Re: Why don't mitochondria have junk DNA?


John Harshman wrote:
> rev.goetz wrote:
>
> > John Harshman wrote:
> >
> >>rev.goetz wrote:
> >>
> >>
> >>>John Harshman wrote:
> >>>
> >>>
> >>>>rev.goetz wrote:
> >>>>
> >>>>
> >>>>
> >>>>>John Harshman wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>>Selection for fast replication? That's the usual idea for bacteria, but
> >>>>>>do mitochondria have to replicate that often compared to the nucleus of
> >>>>>>the same cell? That would depend on the lifetime of a mitochondrion and
> >>>>>>its standing population in the cell. I'll have to look that up.
> >>>>>>
> >>>>>>If not that, then what?
> >>>>>>
> >>>>>>There are mitochondria with junk. In fact the control region has been
> >>>>>>duplicated several times in different groups of birds, and one of the
> >>>>>>copies is clearly non-functional. So it does happen. But why so rarely?
> >>>>>
> >>>>>
> >>>>>Junk DNA is an extavagant byproduct of evolutionary processes because
> >>>>>the rate of neutral mutational insertions from various types of
> >>>>>repeated sequences appears to be significantly more frequent than the
> >>>>>fixation rate of all mutational deletions. And I recall that only
> >>>>>diploid cells have the mechanisms that generate various types of
> >>>>>repeated sequences. (I do not have the time to look up the reasons for
> >>>>>this.)
> >>>>
> >>>>You would seem to be talking about unequal crossing over. That's only
> >>>>one of a host of processes that generate new sequences.
> >>>
> >>>Unequal crossing over is only one of a few mechanisms that help to
> >>>generate non-coding DNA in eukaryotes.
> >>
> >>It's the only one I know of that relies on diploidy.
> >>
> >>
> >>>>>Concerning some junk DNA in mitochondria, this could have occurred by
> >>>>>DNA transfer from the nuclear genome to the mitochondrial genome. I am
> >>>>>not sure if I have heard of cases of DNA transfer from the nuclear
> >>>>>genome to the mitochondrial genome, but I know that I heard of several
> >>>>>examples of gene transfer from the mitochondrial genome to the the
> >>>>>nuclear genome. So I would not be surprised to see if the reverse ever
> >>>>>happened.
> >>>>
> >>>>I don't know of any such case. Like I said, the only mt junk I know of
> >>>>involves a duplication of a mitochondrial region.
> >>>
> >>>I missed that you said it was a duplication of a mitochondrial region,
> >>>so scratch what I said about DNA transfer from the nuclear genome to
> >>>the mitochondrial genome.
> >>>
> >>>In general, mutational insertions/duplications are more likely to occur
> >>>in eukaryotes compared to prokaryotes. And as someone said earlier in
> >>>this topic, many eukaryotes are not harmed by an accumulation of DNA in
> >>>the genome. So many insertions/duplications are neutral in terms of
> >>>fitness in many eukaryotes, but in many prokaryotes a large increase in
> >>>genome size causes a decrease in fitness. So natural selection prevents
> >>>a large increase of "useless DNA"in many prokaryotes.
> >>
> >>As I theorized at the outset. But can this possibly apply to
> >>mitochondria? Larry's mechanism obviously can't, since mt genomes are
> >>tiny by comparison with bacterial genomes. The other suggested
> >>mechanism, selection for speedy replication, also would seem not to be
> >>that strong in mitochondria, though that would depend on their
> >>population genetics. I really have to dig this up and read it again:
> >>Birky, C. W., Jr. 1991. Evolution and population genetics of organelle
> >>genes: Mechanisms and models. Pages 112-134 In R. K. Selander, A. G.
> >>Clark and T. S. Whittam (eds), Evolution at the Molecular Level. Sinauer
> >>Assoc., Sunderland, MA.
> >
> >
> > Even though mitochondria has a small genome size compared to
> > prokaryotes, natural selection favoring a compact genome could still be
> > the primary force that keeps it compact. For example, we know by theory
> > that mitochondria ancestors once had a complete prokaryote genome when
> > they were prokaryotes. And I conjecture that natural selection favoring
> > compactness helped to reduce the mitochondrial genomes to their current
> > sizes. And I see no reason why anything else but natural selection
> > favoring compactness would be needed to keep the mitochondrial genomes
> > near their current sizes.
> >
> > On the otherhand, I know nothing about "selection for speedy
> > replication" so I cannot comment about that.
>
> It's a form of selection for compactness. Unless you can suggest a
> reason why compactness would be selected, all you are saying is that
> selection produces whatever you happen to see, i.e. you are falling
> victim to the panglossian paradigm. I'm saying that I have trouble
> figuring out a reason why compactness (one or two orders of magnitude
> more compactness than in a bacterium) should be selected here.
>
> No selection is required in order for mt genes to be transferred to the
> nucleus, by the way. Just 1) transfer of a functional copy of a mt gene
> into the nucleus followed by 2) decay of the mt copy, no longer
> maintained by selection.

Yes, no natural selection is required. Neutral theory helps to explain
this. On the other hand, the hierarchal transfer of ribosomal protein
small unit (_rps_) genes from mitochondrial genomes to nuclear genomes
most likely resulted from natural selection because the hierarchy
relates to the importance on the functional importance of respective
the _rps_ genes.

.

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