Re: Spliceosomal introns


"Perplexed in Peoria" <jimmenegay@xxxxxxxxxxxxx> wrote in message news:dt86sc$2u2g$1@xxxxxxxxxxxxxxxxxxxxxx
Those interested in possible functions for at least some junk
and those interested in alternative splicing will probably
find much of interest here. Available free online with
registration. I, unfortunately, haven't read it yet, ...

http://www.nature.com/nrg/journal/v7/n3/abs/nrg1807.html

Review
Nature Reviews Genetics 7, 211-221 (March 2006)

The evolution of spliceosomal introns: patterns, puzzles and progress
Scott William Roy and Walter Gilbert

I've read it now. Interesting indeed. Much of the review is
dedicated to the 'introns early' (IE) vs 'introns late' (IL)
debate. Did this class of introns exist in the Eukaryote common
ancestor (and perhaps even earlier, in the LUCA) or did introns
only appear later in Eukaryote evolution? If IE is true, then
a lot of introns have been lost in some lineages. If IL is
true, then a lot of introns have been gained.

Well, the answer that Gilbert and Roy give is that there has
been massive gain AND loss. Some introns appeared early and
were already there in the ur-Eukaryote; others have appeared
much more recently.

Gilbert seems to think that there is still some life in the idea
of exons = domains. Apparently, if you look just at the class
of introns which seem to be most ancient, there is a strong
tendency for such introns to cleanly separate codons, and even
to cleanly separate protein domains. But the correlation is
not so good for the more recently introduced introns. Old
theories never die. Well, in any case, this theory and Gilbert
himself are probably good for at least a few more years.

Box 1 of the review lists some "selective forces that might
favor introns". At the risk of convincing Larry Moran that I
am an incorrigible adaptationist, I would like to add one more
speculative hypothesis to that list.

I suggest that the function of introns is to convert nucleotide
triphosphates (NTPs) to single stranded RNA and pyrophosphate (PP).
And since the extra useless single stranded RNA is fairly quickly
hydrolysed down to nucleotide monophosphates, and since the PP
is very quickly hydrolysed to P + P, it can be seen that the
net effect of having introns is to catalyze the reaction
NTP -> NMP + P + P
It is that simple. ;-)

Well, explaining why this dissipation of the 'high energy phosphate
potential' might be advantageous may not be so simple. I am
assuming here that the intron transcripts are not exported from
the nucleus, but rather are degraded in place by a ribonuclease.
What I have described is a futile cycle. It is well known that
futile cycles waste energy, but it is less widely appreciated that
they sometimes increase the precision of metabolic regulation.
Some futile cycles, used in moderation, are adaptations.

I claim that introns are common in Eukaryotes because Eukaryotes
have a nucleus. Furthermore, in multi-cellular Eukaryotes, the
total level of transcription and the relative usage of particular
bases in the transcript may vary widely between cell types within
a species. Also, I point out that for transcription to operate
accurately, it is important that a whole variety of ratios be held
relatively constant. Ratios of each of the four NTP/NMP. Ratios
among the four nucleotide species. Electrolyte ratios between
nucleoplasm and cytoplasm.

I won't go into details. In fact, I haven't worked out the details.
In fact, I probably wouldn't understand the details if they were
explained to me. ;-) But I will point out that confirming or refuting
evidence for this hypothesis may be found by looking for positive
or negative correlations between the base content of introns and
exons expressed in different types of cells.

Just an idea.


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