LINEs dont do RT like ERVs, HIV, or HBV!

Posted by ERV on January 18, 2010
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The only creatures that existed in the RNA World that still exist today, are viruses.

They are the only creatures that still use RNA to store their genome– they never upgraded to V2.0, DNA.

In fact the creatures that might have written V2.0, retroviruses, are still around today too. They carry their genomes as RNA, but convert it to DNA via reverse transcription in order to take advantage of their hosts.

Ive written a bit about reverse transcription before… its kind of a mess to describe… however every retrovirus, from simple retroviruses like Avian Leukosis Virus (only gag, pol, and env) to wildly complex HIV-1 (gag, pol, env, vif, vpu, vpr, tat, rev, nef) to ERVs, they all do reverse transcription the ‘same’ way: Happens in the cytoplasm, tRNA primer starts reverse transcription, RT hops around a few times, badda-bing, badda-boom, dsDNA moves from the cytoplasm into the nucleus for integration.

Hepatitis B, a DNA virus, has evolved a different way to do things– instead of using a tRNA primer to start reverse transcription, it uses the same RNA structure it uses to package its genome into virions to initiate reverse transcription. This might be a new thing, or it might be a very old, leftover thing. But its totally different from the way retroviruses do it.

And then we have non-LTR retrotransposons like LINEs and SINEs. They make up most of that “half your genome is retroviral” thing you hear me say all the time. Chunks of DNA in your genome that proliferate like bunnies. I have LINEs you dont have. You have SINEs I dont have. Aaaand sometimes that leads to trouble (genetic diseases, yay…).

Even though LINEs code for reverse transcriptase proteins (which SINEs steal), ‘just like’ retroviruses, their reveres transcription process is nothing like that of the retroviruses and ERVs we know and love today. Since its not ‘normal’ it gets its own name– Instead of ‘reverse transcription’, their process is called ‘target primed reverse transcription‘.

LINEs code for an mRNA, which is taken to the cytoplasm to be translated into a protein. Halfway through (after the RT protein is made), the rest of the RNA curls up (not translated), and the RT&leftover RNA is carried back into the nucleus. There, it finds/makes damaged DNA– a nick where the leftover RNA can sliiiiide in, and match up with the exposed DNA. A leftover -OH group on that unlucky bit of DNA is used as a primer for reverse transcription. All of the action happens in the nucleus.

The point is, though LINEs/SINEs are retrotransposons, they dont look like anything alive today. What happened to the retroviruses that behaved like LINEs/SINEs? They are extinct, or, at least we havent found one yet. So ironically, the only survivors of their species are ‘mistakes’ that incorporated into germ-line cells. Nestled in the warm confines of our DNA, being passed on vertically from parent–>offspring for millions and millions and millions of years…

I wonder what they used to look like.

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  2. #2 Tyler
    January 18, 2010

    We have some idea of what LINE ancestors looked like: elements called group II mobile introns in prokaryotes and the mitochondria of some eukaryotes. Often they will have RT open reading frames which are related to those of LINEs and they also use TPRT to insert back into the host genome.

    When trees are made using RT sequences group II intron ones and other like those from the Varkud and Mauriceville plasmids come out near the base with those from LINEs branching off next followed by LTR retrotransposons and then retroviruses like HIV.

    It’s starting to look like LTR elements evolved from a fusion between a LINE, with it’s GAG and POL ORFs, and a DNA transposon providing the proto-integrase ORF in the form of its transposase. Then when some LTR elements acquired ENV and could leave the cell things just took off from their and got more complicated.

  3. #3 MadScientist
    January 18, 2010

    Are you a Sid Harris fan? I vote that they look like Rosenblatt. (No, Rosenblatt didn’t discover it, we named it Rosenblatt because it *looks* like Rosenblatt.)

  4. #4 Optimus Primate
    January 18, 2010

    This might be a new thing, or it might be a very old, leftover thing. But its totally different from the way retroviruses do it.

    Ignorant question alert: Is this a solvable problem? I’m wondering if the rapidity of virus speciation (quasi-speciation?) might have erased the clues one would need to look for an answer, or if there just hasn’t been time (or resources) to answer it? And either way, what would it take to reach a sort of reasonable conclusion one way or another (new thing, old thing, or we’ll never know)?

  5. #5 2nd Edition
    January 19, 2010

    Long time reader (I discovered your blog when you were still on blogger), first time poster. These questions have nothing to do with your post, it’s just out of my curiosity. Let’s say that a cure for the HIV (and/or AIDS?) has been found. Would you still continue the same job that you’re doing right now, or would it change in some way? And if it changes in a way that would give you much less work in the future, would you move on to another virus, or become a teacher, or go back to school and learn a new profession? What would happen?

    By the way, I love your blog (the old one and this one) and think you rock. Oh, and contrary to your belief (if you still believe it), you can write (even though I’m not exactly an expert judge in that subject). Keep up the good work.

  6. #6 Bob
    January 19, 2010

    The most common SINE in the human genome is the Alu element. I have always assumed that its origin was that of a pseudogene where a fortuitous placement of an internal promoter allowed it act as a retrotransposon when a LINE’s reverse transcriptase was available. Is there any evidence that a retrovirus was part of Alu’s history?

  7. #7 Captain Skellett
    January 19, 2010

    Retroviruses wrote v2.0? I always thought viruses had to evolve AFTER their host, as they need the host there to replicate. So something must have evolved to use DNA as a more stable genetic code, and then retroviruses evolved later to take advantage of it. Right?

  8. #8 Christina
    January 25, 2010

    I was under the impression that LINEs and SINEs were thought to have originated from within our genome, rather than from external sources?

  9. #9 Dov Henis
    February 24, 2010

    Life IS INDEED An RNA World
    It Has Always Been And Still Is An RNA World

    Genomes Are RNAs-Made Patterns-Manuals

    “Repeats protect DNA”
    http://www.the-scientist.com/blog/display/57135/

    “More On Evolution In The Still RNA World”
    http://www.the-scientist.com/community/posts/list/260/122.page#4818

    Fitting together the pieces of the “still an RNA world” puzzle ?

    - Rational probability and possibility that the initial, independent pre-biometabolism direct sunlight-fueled genes (life) were RNAs, and that earliest genomes were RNA genomes. The RNA genes
    evolved their DNA-images as continuously updated operational worklogs patterns-manuals libraries, and celled and genomed them. They most probably synthesized (and nucleusized) their DNA manuals as their works memory cores, work functional organs, DNA being environmentally stabler than RNA, than themselves. The genomes are functional organs, just as the outer cell membranes are functional organs, of their resident genes.

    - Rational possibility that ALL RNAs represent the original archae-genes that since their (life) genesis have been and still are the primary actors, assessors, messengers, operators of all life processes.

    - Rational possibility that the RNAs are the environmental feedback communicators to, and modifiers of, the genomes, that the RNAs are the effectors of the desirable biased genes expressions modifications, of enhanced energy constraining for survival.

    Dov Henis
    (Comments From The 22nd Century)
    28Dec09 Implications Of E=Total[m(1 + D)]
    http://www.the-scientist.com/community/posts/list/184.page#4587
    Cosmic Evolution Simplified
    http://www.the-scientist.com/community/posts/list/240/122.page#4427