In article <MAILQUEUE-101.941016104337.480 at molbiol.uct.ac.za>
ED at molbiol.uct.ac.za ("RYBICKI, ED") writes:
>> From: biocukm at okway.okstate.edu (Ulrich Melcher)
>>> I think we (Lartey, Voss and myself, ms in preparation) may have
>come across a
>> case where convergent sequence evolution has occurred during the
>evolution of
>> the ribgrass mosaic virus subgroup of tobamoviruses. In their RNA
>genomes the
>> movement and coat protein cistrons overlap for 25 codons. In
>other
>> tobamoviruses there is no overlap or a shorter overlap. The
>ancestral cistron
>> in the overlap region can be deduced to be the coat protein one.
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>Er...why? Is it not possibly an N-terminal extension of the CP?
>How "homologous" are those regions of the tobamovirus CPs? Enough
>to say that this has not occurred?
The evidence that the coat protein reading frame is ancestral is
as follows:
First, there is very little difficulty in aligning tobamoviral coat
protein amino acid sequences. Very few indels. Second, analysis
of the codon-position-dependent base compositions shows that the
profile for positions 1, 2, and 3 in the coat protein overlap region
show the same preferences as do non-overlapping regions of the coat
and movement cistrons. The exception, the T content, actually supports
the contention, since to derive the overlap, T's have to be suppressed
to avoid stop codons in the overlapping frame (Keese & Gibbs, 1992
PNAS 89:9489). Third, codon usage of the coat frame of the overlap
is closer to the usage in non-overlapping parts of both genes than is
the usage in the movement frame of the overlap.
What measure of "homology" would you like?
>>....I think that is what is meant by convergent
>> sequence evolution. The situation will certainly complicate
>phylogenies based
>> on movement protein amino acid sequences since all alignment
>algorithms will put
>> the C-termini together in some fashion, even though they are
>encoded by non-
>> homologous nucleotides.
>>This is definitely true IF it is the case...so, for all rules there
>has to be an exception!
>> _________________________________________________________________
> [Rybicki sig deleted]
Ulrich Melcher
Dept Biochem Mol Biol
Oklahoma St. Univ.
Stillwater OK 74078
biocukm at okway.okstate.edu
