lamoran at medisun.med.utoronto.ca (Laurence Moran) wrote:
>In article <49cj03$5jm at news.nstn.ca>, Dave Edgell <dedgell at ac.dal.ca> wrote:
>>The 16S rRNA has been sequenced from Thermotoga which places this
>>organism near the base of the eubacteria. A few other genes have
>>been sequenced but none as phylogenetically useful as rRNA. Check
>>out any publication by Woese or cronies for a tree which shows
>>where Thermotoga branches.
>>>>There are several genes that appear to be more phylogenetically useful than
>16S RNA. One of these is the glutamine synthetase gene and dendrograms
>constructed using these sequences tend to show that Thermotoga maritima
>clusters with the gram postive bacteria and the archaebacteria - well
>within the prokaryotic group. Brown et al. (1994) state,
>> "The close proximity of the GSI genes of Thermotoga to those of
> archae and Gram-positive bacteria is an additional and very
> striking conflict with 16S rRNA (ref.) and EF-G (ref) -based
> phylogenies, which tend to place this species as one of the
> deepest branches of the bacterial tree."
True, the glutamine synthetase tree does show an affinity of Thermotoga for
gram positive bacteria. However, there are very few taxa sequenced for this gene
that are relevant to the original posting. 16S rRNA is still one of the most
useful molecular datasets for eubacterial phylogeny as basically all known and
cultivable (and some uncultivable) groups of eubacterial have been sequenced.
The same cannot be said for glutamine synthetase. The same arguement,paucity
of seuqences, can be made for EF-g,. I think we all know the
problems associated with constructing phylogenetic trees without the relevant
groups in question..
Brown et al. then go on to say (after the above quote)
>Brown et al. (1994) then go on to compile a list of all Thermotoga genes
>that have been sequenced and they conclude that the majority support
>a close relationship between Thermotoga and Gram-positive bacteria.
>>Some other Thermotoga genes have subsequently been sequenced (ie. ribosomal
>protein genes; Sanangelatoni et al. (1994)). In most cases the dendrograms
>constructed from these sequences also suggest that Thermotoga is not the
>deepest branch of the bacteria tree but is related to the Gram-positive
>>It's true that Woese and his "cronies" claim that the 16S RNA sequences
>are the best phylogenetic markers. It's also true that many others
>dispute this claim.
I share your sceptical view of the "correct" molecular phylogeny shown by
16S rRNA. However, I still maintain that in the absence of any other dataset
which has as wide a taxon sampling as 16S rRNA, this molecule is still the
most useful for eubacterial phylogeny.
>>Laurence A. Moran (Larry)
>>>Brown, J.R., Masuchi, Y., Robb, F.T. and Doolittle, W.F. (1994) Evolutionary
> Relationship of Bacterial and Archaeal Glutamine Synthetase Genes.
> J. Mol. Evol. 38, 566-576.
>>Sanangelantoni, A.M., Bocchetta, M., Cammarano, P. and Tiboni, O. (1994)
> Phylogenetic Depth of S10 and spc Operons: Cloning and Sequencing
> of a Ribosomal Protein Gene Cluster from the Extremely Thermophilic
> Bacterium Thermotoga maritima. J. Bacteriol. 176, 7703-7710.