Debunking myths on genetics and DNA

Friday, February 10, 2012

Migrating genes

I've been talking quite a lot about mitochondria lately. The fact that these organelles contain their own DNA (called mtDNA) and were the result of a horizontal gene transfer during evolution is simply fascinating. And I know many of you agree, as proved by the wonderful questions my last post on mitochondria sparked (thank you Hollis and Marleen!)

Plastids, plant organelles that are responsible for photosynthesis, also have a circular, double-stranded DNA molecule (called ptDNA). Like mitochondria, plastids originated through endosymbiosis and, in most plants, are inherited from one parent only. Now, here's another fascinating fact:
"During the early phase of organelle evolution, organelle-to-nucleus DNA transfer resulted in a massive relocation of functional genes to the nucleus: in yeast, as many as 75% of all nuclear genes could derive from protomitochondria, whereas ~4500 genes in the nucleus of Arabidopsis are of plastid descent. Cases of present-day organelle-to-nucleus DNA transfer, revealed by the presence of NUMTs and NUPTs [the fraction of nuclear DNA that derives from mitochondria and plastids respectively], are known in most species studied so far. [...] Mitochondrial chromosomes contain segments homologous to chloroplast sequences, as well as sequences of nuclear origin, providing indirect evidence for plastid-to-mitochondrion and nucleus-to-mitochondrion transfer of DNA [1]."
Throughout evolution transfers of genes between plastids and mitochondria have been documented, although in present organisms these transfers gave rise to non-functional sequences. In plants, the transfer of genes from organelles to nucleus seems to be still active, as documented by the RPS10 gene, which is present in the mitochondria of some angiosperms, and in the nucleus of other plants [Henze and Martin, 2001]. In fact, orgenelle-to-DNA gene transfers have been studied extensively in plants: their cells have both plastids and mitochondria and, as a consequence, they are in general more informative than animal eukaryotes.

In [1], Leister revises studies that show that mtDNA in Homo sapiens integrates continuously into the nuclear genome, as both de novo and pre-existing nuclear insertions of mtDNA have been documented. Recent acquisition of nuclear mtDNA have been documented by comparison with chimpanzee genomes.

So, how do these transfers happen? Though it was originally thought that genes would migrate as RNA transcripts, new studies have shown that it's the DNA itself that "escapes" the organelle:
"Escape of organelle DNA and its uptake into the nucleus has been experimentally demonstrated in yeast and tobacco."
Once these bits of DNA arrive to the nucleus, however, they are subject to a much lower mutation rate than they were in their original location. What this means is that mutations appear more rarely in the nucleus than they do in the organelles. As a consequence, they become "conserved," undergo very little changes, and, at all effects, become "molecular fossils," allowing researchers to retrace phylogenies between species.
"Moreover, nuclear organelle DNA insertion polymorphisms, as a subclass of insertion-deletion polymorphisms, are valuable markers for population and evolutionary studies."
Since the process of migration from organelle to nucleus is a constant one, studies have been directed at measuring the rate of continued colonization of organelle DNA into the germline. The rate in humans has been found to be of the order of 10e-05, and even though these insertions in the past had been thought to be essentially harmless, recent studies have confirmed associations with certain types of hereditary diseases. As I was discussing last week, more studies are in the way to investigate possible associations between nuclear mitochondrial polymorphisms and certain types of cancers.

[1] Leister, D. (2005). Origin, evolution and genetic effects of nuclear insertions of organelle DNA Trends in Genetics, 21 (12), 655-663 DOI: 10.1016/j.tig.2005.09.004


  1. Thank you for this nice post. Present-day transfer of mtDNA to nuclear DNA is new to me and very interesting.
    Recently a paper was published in which the authors demonstrated horizontal gene transfer between different species of plants. It concerned the transfer of whole mitochondria to adjacent cells of another species in a graft. Just by itself this is quite interesting. But knowing that the mitochondrial genes may migrate to the cells nucleus, the story becomes even more interesting. This would mean there might exists HGT between the nucleus (via the mitochondria) of different cells of different species !

  2. Thank you, Marleen. Can you send me the reference of the paper you mention?

  3. EEGiorgi, here you find the paper. I was mistaken: this organelle-transfer is not about mitochondria but about chloroplasts. Nevertheless very interesting.

    1. Thanks so much, I'll check it out! Oh, and I have scheduled a post on how DNA has evolved over time for Monday. Did you know it's not universal?? I'm learning all these cool things and I owe it to you guys!! :)

  4. thank you EEGiorgi for a really wonderful post. This is all soooo crazy and wild, I love it ... but of course it's not really crazy, rather we have been a bit ignorant. But times are changing :)

    I tried to +2 the post, actually I would have +10'ed it, but Google wouldn't let me.


    1. Excellent, Hollis, so glad you enjoyed it and it was useful, makes me very happy!

      And yes, it is crazy and wild, but just because we've been asking the wrong questions and having the wrong expectations... ;-)

  5. Still thinking about gene migration ... Did you see Talmudic Question #84 at All Things Considered? Your discussion of "molecular fossils" prompted me to respond to their interesting question:

    1. Thanks so much for posting the link, Hollis. I seem to remember a paper about the proportion between organism complexity and genome length, but right now I can't think of it... been a long day, will see if it comes back later.

      Again, many thanks!!

  6. BTW, did you know that there's a limit to how high a mutation rate in small genomes 9viruses and bacteria) can be? HIV has a pretty high mutation rate, but if one could tweak it even higher, the tweak would grant the rapid extinction of the viral population. I should find that paper and discuss it, it's quite interesting.


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