Nucleotide bias in SS/DS RNA viruses vs. retroviruses
umelcher at BMB-FS1.BIOCHEM.OKSTATE.EDU
Fri Dec 2 16:08:54 EST 1994
Several points regarding D. Shivak's recent query (copy appended below):
1. Kypr and Mrazek (Nature 327:20, 1987) do mention a high A content for
influenza, human papilloma, papova RNA viruses).
2. They also mention a high A content for cauliflower mosaic virus. Kelly
Chenault and I have also noted that, but later (Biochimie 76,3-8, 1994).
Indeed, the near-uniform high A content is present in all sequenced
caulimoviruses and badnaviruses. These are retroid viruses of plants. The
content is very similar to that seen in the lentiviruses.
3. Our analysis of CaMV nucleotide sequences suggested that the main
contributing factor to the high A content is a suppression of A to G
transitions. These were significantly lower than G to A or C to T and T to C
transitions. Of course, we have no clue as to how that suppression occurs
4. The nucleotide composition bias in viruses does, as Bronson and Anderson
point out, influence the outcome of phylogenetic analyses. Chenault and I
noticed that in a phylogenetic study of CaMV isolates ( J. Mol. Evol. 39: 496,
5. The idea proposed by Bronson and Anderson that the composition biases arose
because of competition between two variants on their way to speciating can be
questioned when the plant viruses are included in the thinking. The caulimo and
the badnaviruses are the only two known types of retroid viruses in plants. The
proposed mechanism would require that they have opposite base compositions.
They do not. Alternatively, one could argue that the plant retroid viruses
evolved from a lentivirus after lentiviruses diverged from oncoviruses. One
could argue that, but I don't think many would. Anyone else have any ideas on
why lentiviruses, caulimoviruses and badnaviruses should share high A contents?
6. My interpretation of the Bronson & Anderson article differs a little from
Shivak's "mutational bias due to reverse transcriptase in retroviruses may play
an important role in speciation". I think B & A were arguing that competition
was driving speciation. The competition allowed two variants with complementary
base compositions to co-exist. As a consequence of the variant compositions the
RT adjusted its specificity. True, this is a subtle difference. Yet, I think
In message <D02J1u.H1x at sue.cc.uregina.ca> Dave Shivak writes:
> Network was doing some odd things last night when I posted this, so
> apologies if this is a repeat posting....
> I was wondering if any recent work has been done on SS or DS RNA virus
> phylogeny specifically mentioning nucleotide composition and
> nucleotide bias of RNAdepRNApol as an evolutionary influence. I
> recently read the paper _Nucleotide composition as a driving force in the
> evolution of retroviruses_ (Bronson & Anderson (1994) J. Mol. Evol.
> 38:506-532 article) which suggests mutational bias due to
> reverse transcriptase in retroviruses may play an important role
> in speciation. I was curious as to whether these results may be
> generalized to other viral systems with similar low-fidelity nucleic
> acid replication, such as the SS and DS RNA viruses. Any references
> or comments of use would be much appreciated (please Email).
> Thanks in advance
> Dave Shivak
> shivakd at meena.cc.uregina.ca
Ulrich Melcher biocukm at okway.okstate.edu
Department of Biochemistry umelcher at bmb-fs1.biochem.okstate.edu
and Molecular Biology tel. 405-744-6210
Oklahoma State University FAX 405-744-7799
Stillwater OK 74078-0454
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