A Truly Alive Virus

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."

Comments

Aha!

[Black Parrot]

Now we know what happened to the missing human genes.

Um, no....

[slowtech]

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.

Re:Um, no....

[Ayaress]

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.

Size?

[tod_miller]

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!! :-)

Re:Size?

[aminorex]

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...

[tod_miller]

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...

Spelling nazi

[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.

Evolution proof ?

[Jesrad]

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 ?

[Anonymous Coward]

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 ?

[Ayaress]

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 ?

[DrKyle]

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 10 years or so ago which could only hold maybe 10 to 15kb which had to be removed from the viral genome first to make space. The idea that a mutation which allows this virus to hold more is a good one. If you have the room to store something, and events such as integration, excision and recombination allow for your genome to increase in size when infecting a cell, then the genome will increase in size. Just like anything in life: glove compartments, houses, hard drives - when you get more space you end up filling it rather quickly.

But to say this virus is, or even could be either evolving towards bacterialhood or evolving away from it is quite ludicrous. Sure, you can have a bacteria with less than 300 genes, but those themselves are forced to live as obligate parasites. Even if this virus did manage to get just the right combination of genes which could allow it to "live" outside of a host, it would be like giving me blueprints to build a radio on a deserted island - useless, the virus doesn't have the machinery to use the information itself.

It's called VIRUSES not virii

[hankwang]

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.

Re:It's called VIRUSES not virii

[FFFish]

Spelling it "virii" is A LOT MORE FUN than sticking to "viruses."

Sheesh. Loosen up some!

A Large Virus Named Mimi

[DLWormwood]

What would Drew Carry think?

Um, yes...

[contagious_d]

"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...

[Idarubicin]

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 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.

Living computer virus

[Knights who say 'INT]

How many people thought this was an interesting AI-based computer virus, perhaps employing genetic algorithms?

Re:Um, yes....

[VendingMenace]

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:What is the plural of virii?

[Anonymous Coward]

The whole sequence of plurality is something like: viri, virii, viriii viriv, virv, virvi, virvii, virviii, virix, virx, virxi, et c.

Doesn't produce own proteins outside of a cell

[Bowling Moses]

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.

Hmmm DNA computer template?

[merlin_jim]

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...