Is Carl Woese losing a Kingdom?

L.A. Moran lamoran at gpu.utcc.utoronto.ca
Tue Oct 1 11:20:44 EST 1996

In article <52o42s$m29 at mserv1.dl.ac.uk>,
Graham Clark <g.clark at lshtm.ac.uk> wrote:
>lamoran at gpu.utcc.utoronto.ca (L.A. Moran) writes:
>>One of the main reasons that gene X has been used for phylogeny 
>>reconstruction is the idea that it is vertically transmitted and
>>not subject to lateral gene transfer.
>>You can plug anything you want into "gene X". All such statements
>>have about the same scientific legitimacy. Why do some people feel 
>>that rRNA genes are special in this sense? 
>There ARE good reasons, mostly revolving around co-evolution. The 
>rRNAs do not exist in the cell on their own but as part of an 
>organelle. While most proteins intract with one or two others
>in their funtional role in the cell, the ribosome is made up of
>dozens of distinct proteins many of which are involved in specific
>protein-rRNA interactions that involve specific structures/sequences
>in both molecules.

The problem is that you could say the same thing about many gene products. 
You are no doubt familiar with the fact that transcription initiation complexes
involve many interacting proteins and so do DNA replication complexes. But
there are also complexes of proteins required for metabolism and things
like electron transport. I don't think that ribosomes are very special in
this sense.

Besides, if your argument was valid then you would expect the ribosomal
proteins to be highly conserved but it turns out that they are not. In fact
the ribosomal RNAs themselves are not among the most highly conserved
gene products as you would expect if the argument was valid.

> In other words expressing a heterologous rRNA in
>a cell is unlikely to give rise to functional ribosomes, unless it
>comes from a closely related organism.

This is true of a large number of genes. The exceptions are spectacular,
but they are exceptions.

> In addition to the multiple
>coevolved rRNA/protein interactions forming a barrier to horizontal
>transfer, it has been shown that rRNA promoter and RNA polymerase I 
>also coevolve rapidly in eukaryotes, such that heterologous expression
>is not possible because of promoter incompatibility even between quite
>closely related organisms. 

This is true of most genes. Nothing special about the promoters of rRNA
genes in eukaryotes. Similarly in bacteria there are no guarantees that
an E. coli promoter (of any given gene) will work in cyanobacteria or

>So while coevolution will affect the successful horizontal transfer of
>many genes, the multiplicity of the inter-molecular interactions in
>which ribosomal RNAs are involved means that functional products from 
>such an event are highly unlikely.

I believe that this impression stems from a lack of understanding of
the kinds of complexes that are normally present in most cells. The
ribosome is simply one of the more visible manifestations of such protein

Here's another kind of example for you to ponder. Think about histones and
nucleosomes. We hypothesize that the conservation of histone amino acid
sequences is due to the fact that they interact to form a core particle
and that the multiplicity of such interactions inhibits evolution. Thus
histones are highly conserved. What does this mean? It means that histone
gene are *more* likely to be transferred horizontally because they will
work in most organisms. In this case the presence of a complex leads to
exactly the opposite conclusion to the one that you propose for ribosomal
RNAs. It's the logic of your argument that I am questioning.

Larry Moran

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