "flexible" mechanism for transcription regulation is one of the primary mechanisms for evolution.

So yeah, I am not sure where the popular perception that non-coding DNA is considered to do nothing comes from.

Oh, and as someone already pointed out, the number of chromosomes a particular organism has is completely meaningless (chickens have 78, some primitive plants have hundreds or even thousands).

My DNA...

...include the complete genome for pizza.

Evolutionary Tree not a Tree

This may mean that the idea of the "inheritance tree" needs to be revisited. One speculation for the Cambrian Explosion is that a genetic system evolved that made inter-species gene swapping easier (assisted by microbes and viruses). This could speed up evolution by swapping "good ideas". Species A could steal the eye design of species B, and species B could steal the immune system of species A, etc. But it may make paleontology and fossil evolution interpretation tricky. (As species grew more complicated over time, swapping became more difficult.) Instead of an evo tree in the textbooks, we may start seeing Directed Acyclic Graphs.

Obligatory

"Hey, you got fruitfly in my wolbachia"
"You got wolbachia in my fruitfly!"

Wraith?

Rodney is that you?