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
>> the ribgrass mosaic virus subgroup of tobamoviruses. In their RNA
>> movement and coat protein cistrons overlap for 25 codons. In
>> tobamoviruses there is no overlap or a shorter overlap. The
>> 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
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
>> 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]
Dept Biochem Mol Biol
Oklahoma St. Univ.
Stillwater OK 74078
biocukm at okway.okstate.edu