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Thread: A virus in your genome

  1. #1 A virus in your genome 
    Forum Radioactive Isotope skeptic's Avatar
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    From New Scientist, 1 March 2014, page 16

    Many of you will be aware of how retroviruses insert their own DNA into the nucleus of the host cell. Sometimes a molecule of viral DNA in a gamete producing cell is part of a subsequent gamete that develops into a new human. That human, and all his/her descendants will carry the virus DNA molecule in every nucleus of every cell in their bodies.

    The question is whether that alien DNA will be harmful or useful. Well, it turns out that, at least some of the time, it may be useful, and may help drive evolution of new features. An important such new ability is the ability of cells to fuse together. Viruses have DNA to produce a protein that breaks down cell membranes, to eneable a virus to pump its DNA into the cell, and which will later burst the cell apart to release new virus particles.

    Well, it turns out that the virus protein has its uses in human cells also. That virus protein, from a virus DNA, is used to enable a sperm to burst into an ovum. It is used to build skin structures. It is even used to make the human placenta. It has been suggested that this virus DNA was needed for the first multicellular organisms, to enable cells to merge and fuse together.

    How many other genes essential to human existence were gifts from our virus parasites?

    The other thought I have relates to genetic modification. Lots of people have argued that GM is wrong because it is "unnatural". Well, it looks like mother nature has been inserting genes into genomes in this "unnatural" way for billions of years.


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    Mitochondria might be a type of parasite or symbiont inside cells.

    Endosymbiotic theory - Wikipedia, the free encyclopedia


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    Oh dear... don't tell Robbitybob, we'll never hear the end of it.
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    Quote Originally Posted by Daecon View Post
    Oh dear... don't tell Robbitybob, we'll never hear the end of it.
    I've changed my mind a bit lately.
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    Forum Professor Zwirko's Avatar
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    Changed your mind about what?


    That viruses have shaped the human genome or that viruses serve as a test-bed for the evolution of new proteins?


    The first is a respectable hypothesis with a fair bit of evidential support; the second never made any sense.

    -------------



    This is probably the web version of New Scientist article Skeptic was referring to, for those that are interested: Origin of organs: Thank viruses for your skin and bone
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    Quote Originally Posted by Zwirko View Post
    Changed your mind about what?


    That viruses have shaped the human genome or that viruses serve as a test-bed for the evolution of new proteins?


    The first is a respectable hypothesis with a fair bit of evidential support; the second never made any sense.

    -------------



    This is probably the web version of New Scientist article Skeptic was referring to, for those that are interested: Origin of organs: Thank viruses for your skin and bone
    Why didn't it make sense? If viruses are just clogging our genome with junk DNA that is not make benefit in that is there!
    (I'm reluctant to discuss it here sorry for I had previous restrictions applied.)
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    Quote Originally Posted by dan hunter View Post
    Mitochondria might be a type of parasite or symbiont inside cells.

    Endosymbiotic theory - Wikipedia, the free encyclopedia
    But what's interesting about mitochondria DNA is it didn't join with the eukaryote DNA, but is still an independent reproductive process passed through females (in humans).
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    Quote Originally Posted by Lynx_Fox View Post
    Quote Originally Posted by dan hunter View Post
    Mitochondria might be a type of parasite or symbiont inside cells.

    Endosymbiotic theory - Wikipedia, the free encyclopedia
    But what's interesting about mitochondria DNA is it didn't join with the eukaryote DNA, but is still an independent reproductive process passed through females (in humans).
    But is it true that some of the mitochondrial genes have come across but not all of them. I had read this recently (Virolution) and I thought that was quite cunning for then the mitochondria depend on the cell and the cell depends on the mitochondria.
    But I haven't confirmed that as yet.
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    And it was perhaps a poor example, because mitochondria (and chloroplasts) aren't really virus per say but much more complex and bacteria like.
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    Quote Originally Posted by Robittybob1 View Post
    But is it true that some of the mitochondrial genes have come across but not all of them. I had read this recently (Virolution) and I thought that was quite cunning for then the mitochondria depend on the cell and the cell depends on the mitochondria.
    But I haven't confirmed that as yet.

    Yes, mitochondrial genomes have tended to undergo massive genome reduction to produce a streamlined genome. Human mtDNA is only about 17 kb in size carrying 37 genes. All the rest has either been deleted or transferred over to the nuclear genome.
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    I've mentioned the TWiV (This Week in Virology) podcast many times here before. Here's a timely one: TWiV 275: Virocentricity with Eugene Koonin described as "Vincent and Rich meet up with Eugene Koonin to talk about the central role of viruses in the evolution of all life." This one was recorded on video and uploaded to YouTube.

    I'm currently reading a book by Koonin (decided to buy it after reading many of his papers), so I look forward to watching this video myself when I can find the time.
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    Quote Originally Posted by Zwirko View Post
    I've mentioned the TWiV (This Week in Virology) podcast many times here before. Here's a timely one: TWiV 275: Virocentricity with Eugene Koonin described as "Vincent and Rich meet up with Eugene Koonin to talk about the central role of viruses in the evolution of all life." This one was recorded on video and uploaded to YouTube.

    I'm currently reading a book by Koonin (decided to buy it after reading many of his papers), so I look forward to watching this video myself when I can find the time.
    You certainly have to have plenty of time to listen to that, but if you are reading his book then it will be a timely introduction to the author.
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    Quote Originally Posted by Robittybob1 View Post

    Why didn't it make sense?
    As I noted above, it's commonly accepted that viral genes have been recruited for cellular function at various points in evolutionary history. Skeptic, above, referred to the a particularly well known example. Viewing these recruited genes as being somehow tested in viruses first is just the wrong way to approach this phenomenon.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Robittybob1 View Post

    Why didn't it make sense?
    As I noted above, it's commonly accepted that viral genes have been recruited for cellular function at various points in evolutionary history. Skeptic, above, referred to the a particularly well known example. Viewing these recruited genes as being somehow tested in viruses first is just the wrong way to approach this phenomenon.
    We were pretty close though I believe.
    Does tested mean "evolved functionality". If the viral genes are recruited does the function of the genes, when expressed, vary greatly from it role in the host? Example if a bacteria had the enzyme amylase and through some means that gene to produce amylase was introduced into the mammalian host, the enzyme ( the functional protein) it would still have similar biological activity wouldn't it?
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    Amylase was already produced in mammals though, as a product of the pancreas, there was just an alteration of where the amylase was secreted to include the mouth.
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    Quote Originally Posted by Paleoichneum View Post
    Amylase was already produced in mammals though, as a product of the pancreas, there was just an alteration of where the amylase was secreted to include the mouth.
    It might not have been the best example. I didn't know that aspect so thanks for that. The point I was trying to make related to the activity of the gene. Did its function ever change from one species to the next? If it was coding for amylase in a bacterium would it remain as coding for amylase when transferred?
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    To be honest, I don't fully understand what "tested" means in this context. I just used the word because you used it. All you need say is that a particular gene has been determined to have such and such an origin, rather than say it was first tested out in some particular entity. Then you should note that genes don't just flow from virus to host, but also from host to virus - there's been a lot of gene theft out there. Not only of whole genes, but commonly bits and pieces of genes too.


    Amylases are an ancient group of enzymes found in all domains of life - so perhaps not the best example, but I think I understand the underlying point you are making. If some random gene ends up moving from one organism to another then it may well have a similar function in the new organism. Then again it might not since cell type, developmental state, epistatic effects and so on could give rise to a new function.


    Once recruited, evolution doesn't pack up and go home. That gene will continue to evolve along a different trajectory from that in the donor organism. It could eventually give rise to a whole new family of genes. For example, as Paleoichneum noted, alpha-amylase arose from a pancreatic amylase.


    I think the co-evolutionary arms race between virus and host defence systems has shaped evolution more than the recruitment of viral genes. If we widen the scope of things to include all manner of selfish elements - such as transposons and retrotransposons - then I'd guess that these too have had a more profound effect. Here's a table I nabbed from the internet showing genes of viral origin that have ended up in eukaryotic cells (I've no idea how complete it is):



    Syncytin 1 (also known asERVW1) HERV-W (env) Catarrhine primates: humans, apes, Old World monkeys (25–40 million years) Placenta-specific expression, fusogenic activities 142,143
    Syncytin 2 (also known asERVFRD1) HERV-FRD (env) Anthropoid primates: catarrhines and New World monkeys (40–65 million years) Placenta-specific expression, fusogenic and immunosuppressive activities 144
    Syncytin A (Syna) HERV-F or HERV-H (env) Murid rodents (20–30 million years) Placenta formation (layer I of syncytiotrophoblast); placenta-specific expression, fusogenic activities ex vivo 94
    Syncytin B (Synb) HERV-F or HERV-H (env) Murid rodents (20–30 million years) Placenta formation (layer II of syncytiotrophoblast); placenta-specific expression, fusogenic and immunosuppressive activities 95
    Syncytin-Ory1 Type D retroviruses (env) Leporids: rabbits and hares (12–30 million years) Placenta-specific expression, fusogenic activities 145
    Syncytin-Car1 CarERV3 (class I) Carnivores (65–80 million years) Placenta-specific expression, fusogenic activities 146
    ERVV1 andERVV2 HERV-V (env) Anthropoid primates (40–65 million years) Placenta-specific expression, unknown function 147
    Fv1 MuERV-L (gag) (class III) Mus subgenera: mice (5–10 million years) Confer resistance to murine leukaemia virus (MLV), binds MLV capsid 84,85,148
    CGIN1 (also known asNYNRIN) Retrovirus (pol(RNaseH, integrase)*) Therians: placental and marsupial mammals (125–180 million years) Unknown 149
    EBLN1, EBLN2,EBLN3 andEBLN4 Bornavirus (nucleoprotein) Anthropoid primates (40–65 million years) Unknown, but EBLN2 appears to interact with several cellular proteins 4,17,21
    Iris Kanga errantivirus (F-type env) Drosophila melanogaster and obscura subgroups (25–35 million years) Third instar larva- and adult-specific expression, localized to mitochondria 87,150
    *Refers to the section of the gene that encodes RNaseH and integrase.
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    Quote Originally Posted by Zwirko View Post
    To be honest, I don't fully understand what "tested" means in this context. I just used the word because you used it. All you need say is that a particular gene has been determined to have such and such an origin, rather than say it was first tested out in some particular entity. .....
    "Tested" was like asking where does the enzyme get utilized for the first time? My original thoughts on the subject were that the oceans being full of viruses, bacteria and life forms of all types would be the place where proteins are developed through the process of natural selection, and thereafter through various gene transfers they might make their way into multicellular organisms also depending on selection advantage.
    This was basically made possible by the rapidity of the life cycles of viruses and bacteria and the slow long life cycle of say humans.
    From reading a little on the topic it appears that much of our recent evolution appears to be related to having multiple copies of the same genes in our genome or having the right sequence of genes on the chromosome.
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    It's not all that bad of an idea (at least not exactly worthy of the hostility it has received elsewhere) when worded more sensibly. Most of the genetic diversity in the biosphere is marine; and of that, most of it is viral. That is to say, the vast majority of genes that evolution has ever cared to invent are to be found in the virosphere. Pyutting it another way, we could say that they have explored more of the space of functional possibilities than all other organisms combined. Most of this stuff is commonly referred to a "genomic dark matter" because the sequences have no known homologs in the databases and the function of their gene products are not known. What's even more surprising is that this dark matter may only represent the tip of an iceberg, with no real clues as to how large that iceberg might be.


    Genes in viruses tend, by and large, to be concerned with replication, transcription, encapsidation, and in subverting host defences. Using amylase as an example, it'd be hard to imagine a scenario in which a virus would ever evolve amylase. What good would it do them? I have no doubts that viruses have major roles to play in the biosphere and have been key players in shaping the evolution of ourselves as well as all other cellular organisms. No doubt also that horizontal gene transfers between all players has been rampant too.



    Quote Originally Posted by Robittybob1 View Post
    From reading a little on the topic it appears that much of our recent evolution appears to be related to having multiple copies of the same genes in our genome...
    Gene duplication is thought to be a major source of new genes, at least in the past. They are not brought in to the cell by viruses (although viruses and selfish elements may be indirectly involved in a roundabout fashion).
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    Quote Originally Posted by Zwirko View Post
    It's not all that bad of an idea (at least not exactly worthy of the hostility it has received elsewhere) when worded more sensibly. Most of the genetic diversity in the biosphere is marine; and of that, most of it is viral. That is to say, the vast majority of genes that evolution has ever cared to invent are to be found in the virosphere. Pyutting it another way, we could say that they have explored more of the space of functional possibilities than all other organisms combined. Most of this stuff is commonly referred to a "genomic dark matter" because the sequences have no known homologs in the databases and the function of their gene products are not known. What's even more surprising is that this dark matter may only represent the tip of an iceberg, with no real clues as to how large that iceberg might be.


    Genes in viruses tend, by and large, to be concerned with replication, transcription, encapsidation, and in subverting host defences. Using amylase as an example, it'd be hard to imagine a scenario in which a virus would ever evolve amylase. What good would it do them? I have no doubts that viruses have major roles to play in the biosphere and have been key players in shaping the evolution of ourselves as well as all other cellular organisms. No doubt also that horizontal gene transfers between all players has been rampant too.



    Quote Originally Posted by Robittybob1 View Post
    From reading a little on the topic it appears that much of our recent evolution appears to be related to having multiple copies of the same genes in our genome...
    Gene duplication is thought to be a major source of new genes, at least in the past. They are not brought in to the cell by viruses (although viruses and selfish elements may be indirectly involved in a roundabout fashion).
    It is a topic that has caught my attention, and I'm still going to follow up on the amylase issue, for it appears that I was put wrong when I first read about it, when they said it originated in a bacterium. I have read that plants can get genes laterally transferred to them via a type of bacterium. Look no one has suggested how a bacterial gene can make its way into a multicellular organism but I thought naively at the time it could be a viral event, but I have no evidence for this other than the fact because viruses infect all types of cells it seems that any linkage is possible given the right amount of time.

    Do you know of a mechanism for bacterial genes to get across to mammals?
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    [QUOTE=Robittybob1;537488]






    Quote Originally Posted by Robittybob1 View Post

    Do you know of a mechanism for bacterial genes to get across to mammals?
    In theory, any gene can get from any multicellular organism to any other. The vector is a retrovirus, which infects organism A, and picks up a gene from organism A. That retrovirus then infects organism B, and passes the gene into the nucleus or a gamete, which in turn becomes part of a new generation.

    For example : rattlesnake genes have been found in gophers.

    I am not sure how widespread this process may be. Could a retrovirus that infects a tree also infect a mammal? I don't know. Bacterial genes can get into plants, because the bacterium called Agrobacterium​ is able to carry its genes into plants. Could that gene be passed by a retrovirus to a mammal? Not sure, since I do not know if that virus could infect both plant and animal.
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    Once again, skeptic is posting threads with no question or fundament in it. Don't just go around throwing topics like that
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    [QUOTE=skeptic;537508]
    Quote Originally Posted by Robittybob1 View Post






    Quote Originally Posted by Robittybob1 View Post

    Do you know of a mechanism for bacterial genes to get across to mammals?
    In theory, any gene can get from any multicellular organism to any other. The vector is a retrovirus, which infects organism A, and picks up a gene from organism A. That retrovirus then infects organism B, and passes the gene into the nucleus or a gamete, which in turn becomes part of a new generation.

    For example : rattlesnake genes have been found in gophers.

    I am not sure how widespread this process may be. Could a retrovirus that infects a tree also infect a mammal? I don't know. Bacterial genes can get into plants, because the bacterium called Agrobacterium​ is able to carry its genes into plants. Could that gene be passed by a retrovirus to a mammal? Not sure, since I do not know if that virus could infect both plant and animal.
    Are you talking about a double mistake?
    Like the virus picks up a gene by mistake and passes it onto another host it doesn't normally infect. The chances of that double mistake occurring with a single virus particle and the n to infect the gametes with at stray gene seem so extreme. I tend to think there would have to be some intermediary process. (Purely hypothetical)
    Like a tree has a gene.
    A insect lives in the tree and has a bacterium that infects both the tree and the parasite.
    Birds eat that insect and get infected with a retrovirus that infect both.
    So a tree gene could be transmitted via a parasite and viruses, but because there is a life cycle involved there are repeated chances for the transfer event to happen.


    I had read about Agrobacterium and it ability to transfer DNA to plants. Are there other bacteria that could do this?
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