Thermotoga maratima

Jonathan A. Eisen jeisen at leland.stanford.edu
Sat Dec 2 17:20:31 EST 1995

In article <DIz2nG.H09 at zoo.toronto.edu>, mes at zoo.toronto.edu (Mark
Siddall) wrote:

> In article <jeisen-0112951330230001 at bio-pch9.stanford.edu>
jeisen at leland.stanford.edu (Jonathan A. Eisen) writes:
> >However, there are many reasons why SS-rRNA trees should be good
> >including: lack of parology, low likelihood of lateral transfer, the
> Lack of parology??????
> Are you serious?
> In a gene that has so many copies in the genome?
> In a gene that is known to be subject to concerted evolution to the 
> extreme??
> There is (I suspect) much paraology that is cryptic due to the lineage
> sorting that homogenization effects.

Yes Mark I was serious, but I only meant to refer to rRNA gene evolution
within bacteria.  I will try to clarify what I meant by lack of paralogy. 

In the traditional sense, paralogous genes are those genes which have
diverged after a duplication event (e.g., alpha globins versus beta
globins).  In contrast orthologous genes are those which diverge after a
speciation (e.g. beta globin in humans versus beta globin in mice).  In
the bacteria, although rRNA genes are present in multiple copies, they are
all essentially identical to each other (e.g. in E. coli there are 7 rRNA
operons and although there are differences in the flanking regions and
spacers between the operons, the actual coding regions are identical (or
nearly so) between the different operons).  Thus, although duplication and
gene coversions within a species may make rRNA gene evolution somewhat
different from evolution of other genes, since the homogenization of rRNA
genes appears to be very rapid (at least in bacteria), rRNA genes
essentially evolve in a similar manner to single copy genes (that is, they
can diverge between lineages but not within a lineage).  In contrast,
truely paralogous genes would diverge within a single lineage.

Whether or not paralogy of rRNA genes is a problem for eukaryotes is a
different question (Since the discussion was about Thermotoga I was
writing only about bacteria but my statement implied I meant rRNA genes in
everything).  I would suspect that with the 1000s of rRNA genes within
some species, the homogenization process is not as rapid as within
bacteria and therefore some sequence divergence could accumulate between
genes within a lineage.

So I ask Mark and others out there, are there examples of significant
differences between rRNA genes within a single organism in eukaryotes? 
Or, in other words, how rapid is the homogenization process, and how
complete is it (do all of the 1000s of rRNA genes evolve in concert?).

Jonathan A. Eisen

! Jonathan A. Eisen                       415-723-2425 (lab)         !
! Department of Biological Sciences       415-725-1848 (fax)         !
! Stanford University                     415-497-0599 (home)        !
! Stanford, CA   94305-5020               jeisen at leland.stanford.edu !

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