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Sci-Fi Science

One Species' Genome Discovered Inside Another's 224

Posted by Zonk
from the it's-a-mad-house-a-mad-house dept.
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.'"
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One Species' Genome Discovered Inside Another's

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  • by Anonymous Coward on Thursday August 30, 2007 @06:05PM (#20418157)
    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]
  • by cez (539085) <info AT historystartingyesterday DOT com> on Thursday August 30, 2007 @06:08PM (#20418175) Homepage
    This might have an interesting impact on the 10 year forecast to creating artificial life [slashdot.org] discussion from earlier today.
  • by Anonymous Coward
    as long as i don't get the genes from my neighbour
  • scifi tag? (Score:5, Insightful)

    by haluness (219661) on Thursday August 30, 2007 @06:10PM (#20418193)
    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? (Score:5, Informative)

      by TheMeuge (645043) on Thursday August 30, 2007 @06:14PM (#20418241)
      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? (Score:4, Insightful)

        by linguizic (806996) on Thursday August 30, 2007 @06:34PM (#20418447)
        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).
      • by khallow (566160)
        There doesn't have to be any interaction at the gene level. Remember survival of mitochondria and nucleic DNA are mutually dependent.
      • Re:scifi tag? (Score:4, Informative)

        by wizardforce (1005805) on Thursday August 30, 2007 @06:45PM (#20418567) Journal

        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]
      • by QuantumG (50515)
        I believe the mitochondria DNA is considered part of the human genome, but only by definition.
      • Re:scifi tag? (Score:4, Informative)

        by izomiac (815208) on Thursday August 30, 2007 @06:46PM (#20418579) Homepage
        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.
      • by catbutt (469582)
        I'm not sure I agree. Mitochondria are separate from the nuclear dna, but they are still part of the human genome...just not the nuclear genome.
      • Re: (Score:3, Informative)

        by RDW (41497)
        '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, presumably a result of ancient DNA transfer from the primordial mitochondrial genome to the nuclear genome, so the parent post is substantially correct. The modern mitochondrial genome is pretty vestigial (smaller than that of many viruses). The original arti
      • Re: (Score:3, Interesting)

        by yabos (719499)
        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.
      • by Bob54321 (911744)
        In fact most of what appears to be the genome form the organism that mitochondria are derived from is now in the nuclear genome.
    • It isn't even new. There's plenty known [nih.gov] about bacterial genes [nih.gov] in eukaryotes [nih.gov]. This is just a striking case of large-scale horizontal transfer into an animal genome. It isn't even the first time [nih.gov] transfer from bacteria to animals has been seen. It seems to be a pretty widespread process [nih.gov] in general in eukaryotes. Of course that's also ignoring the gigantic contribution of bacterial genes to eukaryotic genomes from the mitonchondrial symbiont, and the equally huge contribution of cyanobacterial genes from t
  • Mitochondria (Score:4, Insightful)

    by flyingfsck (986395) on Thursday August 30, 2007 @06:14PM (#20418235)
    Hmm, weren't mitochondria, that occur in all our cells, originally symbiotic bacteria?
  • by Erris (531066) on Thursday August 30, 2007 @06:14PM (#20418243) Homepage Journal

    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.

    • by geekoid (135745)
      "There's already evidence that pesticide resistance from GM crops has turned up in weeds."
      oh?
      • Oh yeah. (Score:5, Insightful)

        by Erris (531066) on Thursday August 30, 2007 @08:40PM (#20419547) Homepage Journal

        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.

        • Re: (Score:2, Flamebait)

          by crashfrog (126007)
          Unlike many of his contemporaries, he did not die of cancer.

          You should have looked that up before you said it. Wilhelm Conrad Rontgen, the discoverer of X-rays, died of carcinoma of the colon in 1923.

          Also you're wrong about the bees thing. There's been no established connection between GM crops and bee populations. Indeed, it would be somewhat surprising if there were - bees eat pollen, and GM crops express nearly none of the GM proteins (usually one or another of the Bt complex proteins) in their pollen.
        • 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 wildlife than their conventional equivalent. There were fewer butterflies among modified crops, due to there being less weeds. Verdict: GM fails.


          I'm sorry, but reducing weeds means GM passes, that was it's goal. There's nothing mysterious in observing that
    • 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.
    • by linguizic (806996)
      RoundUpReady crops were genetically modified using a gene that was found in nature, in fact, right outside the the RoundUp factory. So these genes were already in the wild before people started using them to modify food crops.

      I know you didn't state this, but let me put this out there, because there is a lot of confusion about this: there is no RoundUp in RoundUpReady crops. But there is a gene that makes them resistant to roundup, so you can spray with extra strong roundup and kill all the weeds around
    • Provide a cite, please. I follow this and don't recall reading that. Again, cite please.
    • by dbcad7 (771464)
      I think that the resistance to Roundup was already there... What happened is these weeds that had it, now have little competition from other weeds that didn't (since they are dead)... but that's a good thing because Roundup will soon become useless.
    • Puts a new spin on you are what you eat. I need to quit eating the Burger King customers.
    • by catbutt (469582)
      I'm not sure how this is so scary. This is something that happens naturally, so it's presumably been going on since long before humans were around. Issues with pesticide resistance and genetic modification seems peripherally related, at best.
      • by Erris (531066)

        I'm not sure how this is so scary. This is something that happens naturally, so it's presumably been going on since long before humans were around.

        Intensive agriculture is the very antithesis of natural selection. Natural selection has given us cotton that bugs can eat and we can wear. GM is giving us cotton that bugs can't eat and there's evidence that we should not wear it either.

        Harmful organisms we accidentally create may revert to harmless forms given normal evolutionary timeframes. Want to wait

        • by catbutt (469582)
          Great, and pollution is a problem too, but I don't see how it is related to this issue.

          This story is about things that happen naturally. Your concerns are things caused by humans. See the difference?
    • by Artifakt (700173)
      I'm not seeing how you got the "cotton you can't wear" part...
  • Wow (Score:4, Funny)

    by pete-classic (75983) <hutnick@gmail.com> on Thursday August 30, 2007 @06:15PM (#20418247) Homepage Journal
    I thought I was into some kinky shit, but I never tried to stick my genome into someone.

    -Peter
    • by Ardeaem (625311)

      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].
  • 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.
    • Yes, this is in line with Terrence McKenna's theory that there aren't individual <i>species</i> on earth -- instead, there is a "gene swarm" going on.

      If you're high right now, I bet you'd love Terrence McKenna.  Youtube for his DMT videos and other stuff.
  • Dawkins (Score:5, Insightful)

    by Colin Smith (2679) on Thursday August 30, 2007 @06:20PM (#20418301)
    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.

     
    • Re: (Score:3, Interesting)

      by tukkayoot (528280)
      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 the host organism. Non-viral parasites can also co-opt the metabolic functioning of a host organism or even control the hosts' minds [wikipedia.org].

      So this sort of dog-eat-dog, inter-species warfare (as well as friendly symbiosis and back-scratching) between genes for th
  • 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.
    • Re: (Score:3, Insightful)

      by cnettel (836611)
      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 still a significant one, but the foodcrop varieties already in use are already such monocultures. Preserving local varieties in some form is essential, but those varieties are on the other hand not good enough to feed us all.
    • by Absolut187 (816431) on Thursday August 30, 2007 @06:51PM (#20418639) Homepage
      Yes, we are really playing with fire.

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

      • Play with fire all you want. You have every right to take risks on your own behalf. But releasing a fertile, open-pollinated GMO crop is effectively making that risk decision for everyone else. Does Monsanto have the right to do that, in pursuit of profit. I think not.

        Note that the greatest hazard of GMO crops is not the poorly studied potential dangers of the GM organism itself: it's the danger of running afoul of Monsanto's intellectual property [percyschmeiser.com].
  • by brit74 (831798) on Thursday August 30, 2007 @06:35PM (#20418449)
    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.)
    • Unsurprisingly, humans and apes share a remarkable number of matching viral DNA chunks.)

      Well DUH, considering humans ARE apes [wikipedia.org]
    • by weicco (645927)

      Although, the mitochondria (which are small energy producing factories inside most life - including mammals)

      For a second I thought it said midichlorian...

  • phoenix (Score:5, Informative)

    by wizardforce (1005805) on Thursday August 30, 2007 @06:36PM (#20418467) Journal
    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]
  • by Absolut187 (816431) on Thursday August 30, 2007 @06:46PM (#20418581) Homepage
    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..
    • 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 lost -- then that piece of code is never "executed". In programming terms, it's commented out.

      And, yeah, your genetic code contains a whole bunch of commented-out sequences. Dunno, I don't have much trouble believing that they have no impact whatsoever :)

  • by Spy der Mann (805235) <spydermann.slashdot@nOsPaM.gmail.com> on Thursday August 30, 2007 @06:56PM (#20418683) Homepage Journal
    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)
  • by Ethanol-fueled (1125189) on Thursday August 30, 2007 @06:59PM (#20418709) Homepage Journal
    It dosen't stop there. Certain parasites [wikipedia.org] are apparently able to change the behavior of their hosts.
    • by smellsofbikes (890263) on Thursday August 30, 2007 @10:46PM (#20420501) Journal
      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.
  • Clearly a copy/paste error...
  • by ross.w (87751) <{rwonderley} {at} {gmail.com}> on Thursday August 30, 2007 @07:07PM (#20418795) Journal
    it just means the FSM reused his code. Doesn't everyone?
    • Flying Spaghetti Monster! The Spaghetti stands for its code structure liberally sprinkled with tons of GOTO statements. But the bacteria and viruses use an even more archaic and more difficult to debug construct, the COME FROM statements.
      • by jamstar7 (694492)

        Flying Spaghetti Monster! The Spaghetti stands for its code structure liberally sprinkled with tons of GOTO statements. But the bacteria and viruses use an even more archaic and more difficult to debug construct, the COME FROM statements.

        They use COBOL????????????

    • by batkiwi (137781)
      Was that code released GPL? If so, are we now entitled to the entire genome?
      • by ross.w (87751)
        Go for it. But you'll have to write your own compiler, and build the OS and hardware to run it on.
  • by hyc (241590) on Thursday August 30, 2007 @07:15PM (#20418861) Homepage Journal
    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...
    • by glwtta (532858) on Friday August 31, 2007 @12:36AM (#20421123) Homepage
      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).
  • ...how long until we have fruitfly genome in human DNA?

    Answer that, André Delambre/Seth Brundle!

  • My DNA... (Score:3, Funny)

    by NoseBag (243097) on Thursday August 30, 2007 @08:41PM (#20419549)
    ...include the complete genome for pizza.
  • by Tablizer (95088) on Thursday August 30, 2007 @09:04PM (#20419767) Journal
    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.
  • ... feel strangely compelled to think about my new Inner Lords.
  • Oh, it's just the patent lawyers smelling a new revenue stream...

    1. Find an 'embedded' genome
    2. Patent the original (and unimportant) organism's genome
    3. Sue the sellers of the commercial crop with that embedded genome
    4. You know this bit...

    Nobody cares if you patent the genome of some boring bacterium, but if that turns out to be a constituent of, say, rice or racehorses, then you have a goldmine!

  • Obligatory (Score:3, Funny)

    by Klowner (145731) on Friday August 31, 2007 @01:10AM (#20421323) Homepage
    "Hey, you got fruitfly in my wolbachia"
    "You got wolbachia in my fruitfly!"

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