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Biotech

A Truly Alive Virus 67

Posted by michael from the cross-breed dept.
cyclop writes "Microbiologists are puzzled by the genome sequence of the giant Mimivirus. It seems this virus has even more genes than many bacteria, is able to synthesize its own proteins and therefore is, by definition, alive. 'We are seeing an organism here. There is DNA, RNA and plenty of proteins,' says Didier Raoult, who reports the work in this week's Science."
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A Truly Alive Virus More

A Truly Alive Virus

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  • name for the Mimivirus - Slashdotter

  • Aha! (Score:2, Funny)

    by Black Parrot ( 19622 )


    Now we know what happened to the missing human genes.

  • Um, no.... (Score:3, Interesting)

    by slowtech ( 12134 ) on Thursday October 21, 2004 @09:52AM (#10585964)
    Having DNA coding for a lot of proteins does not make a virus alive. This virus has a lot of DNA (the poxvirii do as well), but that does not mean it has a metabolism. Virii use their host's metabolism to produce proteins.

    Whether you think virii are alive or not, there is nothing about this virus that suggests (from the linked PubMed abstract) that this virus is qualitatively different from any other.

    • Spelling nazi (Score:2, Funny)

      by Anonymous Coward
      Check dictionary.com. The proper plural for virus is viruses. It is not "virii". Those who use silly false plurals end up looking like ignoramii.

    • It's called VIRUSES not virii (Score:5, Informative)

      by hankwang ( 413283 ) * on Thursday October 21, 2004 @10:07AM (#10586135) Homepage
      This virus has a lot of DNA (the poxvirii do as well)

      That geeks write "virii" in l33tspeak when they talk about computer viruses is one thing, but it's worse when this spelling pops up in scientific discussions. The plural is VIRUSES!

      If you follow latin rules for constructing the plural form, it would still be viri with a single i at the end [nd.edu].

    • Um, yes... (Score:5, Informative)

      by contagious_d ( 807463 ) on Thursday October 21, 2004 @10:13AM (#10586185) Journal
      "This virus has a lot of DNA (the poxvirii do as well), but that does not mean it has a metabolism. Virii use their host's metabolism to produce proteins....."
      I have this funny feeling you didn't RTFA before you decided that this was a worthless story.
      From Nature: "It can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way. It can even repair its own DNA if it gets damaged, unlike normal viruses."

      • Re:Um, yes... (Score:4, Informative)

        by Idarubicin ( 579475 ) on Thursday October 21, 2004 @04:31PM (#10591771) Journal
        I have this funny feeling you didn't RTFA before you decided that this was a worthless story.

        I have a feeling the parent didn't read the story closely enough to decide that the grandparent was wrong.

        Nature's phrasing is a bit misleading. Mimivirus, like all other known viruses, requires the protein synthesis machinery of a host cell to reproduce and to carry out the synthesis of the proteins described. (For mimivirus, the hosts are amoebae.) I mean, it's impressively large--it carries a lot of genetic material inside its protein coat, and it's comparable in size to some of the smallest bacteria (mycoplasma)--but it's not alive.

        While the Nature blurb says that "it can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way. It can even repair its own DNA if it gets damaged, unlike normal viruses", what they mean is that it carries genes that when expressed by the host cell can carry out those functions. The virus, by itself, can't do protein synthesis, so it can't make the proteins that carry out DNA repair or other described functions.

        It's very interesting and unusual for a virus to carry genes for these functions--all other known viruses rely on their hosts to provide them, or do without--but it definitely doesn't make the virus alive. The grandparent poster is quite right, and it's made quite clear in the linked PubMed abstract [nih.gov] to the original Science article. The Nature piece is in their News section, written by a staff writer. It's not a peer-reviewed article, and the terminology is regrettably confusing.

        • Ahh, you are right. I still think the great grandparent is wrong though, as his whole point was that this virus was not significantly different from other viruses.
    • Can anyone share an insight as to how a virus uses the host's matabolism to make proteins?

      thanks

      .
      -shpoffo

      • Re:Um, yes.... (Score:5, Informative)

        by VendingMenace ( 613279 ) on Thursday October 21, 2004 @11:29AM (#10587469)
        It is quite simple, really. The virus enters the host cell. From there it uses the hosts machinery (enzymes, ribozyme, protiens, ect) to carry out the replication of the viruses DNA (or RNA whatever the case may be).

        However, the virus is not just bare DNA or RNA (gennerally). It also contains a protien coat on the outside that serves to hold and protect the virus genome. So this too must be made in great quantities to hold all the vast numbers of genomes that have just been copied.

        So, in order for a virus to replicate in a cell, it must use the cells system to make BOTH the nucleic acid synthesis AND the protiens for the coat around the virus.

        Since this process of protien sythensis uses energy, the virus IS using the cells matabolism to make protiens.

        I hope that answers your question. :)

      • Re:Um, no.... (Score:4, Insightful)

        by Ayaress ( 662020 ) on Thursday October 21, 2004 @11:41AM (#10587654) Journal
        Well, most viruses just have DNA or RNA. They enter a host cell, and the host (or more particularly, the polymerase and ribozomes in it) then proceeds to treat the new DNA as its own, producing the proteins incoded in it, which is mostly things like the protein "package" for the viral DNA. Viral DNA lacks the control sites that prevents normal cells from overproducing any particular protein, so the cell will continue to produce the viral proteins until it dies.

        However, this virus is unique in that it can produce at least some of its proteins without a host cell. It's not much, but its still metabolism, so it is alive by definition. However, from what I read in the cnrs.fr link from the article, it sounds like it can't, among other things, produce its own ribosomal RNA (feel free to correct me if I'm wrong, I haven't had biology since high school and there are some big words in that article), so its still dependant on host cells for reproduction, which makes it a virus by definition.
        • Your wording is a little ambiguous. This virus carries information to produce these protiens, so it doesn't depend on the host cell's protiens; however, it can't produce them itself.

          It's NOT metabolism by any definition; it's just more information than is common.

          -Billy
          • Really late reply since I was out of town on the weekend, and you'll never read this, but read the article before you act stupid. It does produce the proteins itself. Over 100 of them. Read that carefully. It produces the proteins by itself, without any help from a host cell. Furthurmore, it produces protiens by itself from more genes than most viruses have at all.

  • Size? (Score:3, Interesting)

    by tod_miller ( 792541 ) on Thursday October 21, 2004 @09:57AM (#10586033) Journal
    I thought the amount of genes didn't matter (could be junk genetics?)

    Remember the Macro-virus on Voyager? [IANAT]

    I didn't realise that Viruses weren't 'alive'...

    Since the 1960s, scientists have argued about whether viruses are living organisms or just a bundle of very large molecules.

    aaaah so - definition of life...

    Then the truly dumb dumb dumb stuff:

    A virus has to hijack another organism's biological machinery to replicate, which it does by inserting its DNA into a host. Bacteria, on the other hand, carry all that they need to reproduce independently, and thus qualify as alive.

    Well oil my ovaries, auto-reproduction [there might be a better word for it] here I come! [I am alive right?]

    OK I realise they don't mean asexual reproduction is the only way of being able to reproduce on your own.

    I guess some /.'ers could only reproduce by infecting someone elses DNA!! :-)
    • "A virus has to hijack another organism's biological machinery to replicate, which it does by inserting its DNA into a host. Bacteria, on the other hand, carry all that they need to reproduce independently, and thus qualify as alive."

      YESSSSSSS

      By this definition, the recording industry is DEAD! We just need to decide if virii is on the same level as them, or higher.

    • Re:Size? (Score:3, Funny)

      by aminorex ( 141494 )
      If the gender balance of Slashdot is as similar to
      the gender balance in my upper division undergrad
      science courses as I think it is, the vast majority
      of /.'ers could only reproduce by infecting someone
      else's DNA.

  • 3 categories of life... (Score:3, Funny)

    by tod_miller ( 792541 ) on Thursday October 21, 2004 @10:00AM (#10586072) Journal
    Although biologists sometimes divide life into three categories,

    Alive, dead, and that feeling you get at 3pm on a Sunday afternoon....

    Or:

    Us, them, and my little friends in the test tube...

  • Evolution proof ? (Score:5, Interesting)

    by Jesrad ( 716567 ) on Thursday October 21, 2004 @10:02AM (#10586085) Journal
    This virus is not yet self-reproducting, but I think it might just evolve a bit more and complete that last step. It's a nice demonstration of evolution in action, I think.

    • Re:Evolution proof ? (Score:4, Interesting)

      by Anonymous Coward on Thursday October 21, 2004 @10:44AM (#10586700)

      This virus is not yet self-reproducting, but I think it might just evolve a bit more and complete that last step. It's a nice demonstration of evolution in action, I think.

      Perhaps it was once a bacterium which lost its selfreproductivity in a bid to maximize parasitivity.

      • Re:Evolution proof ? (Score:4, Interesting)

        by Ayaress ( 662020 ) on Thursday October 21, 2004 @11:57AM (#10587893) Journal
        Perhaps it was once a bacterium which lost its selfreproductivity in a bid to maximize parasitivity.

        Evolution or not, that would have been my first guess, too, from its size and the volume of its genome. However, if that were the case, you'd expect the genes it does have to be like their equivalents in bacteria, which isn't the case. The cnrs.fr link says that it shares key gene sturctures in common with viruses like smallpox.

        An interesting possibility would be that it's actually a sort of "hybrid." A mutation in the protien structure of the viral coat might cause the abnormally large size (a reduction in the bonding angles, perhaps), allowing for the fused genome of the host bacterium and the original virus, along with various key molocules from the bacterium to all be packaged into the virus, instead of just the viral DNA alone.

        • Re:Evolution proof ? (Score:3, Informative)

          by DrKyle ( 818035 )
          A mutation in the protien structure of the viral coat might cause the abnormally large size (a reduction in the bonding angles, perhaps), allowing for the fused genome of the host bacterium and the original virus, along with various key molocules from the bacterium to all be packaged into the virus, instead of just the viral DNA alone.

          It's long been known that the viral coat proteins can only accept a certain amount of DNA to be packed inside them. A good example of this is the use of Lambda libraries 1

  • A Large Virus Named Mimi (Score:3, Funny)

    by DLWormwood ( 154934 ) <wormwood@meCOMMA.com minus punct> on Thursday October 21, 2004 @10:09AM (#10586150) Homepage
    What would Drew Carry think?
  • ... I'm not convinced it's alive. Certainly it's perkier than a prion, but...

  • Living computer virus (Score:3, Funny)

    by Knights who say 'INT ( 708612 ) on Thursday October 21, 2004 @10:33AM (#10586524) Journal
    How many people thought this was an interesting AI-based computer virus, perhaps employing genetic algorithms [wikipedia.org]?

  • The Mimi virus (Score:1, Redundant)

    by tcc ( 140386 )
    Let's wait till Drew gets a hold of this :)

  • Now we have to attribute and possibly congradulate the lowest scum of the earth (virus writers) for making possible real artificial intelligence. I can just see these virii as the stepping stones towards self-awareness in computer networks. Who'da thunk it!

  • Doesn't produce own proteins outside of a cell (Score:4, Informative)

    by Bowling Moses ( 591924 ) on Thursday October 21, 2004 @03:59PM (#10591361) Journal
    From the Science article: "Surprisingly, Mimivirus genome sequence now reveal genes relevant to all key steps of mRNA translation: tRNA and tRNA charging, initiation, elongation and termination, with the exception of ribosome components themselves." I'm sure many people knew that when the Nature News link said "Mimi carries about 50 genes that do things never seen before in a virus. It can make about 150 of its own proteins, along with chemical chaperones to help the proteins to fold in the right way." they meant within a host cell, but I'm sad to say I didn't get that right away. I really should have--there's a guy in the lab next door who does EM and crystallography on virus particles so I know that the inside of a virus capsid is ~crystaline DNA or RNA so no protein production would be expected to take place within the capsid itself.

    Mimivirus does contain a lot of weird, weird stuff for a virus, including a number of DNA repair proteins, and truly bizarre, protein folding chaperones and a proline cis-trans isomerase. Doesn't make a damn bit of sense to me, but it'll be interesting to find out why it has them.

    Oh yeah. You know it's news when Science gives you 13 freakin' pages for your stuff as opposed to the usual miserly 3.
    • Mimivirus does contain a lot of weird, weird stuff for a virus, including a number of DNA repair proteins, and truly bizarre, protein folding chaperones and a proline cis-trans isomerase. Doesn't make a damn bit of sense to me, but it'll be interesting to find out why it has them

      Mimi is packed for a long trip. He knows, where he has his towel.
  • For those interested in a bit more background on the Mimivirus (and have access to Science's archives), you can check out the group's previous report on the virus at:

    La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D (2003) A Giant Virus in Amoebae. Science 299(5615):2033

  • Hmmm DNA computer template? (Score:3, Interesting)

    by merlin_jim ( 302773 ) <{James.McCracken} {at} {stratapult.com}> on Friday October 22, 2004 @11:19AM (#10598328)
    Wow this virus is self contained, has 800 kilobase pairs, can replicate its own proteins, uses a circular genome (think of a turing machine tape), and is capable of DNA self-repair, unlike every other organism in the world. And the scientists believe that over 90% of its DNA is actively used throughout its lifecycle.

    Sounds like an ideal building block for a genetic computer. I'm half-seriously wondering based on that 90% figure if it is in fact the left over of some pre-historic genetic computer?

    There are more mysteries here; the virus has genes common to all cellular life, but it itself is clearly not cellular. Unless this virus is a close relative of some precursor virus that initially combined with a bacteria to from the first nucelied cell, then this is an EXTREMELY improbable occurance.

    I mean form follows function, but in this case the form is present but not necessarily the function... parallel evolution doesn't really explain that...

    All the same, if I was a genetic computing microbiologist I'd be very interested in this guy...
    • and is capable of DNA self-repair, unlike every other organism in the world.

      Pardon, but every organism in the world does DNA self-repair. If they didn't there would be almost NO succesful reproduction. von Neumann considered self-repair to be one of the three crucial elements of a self-preproducing machine (the other two are reproduction and self-diagnosis).

      And I'm not sure what you meant, but this virus doesn't replicate its own proteins -- it simply has the instructions for its own proteins encoded in
      • Pardon, but every organism in the world does DNA self-repair. If they didn't there would be almost NO succesful reproduction. von Neumann considered self-repair to be one of the three crucial elements of a self-preproducing machine (the other two are reproduction and self-diagnosis).

        I was unaware of that. However, this is still unique in that its a virus that does DNA self-repair...

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