HSP70 evolution

Peter Gogarten peter at carrot.mcb.uconn.edu
Wed Jan 25 14:59:37 EST 1995

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.


* 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
  Phone:  USA 203 486 4061
  FAX:    USA 203 486 1784
  E-Mail: gogarten at uconnvm.uconn.edu 

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