cherry at watneys.genetics.utah.edu (Joshua Cherry) wrote:
>In article <4l05om$hhh at News.Dal.Ca> "Andrew J. Roger" <aroger at ac.dal.ca> writes:
>> Maybe it was a case where the ancestral eukaryotic GAPDH could not
> work well in concert with a eubacterial TPI (and the enzymes above
> it in the pathway)- so for a while several enzymes existed and
> the one which worked best eventually was retained while the
> other was lost.
>>This seems unlikely since, as far as I know, TPI and GAPDH don't
>interact in any way; a product of one is just a substrate for the other.
>But, more importantly...
But perhaps common feedback mechanisms which are meant to affect
both enzymes in the same way, do not for enzymes from deeply distant
taxa.This sounds a bit hand-waving too, I admit. Alternatively, there may
be more interaction between sequential enzymes in this pathway
than we know-- certainly some pathways are accomplished by
multimolecular enzyme systems (tryptophan biosynthesis for instance).
OR-- the retention of one of the two enzymes was entirely random.
>> The problem is that there are several classes of eubacterial GAPDHs.
> There is a huge bacterial assemblage which is quite distant to
> the eukaryotes (in fact the new archaebacterial sequence from
> Haloarcula vallismortis is a little more similar to the eukaryote
> enzymes than this eubacterial group is). Then there are GAPDH
> enzymes found in cyanobacteria (Anabaena and Synechocystis) and
> enzymes found in gamma-proteobacteria (ranging from E.coli to
> Haemophilus) which fall RIGHT in the eukaryote clade (they are
> far more similar to euk enzymes than either archaebacterial ones
> or the big eubacterial assemblage). Moreover, there are multiple
> copies of GAPDH in E.coli and the cyanobacteria- the above mentioned
> ones and ones which fall in the eubacterial assemblage.
>> So the explanation is likely either:
>> 1) cyanobacteria and E.coli received these eukaryotic-like GAPDH
> genes from lateral transfer from eukaryotes
> 2) eukaryotes received their GAPDH genes from bacteria (this
> scenario invokes a minimum of 2 transfers if one pays attention
> to the topology of the GAPDH tree)
>>There is an important other possibility which does not involve horizontal
>transfer at all. What you're calling the 'eukaryotic group' and the
>'bacterial group' may in fact be the results of a duplication which
>occurred prior to the divergence of eukaryotes and eubacteria. Everything
>you said about GAPDH is consistent with this scenario.
Yes paralogy of the sort you are suggesting is possible also. However,
there are details of the phylogeny of the "eukaryotic" group and the
"eubacterial" group which makes me think this unlikely. For instance, the
gamma-proteobacteria show a particular sister group relationship with
the kinetoplastid gapC enzyme (it is an extremely highly supported
clade in bootstrap analysis using distance, parsimony and likelihood
methods). The cyanobacterial enzyme is entirely distinct from the gamma-proteo
bacterial enzyme falling closer (but not at) the base of the eukaryotic
subtree. The other problem for your paralogy scheme is that one must postulate extensive
loss of multiple copies of GAPDH-- for instance one must postulate
loss of the eubacterial-type enzyme in every eukaryotic group except
for trichomonads. When weighing several events of lateral transfer
against possibly scores of events of loss of the eubacterial enzyme
in eukaryotes, I tend to favour the lateral transfer scenario.
>in some organisms of enzymes from both clades supports the possibility
>of an advantage to maintaining both (perhaps one is specialized in
>some way for glycolysis, and the other for gluconeogenesis, for example).
>One should always consider this possibility befor jumping to a conclusion
>of horizontal transfer. Think of the havoc that could be wreaked by
>someone naively considering trypsin sequences from some animals and
>chymotrypsin sequences from others.
>I see your point. However, explanations ad paralogy also come at a cost.
The reason we know that alpha and beta hemoglobin are paralogous
is because they are present simultaneously in many organisms and the
alpha tree and the beta tree are mirrors of each other. For GAPDH,
eubacterial and eukaryotic enzymes exist simultaneously ONLY in eubacteria (in fact
the explanation I'm using calls on ancient paralogy within eubacteria).
Eukaryotes which have "eukaryotic" enzymes (everyone except for
trichomonads) ONLY have these. Trichomonads ONLY have the eubacterial
sub-type enzyme. Archaebacteria, as far as we know, only possess
ONE type of GAPDH per cell. Ancient paralogy requires us to postulate
at least 3 type of GAPDH in each of these types of cells ancestrally-
for euks and archaes there is little evidence for this.
Andrew J. Roger