HSP70 evolution

Peter Gogarten peter at carrot.mcb.uconn.edu
Fri Dec 16 16:36:01 EST 1994


In article <D0wvon.99z at gpu.utcc.utoronto.ca>, 
lamoran at gpu.utcc.utoronto.ca (L.A. Moran) says:

>
>

stuff deleted

>Peter Gogarten continues,
>
>     "The front half of the HSP70 homologues is homologous to the MreB 
>      proteins of E.coli and Bacillus (i.e. a gram positive and a gram 
>      negative). We (Elena Hilario and I) did some so far unpublished 
>      analyses including these proteins in a phylogenetic analyses of 
>      the HSP70 homologues.  Using parsimony, distance matrix or maximum
>      likelihood analysis, the MreB proteins always group between Eukaryotes
>      on one side and all the prokaryotes on the other."
>
>I have a problem with this. According to the published alignments of MreB
>and HSP70's there is no homology. For example, Gupta and Golding (1993)
>show an alignment of about 340 aa's with about 40 identities and 9 gaps.
>(The number of identities depends on which MreB or HSP70 sequences are
>looked at.) This corresponds to about 12% similarity and a normalized  
>alignment score (NAS) of about 50. According to Doolittle, NAS has to be well
>above 200 (!) in order to claim homology. It looks to me like there may
>be an ATPase binding motif that has arisen independently in many proteins
>by convergent evolution. (Most of the MreB and HSP70 similarities are in
>short stretches of sequence that are involved in ATP binding.)
>

I used the Needleman Wunsch algorithm in conjunction with the unitary 
matrix to calculate % identity and alignment scores for the different aa 
sequences. The results I got leave little doubt concerning the homology 
between mreB protein and the ATPase domain of HSP70 homologues:

                               z-values:

                      ATPase domain of HSP70 homologues from
                      E.coli     Halobacterium   Drosophila 
                                 marismortui     melanogaster

E.coli mreB            9.9         7.2              4.4

B.subtilis mreB        6.8         8.7              5.0

calculated using the unitary matrix and 50 randomizations each; 
usually z-values above 3 are considered as suggestive of homology, 
as far as I know values above 5 have only been obtained for homologous
sequences.  


                               % identity :

                      ATPase domain of HSP70 homologues
                      E.coli     Halobacterium   Drosophila 
                                 marismortui     melanogaster

E.coli mreB           28.2        28.2             21.8

B.subtilis mreB        27         26.3             24.6

 



>     "The insertion that according to Gupta et al unites gram negative
>      eubacteria and eukaryotes appears in our analysis as an insertion 
>      that unites gram positives and archaebacteria."
>
>I assume that you meant to say a "deletion" that unites gram positives and
>archaebacteria? That's what our data shows. 

Yes, I meant "deletion that unites gram positives and archaebacteria".


Peter Gogarten



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