Methionine adenosyltransferase as a useful molecular systematics tool revealed by phylogenetic and structural analyses

Structural and phylogenetic relationships among Bacteria and Eukaryota were analyzed by examining 292 methionine adenosyltransferase (MAT) amino acid sequences with respect to the crystal structure of this enzyme established for Escherichia coli and rat liver. Approximately 30% of MAT residues were found to be identical in all species. Five highly conserved amino acid sequence blocks did not vary in the MAT family. We detected specific structural features that correlated with sequence signatures for several clades, allowing taxonomical identification by sequence analysis. In addition, the number of amino acid residues in the loop connecting beta-strands A2 and A3 served to clearly distinguish sequences between eukaryotes and eubacteria. The molecular phylogeny of MAT genes in eukaryotes can be explained in terms of functional diversification coupled to gene duplication or alternative splicing and adaptation through strong structural constraints. Sequence analyses and intron/exon junction positions among nematodes, arthropods and vertebrates support the traditional Coelomata hypothesis. In vertebrates, the liver MAT I isoenzyme has gradually adapted its sequence towards one providing a more specific liver function. MAT phylogeny also served to cluster the major bacterial groups, demonstrating the superior phylogenetic performance of this ubiquitous, housekeeping gene in reconstructing the evolutionary history of distant relatives.