In article <timi-230195180310 at kos4mac15.berkeley.edu>, says
>>About the comparisons to the gram positives...
>Are there any HSP70 sequences from the high-GC gram positives or are
>they all from the low-GC, (Bacillus, Clostridium, Mycoplasma) branches?
>It's just that the low-GC's seem to have really been on the move,
>evolutionarily speaking. They're quite divergent. I just wonder how
>the comparison goes when one includes a representative sampling from
>the "Actinomycetes" (high-GC) subgroup of the gram-positives, which
>appear a bit more like the gram-negatives in many ways.
>>Regards, Tim Ikeda (timi at mendel.berkeley.edu)
I included HSP 70 homologs from both low (Clostridium, Bacillus, Stapylococ., Lactococcus) and
high GC gram positives (Mycobact., Streptomyc.) in my analyses. In the most parsimonious tree
Methanosarcina HSP70 groups with the low GC gram positives, Haloarcula groups with the high GC
gram positives, in 3% - 10% of the bootstrapped samples (depends on the alignment) the two
archaebacteria group together. If you want a copy, send me your FAX number.
In article <1995Jan23.114743.32832 at ac.dal.ca>, aroger at ac.dal.ca says...
>>For the sake of clarity, it should be explained the
>trees A and B, of Moran's posting, differ only in the
>placement of the root. Without a root these trees are
>topologically identical. Thus the central issue in Moran's
>posting could be phrased as simply: "where does the root of the
>HSP70 tree fall?".
>>Unfortunately, I think that given the data that Moran and others have
>offered, it is an issue which cannot be adequately addressed. In
>order to justifiably root this tree with another sequence, one must have
>reason to believe that the gene duplication giving rise to the pair
>of genes preceeded the divergence of all of the organisms in question.
>Since all of the sequences described as possible outgroups to these
>trees are found in only ONE of the three "urkingdoms" of life (MreB,
>the Ecoli hsc70 and the others mentioned), we have no strong data upon
>which to base this assumption. All of these potential paralogs of
>hsp70 could owe their low sequence similarity to an increased rate
>of non-synonymous substitution following gene duplication in that
>urkingdom; in other words distant sequences don't always imply ancient
>gene duplications gave rise to them.
>Stuff deleted
>
I agree with nearly everything that Andrew wrote, except that I don't see the rooting problem as
non-informative as he does. He correctly points out that there is no way to assure that the
HSP70 paralogous MreB proteins are present in all three domains; therefore, they do not provide
a proper outgroup for the HSP70 protein family. However, the MreB proteins are found in both
gram positives and gram negatives suggesting that MreB and HSP70 were both already present in
the ancestor of the gram positives and gram negatives. Thus the point where the MreB proteins
join the HSP70s either reflects the root or a point between the root and the separation between
gram positives and gram negatives. The placement of the mreBs with respect to the HSP70s (see
the sketch below*) thus provides the following information: The gram negative and
cyanobacterial HSP70s do not group together with the eukaryotic HSP70s. The archaebacterial
HSP70s group together with the HSP70s from gram positives (i.e. with respect to the HSP70s the
prokaryotes are not divided into a eubacteria and archaebacteria). The finding of the same
close association between gram positives and archaebacteria for a variety of other markers (see
my earlier posting) seems to indicate that the archaebacteria received several genes (many of
them involved with amino acid metabolism) from gram positive bacteria. The problem with this
analysis is that the branch connecting the prokaryotic and eukaryotic HSP70s is very long, and
that only few amino acid positions can be aligned with confidence between HSP70s and mreBs (most
of which are identical and thus do not contain phylogenetic information either). If one
includes most positions from a computer generated alignment the bootstrap values for both the
eukaryotic and the prokaryotic grouping are 100% (long branches attract); however, if one uses
only positions with reasonable alignment, the bootstrap value for the prokaryotic grouping drops
to 66%.
Andrew Roger continues :
>Rooting trees with very divergent sequences may yield a tree abberrantly
>rooted along the longest branch of the tree- long branches attracting
>may be a serious problem.
Yes!
* from an earlier posting:
|-------- mreB E.coli
|----------|
| |-------- mreB Bacilli
|
| |--------- eukaryotic HSP70 hom.
| |
|---------
| |--- gram negative bacteria
|-----|
| |-- gram positive bacteria
|---|
|-- archaebacteria
--
********************************************
J. Peter Gogarten
University of Connecticut
Dept. Molecular and Cell Biology
75 North Eagleville Rd.
Storrs, CT 06269-3044
USA
Phone: USA 203 486 4061
FAX: USA 203 486 1784
E-Mail: gogarten at uconnvm.uconn.edu
**********************************************
