HSP70 evolution

Brian Foley brianf at med.uvm.edu
Tue Jan 17 11:32:48 EST 1995

L.A. Moran (lamoran at gpu.utcc.utoronto.ca) wrote:

:           |---- BiP                            |------ BiP
:         |-|                                 |--|
:         | |---- hsc70/hsp70                 |  |------ hsc70/hsp70
:      |--|                                   |
:      |  | |---- organelles                --|    |---- organelles
:      |  |-|                                 |  |-|
:    --|    |---- gram neg.                   |  | |---- gram neg.
:      |                                      |--|
:      |  |------ archaebacteria                 | |---- archaebacteria
:      |--|                                      |-|
:         |------ gram pos.                        |---- gram pos. 

:               A                                      B

:      "...it is clear that all of the eukaryotic HSP70 homologs ... share
:       a number of sequence features in common with the Gram-negative group
:       of bacteria. The most prominent of these features is the presence
:       of a relatively conserved insert (sic) of between 23 and 27 amino
:       acids in the N-terminal quadrant following the sequence KRLIG, which
:       is not found in any of the homologs from archaebacteria or Gram-
:       positive bacteria. The presence of various unique, shared sequence
:       features between these species and detailed phylogenetic analyses
:       of the HSP70 data (the results of which are not affected by excluding
:       this region) provide strong evidence that the eukaryotic HSP70
:       homologs have evolved from a Gram-negative eubacterial ancestor."

: I do not agree. My analyses show that all prokaryotic sequences cluster
: together in a monophyletic group that is distinct from the eukaryotic
: sequences (tree B). This result is obtained even when the region containing
: the insert/deletion is included but it is much more apparent when this
: region is excluded.

	I'm not sure what the overall point is here:  To decipher the
evolutionary tree of organisms, or the tree of Heat Shock proteins?
If you wish to decipher the tree of oprganisms, you should look at many 
genes from different families, and not just one.  Cammarano et al in
J. Mol. Evol. 34: 396-405 (1992) used EF-G and EF-2 sequences and 
compared their results to results obtained using EF-1alpha/EF-Tu 
sequences.  They discuss why the two genes/proteins result in different 
phylogenetic trees.  Braithwaite and Ito in Nucleic Acids Research 21: 
787-802 (1993) used the DNA polymerase proteins to build phylogenetic 
trees.  Just as classical taxonomists use a weighted average of many 
features, and not just one feature like "wing shape" to generate 
phylogenetic trees, molecular evolutionists must consider many 
gene or protein sequences, and not just one or two.
	If it is a tree of heat shock proteins which you seek, beware 
that some gene and protein sequences are mis-labelled and this might 
result in circular logic.  Many genes are clones and sequenced based on 
sequence similarity (probing libraries, designing PCR primers, etc...) 
and many others are sequenced at random and then assigned a name based on 
sequence similarity (sequence a random piece of DNA, compare it to the 
database, it is most similar to HSP70, so name it HSP70).  For example in 
the study of EF-1alpha/EF-Tu one could be mislead by the fact that many 
EF-1alpha proteins are named as "the" EF-1alpha for that species, when in 
fact there are a whole family of EF-1alpha proteins expressed at 
different developmental stages.  One may then end up comparing the 
Drosphila embryonic EF-1alpha to the Xenopus adult liver EF-1alpha 
without realizing it.  One must be careful to analyze how much is known 
about the uniquenss of a gene in a genome.  If more than one member of a 
gene family is present, then intra-genomic recombination could occur 
which would allow for an evolutionary tree to be non-binary.  
Inter-genomic recombination between say an archaebacterium and a plant, 
is much less likely to occur, but still possible.

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

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