The phylogenetic position of the Mollicutes has been re-examined by using phosphoglycerate kinase (Pgk) amino acid sequences. Hitherto unpublished sequences from Mycoplasma mycoides subsp. mycoides, Mycoplasma hyopneumoniae and Spiroplasma citri were included in the analysis. Phylogenetic trees based on Pgk data indicated a monophyletic origin for the Mollicutes within the Firmicutes, whereas Bacilli (Firmicutes) and Clostridia (Firmicutes) appeared to be paraphyletic. With two exceptions, i.e. Thermotoga (Thermotogae) and Fusobacterium (Fusobacteria), which clustered within the Firmicutes, comparative analyses show that at a low taxonomic level, the resolved phylogenetic relationships that were inferred from both the Pgk protein and 16S rRNA gene sequence data are congruent.
AltschulS. F.,
MaddenT. L.,
SchäfferA. A.,
ZhangJ.,
ZhangZ.,
MillerW.,
LipmanD. J.1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402[CrossRef]
BalishM. F.,
KrauseD. C.2002; Cytadherence and the cytoskeleton. In Molecular Biology and Pathogenicity of Mycoplasmas pp 491–519 Edited by
RazinS.,
HerrmannR.
New York: Kluwer;
BrownJ. R.,
DouadyC. J.,
ItaliaM. J.,
MarshallW. E.,
StanhopeM. J.2001; Universal trees based on large combined protein sequence data sets. Nat Genet 28:281–285[CrossRef]
CiccareseS.,
TommasiS.,
VonghiaG.1989; Cloning and cDNA sequence of the rat X-chromosome linked phosphoglycerate kinase. Biochem Biophys Res Commun 165:1337–1344[CrossRef]
DandekarT.,
SnelB.,
SchmidtS.,
LatheW.,
SuyamaM.,
HuynenM.,
BorkP.2002; Comparative genome analysis of the Mollicutes
. In Molecular Biology and Pathogenicity of Mycoplasmas pp 255–279 Edited by
RazinS.,
HerrmannR.
New York: Kluwer;
DaubinV.,
GouyM.,
PerrièreG.2002; A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12:1080–1090[CrossRef]
FelsensteinJ.1993; phylip (phylogeny inference package). version 3.6 Department of Genetics, University of Washington; Seattle, USA:
Fothergill-GilmoreL. A.1986; Domains of glycolytic enzymes. In Multidomain Proteins: Structure and Function Edited by
HardieD. G.,
CogginsJ. R.
Amsterdam: Elsevier;
JohanssonK.-E.,
PetterssonB.2002; Taxonomy of Mollicutes
. In Molecular Biology and Pathogenicity of Mycoplasmas pp 1–31 Edited by
RazinS.,
HerrmannR.
New York: Kluwer;
JohanssonK.-E.,
HeldtanderM. U. K.,
PetterssonB.1998; Characterization of mycoplasmas by PCR and sequence analysis with universal 16S rDNA primers. Methods Mol Biol 104:145–165
LudwigW.,
KlenkH.-P.2001; Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 1 pp 49–65 Edited by
BooneD. R.,
CastenholzR. W.,
GarrityG. M.
New York: Springer;
ManiloffJ.2002; Phylogeny and evolution. In Molecular Biology and Pathogenicity of Mycoplasmas pp 31–45 Edited by
RazinS.,
HerrmannR.
R. New York: Kluwer Academic/Plenum Publishers;
NeimarkH.1979; Phylogenetic relationships between mycoplasmas and other prokaryotes. In The Mycoplasmasvol. 1 pp 43–61 Edited by
BarileM. F.,
RazinS.
New York: Academic Press;
NelsonK. E.,
ClaytonR. A.,
GillS. R.26 other authors1999; Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
. Nature 399:323–329[CrossRef]
PollackJ. D.2002; Central carbohydrate pathways: metabolic flexibility and the extra role of some “housekeeping” enzymes. In Molecular Biology and Pathogenicity of Mycoplasmas pp 163–201 Edited by
RazinS.,
HerrmannR.
New York: Kluwer;
PollackJ. D.,
MyersM. A.,
DandekarT.,
HerrmannR.2002; Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing “household” nucleoside diphosphate kinase gene and activity by glycolytic kinases. OMICS 6:247–258[CrossRef]
StrimmerK.,
von HaeselerA.1996; Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969[CrossRef]
ThompsonJ. D.,
HigginsD. G.,
GibsonT. J.1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680[CrossRef]
Van de PeerY.,
De WachterR.1994; treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570
WhelanS.,
GoldmanN.2001; A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691–699[CrossRef]