Are introns just junk?

birney at birney at
Sun Oct 24 05:57:12 EST 1993

In article <CFDGHs.Jzq at>, John Logsdon <jlogsdon at> writes:

This is part of the running debate of introns early and introns late.
I think it is, as pointed out by John Logsdon, naive to think that
because a couple of proteins seem to have shuffled their exons
in way that makes sense in the domain structure of the protein that
this function explains the presence of introns. The vast majority of
exons, say in duplicated domain proteins do not make sense in a 
protein folding way: it is a neat theory, just doesn't seem to be
backed up with good evidence (In my opinion). 

John Logsdon wrote...
> The phylogenetic distribution of introns is as follows: Introns present
> in large numbers in multicellular eukaryotes (arose ca. <1 BYA), introns
> present in smaller numbers in some single celled euks, such as ciliates
> and slime molds (arose ca. 1-1.5 BYA), introns absent in euks which
> (ancestrally) do not contain mitochondria, and some other early arising
> mitochondriate euks such as Giardia and trypanosomes (arose ca. 2.5 - 1.5
> BYA)., introns absent in all Archaebacteria and Eubacteria (split ca. 3.5
> BYA).

Why no mention of the group II intron in the cyanobacteria? I realise that
the splicesomal introns are a different kettle of fish, but if you 
not too sceptical then there are realistic similarities between the
group II and spliceosomal introns, and not simply a lariat intermeadaite.
The fact now that you see group II introns in cyanobacteria but perhaps
not in other eubacteria is important (here I am ignorant: Does anyone
know how likely a group II intron would have been found in E. coli
or some other bacteria given the current amount of genome that had been
sequenced? Are there good reasons why one might expect a heavy
selection against introns in E. coli and not in cyanobacteria?) 

To further the debate, if we accept an intron late hypothesis as
being introduced sometime around the symbiosis of mitochondria...what
is the function of the nucleus in the ancestral eukaryote? I am asking
this because I think that most people would say that one of the major
functions of the nucleus in eukaryotes is to provide for the extensive
RNA processing, in particular splicing, that goes on.

So here are some more specific questions:

In eukaryotes that have no introns, is there poly A addition to their
mRNAs? Also is the nuclear structure changed compared to splicing
eukaryotes? What to people think the real benefit to having a nucleus
is, if we accept that splicing out introns is not an ancestral function?

ewan birney

birney at

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