Peter Gogarten says,
"Concerning the close relationship between gram negative bacteria and
eukaryotes I think the authors and others completely mis- (or over-)
interpret the data. The trees they Gupta et al. calculated are all
unrooted. If one uses midpoint rooting (i.e., one assumes a molecular
clock) the root is placed between the eukaryotes on one side and all
the prokaryotes on the other side (This was done by Sharon Shtang in
her dissertation at the Univ. of Toronto). The same result is obtained
if one uses an 'outgroup':"
I agree that Gupta and Golding (1993) have mis-interpreted their data. Their
dendrogram clearly shows clustering of bacterial and eukaryotic sequences
and a close relationship between arachaebacteria and gram positives. But in
deriving their model (fusion of gram negative and archaebacterial ancestors
to produce eukarotes) they re-root and re-draw their tree so that the
archaebacterial sequences form a distinct cluster and the gram positive
and gram negative bacteria have a monophyletic origin! Many of Sharon's
trees are unrooted but when a molecular clock is assumed we placed the root
between prokaryotes and eukaryotes. This seems very reasonable.
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 We (Elena Hilario and I) did some so far unpublished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.)
"As far as I can see there is no indication in the HSP70 data what so
ever indicating a close association between gram negative bacteria
Right. None of the analyses that we have done gives any indication of a
relationship between eukaryotic genes and those from gram negative bacteria.
"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. Gupta and Golding claim that
the ancestral HSP70 gene contained a gap and that gram negatives and
eukaryotes acquired an insertion. This makes no sense and can't be reconciled
with their HSP70 dendrogram. They claim that HSP70 genes arose from a
duplication of sequences in the N-terminal region and that the duplicated
region does not contain the insert. Here is their scheme,
********** ancestral gene
**********/********** internal duplication
*******000***/********** insert acquired in -ve's and euks.
As support for this scheme they claim that modern HSP70's contain evidence
of the internal duplication but we have analyzed 144 HSP70 sequences and
we fail to find any significant similarity between the first and second
quadrants. If there has not been an internal duplication then there is
no reason to suppose that an insertion has occurred. We think that the
ancestral gene contained all of the amino acids found in the eukaryotic and
gram -ve bacteria and that the branch leading to gram +ve's and the archae-
bacteria is derived from a gene with a deletion.
Laurence A. Moran (Larry)