The first lines of divergence in the Bacteria domain were the hyperthermophilic organisms, the Thermotogales and the Aquificales, and not the mesophilic Planctomycetales
Introduction
There is clearly a controversy between those who claim that the first line of divergence in the Bacteria domain is represented by mesophilic or moderately thermophilic Planctomycetales (Brochier and Philippe, 2002) and those who claim that it was the hyperthemophilic organisms, the Thermotogales and the Aquificales, which first diversified in this domain (Bocchetta et al., 2000, Brown et al., 2001, Daubin et al., 2001, Di Giulio, 2003a, Di Giulio, 2003b, Di Giulio, 2003c). The solution to this controversy might be important in order to establish whether the last universal common ancestor (LUCA) was a mesophilic or hyperthermophilic ‘organism’, under the hypothesis that the node of the ancestor of Bacteria in the tree of life was close to that of the LUCA. Therefore, it would be possible to establish where the first organisms lived and, hence, where life may well be thought to have originated (Pace, 1991).
On the other hand, if the root of the tree of life were situated, for instance, in the Archaea domain as some authors suggest (Xue et al., 2003), then the LUCA node would be located far from that of the ancestor of Bacteria and, therefore, establishing the nature of the first line of divergence in this domain would not be particularly significant for understanding the nature of the LUCA. Clearly, under the latter hypothesis, establishing the nature of the first line of divergence in the Bacteria domain would have a more limited and less general significance and would therefore only clarify the evolutionary aspects pertinent to the Bacteria domain and its relationships with those of the Archaea and the Eukarya.
Brochier and Philippe (2002) have come to the conclusion that the mesophilic Planctomycetales were the first line of divergence in the Bacteria domain by examining the ribosomal RNA. Di Giulio (2003a) analysed their data set and concluded that, on the contrary, the hyperthermophilic organisms, the Thermotogales and the Aquificales, were the first lines of divergence in this domain. In order to help to clarify this apparent contradiction, we have used the fusion of 20 different proteins, i.e. we have built a long concatenamer of proteins in the hope of increasing the phylogenetic signal present in the data set and, thus help to better define the relative phylogenetic positions of the three species under study. This is the aim of the present paper.
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Materials and methods
All the protein sequences were taken from the KEGG data base (www.genome.jp/kegg/). The data set includes 15 species from the Bacteria domain and 4 from that of Archaea (Table 1). The organisms were chosen on the basis of phylogenetic considerations. In order to construct the initial concatenamer we used 17 ribosomal proteins, one RNA polymerase, and two elongation translation factors. For the multiple alignment of the proteins we used CLUSTALX (Thompson et al., 1997) with all the default
Construction of the data set: concatenamers
In order to construct the initial concatenamer we used 17 ribosomal proteins, one RNA polymerase, and two elongation translation factors. For many of these 20 proteins no cases of horizontal gene transfer were noted (Bocchetta et al., 2000).
For each individual protein, multiple alignment was performed using the CLUSTALX program (Thompson et al., 1997). The poorly conserved regions were removed from the individual alignments. Concatenating all 20 proteins produced an initial concatenamer of 6921
Conclusions
The present phylogenetic analysis makes it extremely different to claim, as Brochier and Philippe (2002) do when analysing an alignment of rRNA, that the Planctomycetales are the first line of divergence in the Bacteria domain. This is the main conclusion of the present work. However, there is evidence to support the hypothesis that the first lines of divergence in this domain were the hyperthermophilic organisms, Thermotogales and Aquificales, as claimed in other analyses (Bocchetta et al.,
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