Re: Dinofarts / Sauropod methane emissions

[Erik Boehm <erikboehm07@yahoo.com>]

"Linear DNA strands are easily thin enough to fit through a nuclear pore,"
Yes, 2nm wide strand, 9 nm opening, but its still going to take a while for it 
to randomly enter - and again, the DNA should get degraded after a while.
Surely it occassionally gets in before it is degraded, but then you have to 
have even more luck for it to be stably maintained in the nucleus.

This paper suggests that DSBs are the primary source of integration:
http://www.ncbi.nlm.nih.gov/pubmed/20168995

This paper would seem to support that:
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Search&doptcmdl=Citation&defaultField=Title%20Word&term=Ricchetti%5Bauthor%5D%20AND%20Mitochondrial%20DNA%20repairs%20double-strand%20breaks%20in%20yeast%20chromosomes.
- But it also shows a function of that import -> Is there now a system to 
actively get the DNA into the nucleus? it is doubtful there was one initially.
I can't find a paper now, but I do recall hearing (from the head of a lab 
working with mitochondria) that there was evidence for a pathway/directed 
import/targeting of mt DNA to the nucleus - a way you could readily induce 
mitochondria to lose their DNA and have it go to the nucleus.

Then you've got this paper
http://www.ncbi.nlm.nih.gov/pubmed/10541855

and this one:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030943

"Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. 
COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of 
mitochondrial encoded reverse transcriptase machinery. Furthermore, these 
reductions correlated with increases in the transcript levels of the nuclear 
loci (MSY1 and RSM7). We propose that these interactions represent an 
inter-organelle DNA mediated communication system and that reverse 
transcription of mitochondrial RNA plays a role in this process."

We have many ways that mtDNA may end up in the nucleus. Many may even perform 
some function, rather than just randomly having mtDNA end up in the nucleus.

Did these possible "communication
to the nucleus? or did they facilitate its transfer?

> "In vertebrates, mitochondria have a modified genetic code. Therefore, mt 
> genes that end up in the nucleus are automatically pseudogenes."

Not necessarily - the code isn't *that* different - and its not just 
vertebrates where mitos have a different genetic code. It would only really be 
automatically a pseudogene if the mito gene uses the "other" met codon as a 
start codon, or if it has a premature stop codon - I haven't looked through all 
17 proteins encoded in the human/mammal genome to see when this would or would 
not cause a premature stop or a late start. Still I suspect your statement that 
it would automatically be a pseudogene is overly broad
(I had a webpage showing all the deviations from the universal genetic code, 
and in which groups they are found, but I can't find it at the moment, I will 
look more if you are interested)
-and of course there is the debate as to what constitutes a "gene" - would you 
not consider the DNA encoding the transcript for an rRNA/tRNA to be a gene? 
they are discrete heritable units with a definite function, but they also don't 
use the "genetic code" (a term I never really liked)

Just because it happens now, does not mean it was happening back then - what 
happens now may actually have a function, even if it is poorly understood. Its 
also a lot easier to transfer a 17kbp DNA sequence, than a 1,000 kbp sequence 
(as the ancestral mito presumably was this size or larger)

There is no hard evidence that it was simply diffusion through the pore 
followed by recombination. It is certainly very plausible, but there are other 
mechanisms that can't be ruled out

I still say we aren't sure of the primary mechanism by which the mtDNA found 
its way to the nucleus. Given the time that has passed, I doubt we will ever be 
able to say with any certainty specifically how it happened.
We can propose many scenarios/mechanisms, and combinations and variations 
thereof.
It is certainly no miracle that it happened.

--- On Wed, 5/9/12, David Mar
anovic@gmx.at> wrote:

> From: David Marjanovic <david.marjanovic@gmx.at>
> Subject: Re: Dinofarts / Sauropod methane emissions
> To: "DML" <dinosaur@usc.edu>
> Date: Wednesday, May 9, 2012, 3:11 AM
> >  Yes, but that doesn't
> answer the mechanism by which it crosses the
> >  nuclear pore, or integrates with the nuclear
> chromosomes.
> 
> Again, it still happens today; numts are common. Linear DNA
> strands are easily thin enough to fit through a nuclear
> pore, and "homologous recombination" (a misnomer) is almost
> universal.
> 
> In vertebrates, mitochondria have a modified genetic code.
> Therefore, mt genes that end up in the nucleus are
> automatically pseudogenes. But that's not the case in many
> other eukaryotes.
> 
> >  The nuclear envelope disappears during mitosis -
> 
> Not in all eukaryotes by far. I don't know what the
> plesiomorphy is.
> 
> >  All of the above?
> 
> Probably all of the above at different points.
>