Thursday, August 11, 2011

Retrotransposons/Endogenous Retroviruses

 
RNA viruses are viruses that contain RNA instead of DNA. When the RNA molecule is injected into the cell it serves immediately as a template for translation. All RNA viruses have genes for making new viral particles and new copies of the RNA genome.

In eukaryotes, there is a large class of RNA viruses known as retroviruses. They have an obligatory stage where the RNA is reverse transcribed into DNA and the DNA is inserted into the genome where it resides as a provirus.

The structure of the integrated retrovirus genome is shown above. The ends of the viral genome contain long terminal repeat (LTR) sequences of several hundred base pairs. Both LTRs are arranged in the same orientation and the outside ends of each are flanked by short inverted repeats. The host DNA at the site of the insertion contains a short (5- bp) repeated sequence that is produced on integration as in transposons [Transposons: Part I].

There are three open reading frames (ORFs) in the retrovirus genome. One of these encodes a protein called gag that's involved in packaging the retroviral RNA in the virus particle. The gag protein is cleaved after translation to produce a number of individual proteins.

The pol ORF (gene?) encodes another polyprotein that is cleaved to produce reverse transcriptase, integrase, and a protease. The key enzymes are the reverse transcriptase, which copies RNA into double-stranded DNA, and integrase, which catalyzes the insertion of retroviral DNA into the host genome.

The third ORF encodes the coat proteins of the mature viral particle.

All eukaryotic genomes contain integrated retroviruses. Some are still capable of producing new viral particles under the right conditions while others have become defective over the course of millions of years of evolution. The defective retrorvirus genomes are a kind of pseudogene. Collectively they are known as endogenous retroviruses. [See ERV.] About 8% of mammalian genomes consists of defective retroviruses [What's in Your Genome?].

A common class of eukaryotic transposons is derived from retroviruses. These retrotranspsons contain the pol gene for reverse transcriptase and integrase and usually part of the gag gene that encodes a protein that interacts with DNA. When the transposon is transcribed the reverse transcriptase converts the RNA into double-stranded DNA and the integrase allows it to be inserted into the genome. Like many other transposons, these retrotransposons are examples of selfish DNA whose only "function" is to propagate itself within the genome [Transposons: Part II]. The yeast Ty element and the copia transposon of Drosophila melanogaster are the classic examples of retrotransposons.


The key features of these transposons are the pol gene and repeat sequences at the terminii. These repeats are usually called LTRs as in retroviruses but sometimes the have a different name. The yeast Ty repeats are called δ elements. Those features are all that are necessary for these genes to propagate in the genome.

Unlike the transposons described earlier, the retrotransposons do not excise from the genome in order to jump to a new spot. Instead, the existing transposon sequence is transcribed and then a DNA copy of the transcript is re-inserted. Thus, the number of retrotransposons increases whenever a new integration occurs.

There are about 35 copies of the Ty transposon in the genomes of most strains of yeast. In addition, there are many copies of defective transposons containing pieces of the original intact Ty element. The typical fruit fly genome has about 100 copies of copia and about 5000 copies of all types of retrotransposons. Many of these are defective and they contribute to a substantial percentage of the junk DNA in the Drosophila genome.


29 comments :

  1. Matthew Meselson posits that the major evolutionary driving force for sexual reproduction is the recombinagenic knockdown of retrotransposon copy number.

    -AJP

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  2. Like many explanations of sex, that one postulates that sex arose for some future benefit to the species and not because of an immediate selective advantage for the individual. That's why it's not one of the leading contenders in the field.

    Meselson is a brilliant scientist but I think he's wrong on this one.

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  3. I would query the figure of 1% - isn't it closer to 8% of our genome that's made up of ERVs?

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  4. Is the mechanism for limiting Ty elements in yeast known? Why aren't there hundreds or thousands of copies?

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  5. Matthew Meselson posits that the major evolutionary driving force for sexual reproduction is the recombinagenic knockdown of retrotransposon copy number.

    How do prokaryotes deal with retrotransposition? They seem to keep very lean genomes, while eukaryotes seem broadly unconcerned by huge amounts of crap. I don't think there is likely to be strong pressure in this direction - and it conflates the origin of sex (ie syngamy) with that of homologous recombination, which are unlikely to have been contemporary events.

    Bloated eukaryotes were not outcompeted by lean prokaryotes, while every eukaryote investigated has ancestral meiosis genes and junk: recombinational sex seems more a cause of genome inflation than a cure.

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  6. anonymous says,

    Is the mechanism for limiting Ty elements in yeast known? Why aren't there hundreds or thousands of copies?

    The yeast genome is very compact. Almost every insertion is going to be lethal.

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  7. Allan Miller says,

    ... it conflates the origin of sex (ie syngamy) with that of homologous recombination ...

    In the scientific literature, the origin of sex is intimately connected to the origin of homologous recombination. Syngamy is something that evolved much later. Many species of bacteria, for example, have sex (conjugation) but not syngamy.

    Bloated eukaryotes were not outcompeted by lean prokaryotes, while every eukaryote investigated has ancestral meiosis genes and junk: recombinational sex seems more a cause of genome inflation than a cure.

    In a haploid organism, recombination between two homologous regions (e.g. transposons) in different parts of the genome will often be lethal. This isn't as much of a problem in diploid organisms.

    BTW, recombination isn't confined to meiosis. I'm sure you know that but I just want to make sure that other readers aren't confused by your reference to meiosis.

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  8. "Unlike the transposons described earlier, the retrotransposons do not excise from the genome in order to jump to a new spot. Instead, the existing transposon sequence is transcribed and then a DNA copy of the transcript is re-inserted. Thus, the number of retrotransposons increases whenever a new integration occurs."

    What is the evolutionary value of that process? In other words what benefit does the cell gain from that activity? And if it gains none, why does it occur?

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  9. Allan Miller says,

    ... it conflates the origin of sex (ie syngamy) with that of homologous recombination ...

    Larry says:

    In the scientific literature, the origin of sex is intimately connected to the origin of homologous recombination. Syngamy is something that evolved much later.


    This is precisely why there is such confusion over sex. If you lump bacterial conjugation with eukaryotic syngamy, and eukaryotic homologous recombination with that occurring during transduction, that's fair enough, but one needs to remain clear that one may be looking at two completely different processes that look a bit similar and have similar names. A common logical fallacy is to draw the conclusion that their similarities demand some consistency of explanation at their heart.

    Let's be clear: sex in eukaryotes is a cycle, consisting of syngamy and reduction - haploidy and diploidy in alternation. That's all it is, whatever bacteria do. As an optional extra, immediately prior to the division step, there may be homologous recombination between the diploid elements. This second process is nested within the first, and cannot occur without it. There is no particular reason to suppose that this cycle arose from some prior bacterial precursor - except inasmuch as the repair of meiotic DSB's is mediated by many derivatives of bacterial pathways - basic DNA management is ancient.

    The world won't go with me, but I'd prefer a different nomenclature: stop calling bacterial genetic exchange sex, and using the same name for whole-chromosome recombination in diploids as is used for fragments (up to whole chromosomes) in prokaryotes. Completely different phenomena.

    Larry wrote

    BTW, recombination isn't confined to meiosis. I'm sure you know that but I just want to make sure that other readers aren't confused by your reference to meiosis.

    This illustrates the point well. The kind of recombination I am referring to - the recombination that evolved as a part of meiosis - is confined to meiosis! Homologous-recombination-between-diploid-chromosomes, to be explicit. Haploids evidently have the means to recombine homologous regions on both the same and in different DNA fragments, and it is evident that these mechanisms provided much of the toolkit that enables alignment, resection, ligation etc within meiosis. The doesn't mean that syngamy arose as an enhancement to some ancestral mechanism of recombination.

    As far as eukaryotic sex is concerned, syngamy/reduction is the basic process, with recombination immediately preceding reduction if it occurs. They may have been contemporary, but my own view is that theories demanding that syngamy evolve in order to perform recombination on the united chromosomes are incorrect.

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  10. anonymous asks,

    What is the evolutionary value of that process? In other words what benefit does the cell gain from that activity? And if it gains none, why does it occur?

    We know a lot about the process in bacteria. In fact there's a whole book about it (The Genetic Switch). The virus integrates into the genome when the cells are starved for nutrients. When the cell encounters a richer environment the virus pops out and make lots and lots of new viruses (and kills the cell).

    In the case of retroviruses, the integration allows the virus to produce produce a low level of new virus particles over a long period of time—years in the case if HIV. The only way the virus can remain in a stable state for such a long time is to copy its genome into DNA and hide in the cell's chromosomes.

    The cell gets nothing out of it. This is all for the benefit of the virus.

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  11. "The only way the virus can remain in a stable state for such a long time is to copy its genome into DNA and hide in the cell's chromosomes."

    Does this mean it knows that by copying itself into DNA and hiding in the cell's chromosomes?
    That would mean that it knows a beneficial future state and aims for it.
    That would be contrary to evolution theory.

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  12. anonymous the IDiot says,

    Does this mean it knows that by copying itself into DNA and hiding in the cell's chromosomes?
    That would mean that it knows a beneficial future state and aims for it.
    That would be contrary to evolution theory.


    How stupid of me not to have realized that retroviruses refute evolutionary theory!

    What church should I join?

    (There's a remote possibility that you actually want to understand evolution so why don't you read The Genetic Switch. It explains exactly how bacteriophage lambda evolved to see into the future.)

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  13. Moran posted:
    "How stupid of me not to have realized that retroviruses refute evolutionary theory!
    What church should I join?"

    When Moran is stuck he becomes a little over the top.

    And I wish I had a dollar for every time someone who was stuck, points to some book rather than give an answer himself.

    I am still interested in an answer to my question, so if there is someone here who can answer it please do.

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  14. anonymous the IDiot asks,

    I am still interested in an answer to my question, so if there is someone here who can answer it please do.

    I devoted ten pages and 15 figures to explaining the basic biology of bacteriophage λ in my 1994 textbook. I then devoted an additional 6 pages and 6 figures to explaining the genetic switch.

    This is basic molecular biology that's covered in most high quality gene expression courses.

    Nobody is going to try and teach that stuff to you in the comments section of Sandwalk for 2 reasons.

    (1) It would take too much time.

    (2) You won't believe it anyway.

    Your history here reveals that we are wasting our time trying to teach you anything. You do not want to learn.

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  15. There are a relatively small set of excuses for not answering questions. I have heard them all.
    When people are stuck they sometimes give the kind of answer that Moran has given.
    And each time they think it is fresh and original.

    Let's think for a moment.
    EVERY question that is asked always has a huge amount that could be said about it. That is simply a fact.
    And yet people answer questions all the time.
    It is only when someone cannot answer a question that they fall back on the kind of predictable dodge that Moran has given.

    The simple fact is that the question I have asked is not answered anywhere.
    What is described at length in textbooks is the PROCESS that is observed.
    But that is not an answer to the kind of question I have asked.

    For example, it is a principle of evolution theory that EACH small change must have survival value.
    The retrotransposon we have been talking about goes through a huge number of steps before it arrives back in the genome where it is of any value.

    Nobody has ever shown how the intermediate steps are valuable.
    If you think someone has specifically shown the value of intermediate steps, then please give a reference. And not a general reference to a textbook that only describes the PROCESS.

    The fact is that the intermediate steps are of no value and the presence of retrotransposons contradicts evolution theory.

    This is not a religious or ID argument. This is a scientific question.

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  16. "The only way the virus can remain in a stable state for such a long time is to copy its genome into DNA and hide in the cell's chromosomes."

    Does this mean it knows that by copying itself into DNA and hiding in the cell's chromosomes?
    That would mean that it knows a beneficial future state and aims for it.
    That would be contrary to evolution theory.


    I'll play. The only elements that have remained stable are those that have copied themselves into the chromosomes. They didn't know it would work but - by golly, it did! Those lacking that insertional capacity are no longer around.

    Compare this: "the only objects that can pass through the sieve are smaller than a threshold size". "Does that mean they know that by being small they get through?"

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  17. Hi Allan Miller.
    How do you respond to my post about the intermediate steps.
    Are you saying that EACH step of that long complicated process aids survival?

    Do you see that it is no help concerning just the final step to simply say:
    "They didn't know it would work but - by golly, it did! Those lacking that insertional capacity are no longer around."

    Do you acknowledge the problem?
    It is a scientific question.

    If anyone else acknowledges the problem, what do you say?

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  18. Allan Miller writes:

    I'll play.

    Ah, you must be new here. :-)

    Anonymous never admits any of his questions have been answered. One of my favorites was his insistence that no one could successfully show the common ancestors of apes and humans hadn't all starved to death for lack of a vital nutrient in their diets. The fact that there are currently apes and humans didn't seem to impress him as an adequate response.

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  19. @Anonymous

    Are you suggesting that if I can’t provide, to your satisfaction, a plausible pathway, then evolutionary theory has a problem? Or if I can’t find someone who can? Nah, you need to find something that can’t be explained by naturalistic processes, not something that hasn’t been. There are many unexplained issues in biology, which is why it continues to be an active science. It’s no good whining that ET is therefore unfalsifiable, because somehow it is not destroyed by the existence of such uncertainties in specific instances. If you want to falsify it, you are free to try, but you need to understand the difference between facts that contradict theory and those (such as unknowns) that are completely silent on the matter.

    But the matter of becoming incorporated into a genome is a relatively straightforward one – and nothing much to do with evolutionary theory per se. Reverse transcriptase will construct double-stranded DNA from a single-stranded RNA template. The virus does not need to ‘invent’ a RT of its own; it merely needs to incorporate an existing RT gene from a host within its viral sequence. This happens entirely by accident – but the virus resulting from such an accident has hit the evolutionary jackpot. Genomes abound with such skulduggery, and countermeasures that have been selected for. ‘Conventional’ genomes are probably where viruses came from in the first place. There are mobile genetic elements that never leave the cell, but still construct a protein coat as they jump from one part of the genome to another. The cell defends itself against such activity, and the proto-virus responds by disguising or protecting itself. So a proto-virus can actually ‘practice’ insertion without having to go the whole hog. It starts off simply being retrotransposed around the genome. It acquires a coat that protects it from the cell’s own defences against such damaging behaviour. It then only needs such an element to ‘go viral’ – to exit the cell with its coat on, and the means of subsequent infection incorporated within it – to make a brand new disease. In this scenario, genome insertion is the first step, not the last.

    Or do you think that HIV was intelligently designed?

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  20. Hello Allan Miller.
    Before I respond at length to your post, can I suggest that when you say "exit the cell" you mean exit the nucleus.
    Do we agree on that?

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  21. @Jud

    Allan Miller writes:

    I'll play.

    Ah, you must be new here. :-)


    :0)

    Not entirely unfamiliar with this kind of approach - reminiscent of a recent debate relating to the impossibility of bipedal evolution due to the superior tree-climbing ability of competitive proto-chimps!

    However, I have my deflector shields up - if Senor Anonymouse doesn't get the point, someone else might. And if no-one does (because I have no point, or I express it badly, or I'm wrong), then I quite enjoy the process of articulation anyway. I might learn something!

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  22. Allan Miller writes:

    ...I quite enjoy the process of articulation anyway. I might learn something!

    Have at it, then, though I would advise for the process of sharpening one's mental equipment, steel (Dr. Moran) works better than a blunt object (Anonymous).

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  23. Very good and informative post, but I feel a surge of pedantry compelling me to quibble with the second sentence: Dr.Moran writes "When the RNA molecule is injected into the cell it serves immediately as a template for translation"- this is the case only for +sense single stranded RNA viruses (Baltimore class IV, e.g. rubella, polio). For viruses of this class, the naked viral genome injected into a cell can therefore produce an infection.
    However two other classes of RNA viruses, double stranded (class III, e.g. rotavirus), and -sense single stranded RNA viruses (class V, e.g. Influenza) must go through some additional step(s) before a viral mRNA molecule is produced that can be translated is produced. Indeed the retroviruses (class VI) do not produce viral proteins until mRNAs are transcribed from the integrated provirus using the polymerase provided by the host.
    Of course Dr.Moran is more knowledgable about all this than me. I just felt that the first paragraph might divert readers from the fascinating diversity in the processes by which RNA viruses produce proteins and new virions.

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  24. Hello Allan Miller.
    Before I respond at length to your post, can I suggest that when you say "exit the cell" you mean exit the nucleus.
    Do we agree on that?


    Not really. In order to exit the cell, a sequence that is integrated into nuclear DNA must of course exit the nucleus (in those organisms that have a nucleus). But for a sequence to act as a virus, it must exit the cytoplasm as well.

    For any DNA sequence, 'success' is a matter of survival and copying. If a short boxed sequence contains a reverse transcriptase and an integrase, then it has the basic means to increase its copy number within its present genome. It's not a virus. Its path into the future is still via replication of its host genome. Therefore, there is selection to moderate the disruptive effects of the sequence on organismal fitness.

    But if the virus 'discovers' independent transmission, by capsid protection, cell rupture, and infectivity, then it is uncoupled from fitness effects on the genome, other than the need to keep a host alive long enough to make virus copies. It's classic parasitism, little different in principle from those lovely little (designed?) wasp grubs that consume paralysed larvae from the inside out before bursting forth.

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  25. Hello Allan Miller.
    I am talking about retrotransposons.
    You seem to be talking about retroviruses.
    Are you assuming that all retrotransposons began life as a virus?

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  26. Hello Allan Miller.
    I am talking about retrotransposons.
    You seem to be talking about retroviruses.
    Are you assuming that all retrotransposons began life as a virus?


    No. I’m suggesting that some retroviruses may have begun life as retrotransposons.

    I came into the discussion in response to this:

    "The only way the VIRUS can remain in a stable state for such a long time is to copy its genome into DNA and hide in the cell's chromosomes."

    Does this mean it knows that by copying itself into DNA and hiding in the cell's chromosomes?
    That would mean that it knows a beneficial future state and aims for it.
    That would be contrary to evolution theory.”


    You were wondering how a VIRUS might know how to disguise itself, and how the steps may have emerged in evolutionary sequence. I gave you an answer. Or perhaps that was a different Anomymous. In which case, how do you propose to have a rational discussion, if you won’t even assume a nom-de-guerre?

    Ultimately ... I don’t know WHAT you’re talking about. And this ain’t the place to do it. Larry has been obliged to moderate comments due to the actions of some religiously-motivated knobhead(s). This, in conjunction with the inability of people to identify themselves, renders it an inappropriate forum for such a back-and-forth discussion. Someone Anonymous, maybe you , maybe someone else asked a question about viruses, and how their ability to hide in DNA might be explained in stepwise, evolutionary terms. I did that. You want to know more, subscribe to my correspondence course, $100 a module.

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  27. Allan Miller, we have had an honest misunderstanding.
    But if you feel better by venting your spleen, then so be it.

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  28. @Anonymous

    I apologise for my terseness. The issue is that retrotransposons and retroviruses are not radically different entities - they are both simply bounded segments of DNA containing within them the means to propagate by reverse transcription and integation. The difference is simply in the boundaries that they are able to transgress in propagating - transposons are condemned to a "germ line" fate, ultimately depending on the organism's reproduction to survive. Viruses can transcend that fate through virulence, creating packaged infective particles that do not need the host genome to reproduce. But they use fundamentally the same mechanisms to reverse transcribe and integrate into genomes.

    Effectively, there is two-way traffic - a retrotransposon can become a retrovirus, and vice versa, due to the acquisition and loss of the components of virulence. Furthermore, bits of each can be swapped between virulent and non-virulent entities as they meet up in genomes. Genomes form an 'environment' for these elements, and they prosper by their ability to exploit it.

    We can look at the sequence homology of the elements and construct evolutionary trees that give a complex, but resolvable history. It depends on your take on sequence homology. Evolutionists take the reasonable position that sequence homology indicates commonality of origin. You might think that it only indicates commonality of 'purpose'. I don't think, if you were to delve deeper, that you would find that position sustainable.

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