Intro to ERVs: **gag**

When I first joined SciBlogs, there were several new readers who didnt get ‘the joke’:

If were made in Gods image, Gods made of gag, pol, and env.

Short explanation: Genomes are full of crap. Crap DNA. No, no not super special DNA front loaded by The Lord to be [insert stupid creationist claim here], I mean crap. Clearly retroviral DNA in humans, just chillin. Old, decrepit gag, pol, and env genes (and promoters/insertional markers, but that makes the joke less catchy :P) which are the basic building blocks of retroviruses.

Thus, if humans are made in the image of a god, that god looks like this.
;)

gag isnt just the noise Creationists make when you bring up endogenous retroviruses, its also the gene that encodes the major structural proteins of retroviruses.


Researchers originally named this gene gag for group specific antigen, because they thought it was a good target for antibodies… but that didnt work out so well (env is actually the main target for antibodies).

Now, one of the super cool features of retroviruses is that they have lots and lots of proteins that have to be expressed at just the right time in just the right amount… But they only have one promoter! One promoter, for sometimes a dozen or more proteins! How do they do it? They have lots of tricks I will go through, but the first way of getting multiple proteins out of one promoter is to transcribe–>translate one great big gene into one great big protein, then cutting that protein up into smaller proteins with different functions. Like making a cake and cutting it into a dozen pieces, rather than making a dozen cupcakes :)

Thats what gag does! ‘gag’ the gene encodes for ‘Gag’ the giant protein, which gets chopped into several smaller proteins, Matrix, Capsid, and Nucleocapsid (and sometimes a few more tiny ones, depending on the retrovirus).

Matrix is the structural protein just inside the envelope (the membrane the virus stole from its host cell). It has ‘outside’ functions (targeting the virus assembly to the right kind of cell membrane, keeping the outside protein, Env, in order) and ‘inside’ functions (targeting the reverse transcribed DNA to the new host cell nucleus). Jack of all trades protein, like lots of retroviral proteins. They run a tight ship.

Capsid
forms the viral ‘core’. Normally when you think of a ‘virus’, you think of this shape, an icosahedron.

Retroviral ‘cores’ really look more like a cylinder-cone-thingie, like the bottom pic here. That particular pic is also worth a second look– More protein cuts to Capsid need to take place after a baby virus buds off from its host cell to make an immature virus mature. Blocking this maturation step is what the next family of anti-HIV-1 retrovirals do. *thumbs up*

Nucleocapsid
is a structural protein that wraps up the retroviral genome to make sure its packaged properly into the Capsid.

**gag** One ‘protein’ chopped into 3 main proteins with very, very different structures and functions.

Comments

  1. #1 SteveWH
    May 27, 2008

    I really like the analogy of making a cake and cutting it into slices rather than making a dozen cupcakes. It would be a good image to use when teaching an intro class.

  2. #2 ERV
    May 28, 2008

    Glad you like it– I almost went with horsey cake instead of cupcakes, but I thought that might be too much :P

  3. #3 Patrick
    May 28, 2008

    I think we need your **gag** on a T-shirt. I know I want one…

  4. #4 EyeNoU
    May 28, 2008

    Thanks for the very educational post.

  5. #5 bunnycatch3r
    May 28, 2008

    Furthermore, if scripture is to be trusted, God is male (has both a penis and a Y chromosome). He is presumeably circumcised. However, it is not certain how that procedure was performed. That’s a question, no doubt, we’ll have to ask when we get to heaven.

  6. #6 Felstatsu
    May 28, 2008

    Why would he be circumcised? Men aren’t born that way, and according to scripture Man was made in His image, but that doesn’t mean that changes to man while in life are also changes to God.

    Even if we take the flying leap of assuming he’s real though, what’s to say he didn’t tell his “chosen people” that just for grins and see if they’d really do it. He could’ve been like “Ain’t nobody gonna do that to my man-bits” after seeing them actually follow through, which surely would be amusing to see some form of real divinity say. We have nothing but what he’s said to determine what sort of god he is, and it’d be trivial for a god to say “trust me, I’m good” even if it wasn’t a good god. The Christian god could really be some grand trickster that doesn’t care about people and want to make his followers look silly, which certainly seems more likely to be true than what the Christian creationists say about him.

  7. #7 laneman
    May 28, 2008

    “I think we need your **gag** on a T-shirt.”

    For research purposes only of course. ;)

  8. #8 Peter Mc
    May 28, 2008

    Felstatu: circumcision is what happened on the eighth day. It got edited out at the Council of Nicaea.

  9. #9 Felstatsu
    May 29, 2008

    Ah, I must’ve missed hearing about that.

    Though I still want to see in some comedy movie or something similar, a representation of that worlds divinity saying the Ain’t nobody quote, more-so if that worlds divinity is a woman with the quote still remaining the same as above.

  10. #10 octopod
    May 30, 2008

    Felstatsu: What, you’ve never heard of the Feast of the Circumcision? Silly Catholics, bowlderizing the church holidays.

    This is an awesome post, ERV. Despite my SCIENCE! degree I don’t know squat about viruses, so this is pretty fascinating stuff.

  11. #11 Torbj´┐Żrn Larsson, OM
    May 30, 2008

    Researchers originally named this gene gag for group specific antigen, because they thought it was a good target for antibodies…

    Actually I hear that they originally named it after the likeness to Klingon Gagh serpent worms, but that it was too tough an act to swallow.

    @ octopod:

    The Christian Catholic Church seems to have a thing for “C” as in Contraceptives (Jesus was born in spite of any), Circumcision (Jesus was roundly circumcised) and Crucifixion (Jesus was happily crucified).

    Silly, as we all know the answer is really “42″.

  12. #12 Ohhello
    March 10, 2009

    Well, ERV, perhaps people didn’t get the joke because the joke is flat out stupid.

    God creating man in His image doesn’t mean our animal bodies, but our souls. You know, that OTHER important belief next to God Himself in many religions?

    And in Abrahamic faiths anyway, the entire idea is to defy our animal nature. Then God sorts out the successful into Heaven and sends those who chose otherwise to Hell.

    Simple. Kids learn this probably on the first day of sunday school. Yet despite being a grad student, this escapes you. Ironic. And raises frightening questions about your competence. Graduate school really does kill your brain.

  13. #13 ERV
    March 10, 2009

    EFG on ERV?

    Win!!

  14. #14 minimalist
    March 11, 2009

    “Oh my god you guys I can’t believe you would be so ignorant as to say that Picard is better than Kirk! *wheeze* *wheeze* Everyone, even little babies know that Kirk kicks ass, how could you even make a so-called ‘joke’ about that?!? *wheeze* *gasp* *inhaler noises* *faaaarrrrrrrt*”

  15. #15 dustbubble
    July 15, 2011

    The link for the retroviral cylinder-cone doobry is whingeing at me

    Reason: The web page address (URL) that you used may be incorrect. It specifies a figure that does not exist.

    URL: http://www.ncbi.nlm.nih.gov/books/NBK19370/figure/A289/

  16. #16 Woden
    July 28, 2011

    dustbubble:

    While I’m pretty sure this isn’t the original image, I think this still shows off the shape of the viral core that she was describing. :)

    http://www.vetmed.auburn.edu/uploads/5e/13/5e1327b915fc8a1932060c4ccf6cb936/Retrovirus.jpg

    If that doesn’t work, then this is the report the above image came from:
    http://www.vetmed.auburn.edu/fiv_feline_immunodeficiency_virus

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    May 30, 2012

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