| The large and complex aromatic amino acid biosynthesis pathway presents numerous examples of the expansion or reduction of genomes in the form of homolog/analog emergence or loss. (1) Two distinct homology classes (AroA I and AroAII) of 3-deoxy D-arabino-heptulosonate 7-phosphate (DAHP) synthase exist. Phylogenetic-tree analysis shows that AroA II originated within the Bacteria domain, and it seems probable that higher-plant plastids acquired AroAII from a Gram-negative bacterium via endosymbiosis. (2) My analysis has facilitated the recognition of a subclass of Chorismate mutase (aroQ) genes (*aroQ), which have a cleavable signal peptide and are located in the periplasmic compartment. The joint presence of *AroQ, cyclohexadienyl dehydratase, and aromatic aminotransferase in the periplasmic compartment comprises a complete chorismate-to-phenylalanine pathway and accounts for the “hidden overflow pathway” to phenylalanine previously described in the literature. (3) Two distinct subgroups of the tryptophan synthase beta chain are found in nature. Representatives of Archaea, Bacteria and higher plants all exist that possess both TrpEb_1 and TrpEb_2. My analysis suggested that the stand-alone function of TrpEb_2 might be to catalyze the serine deaminase reaction, an established catalytic capability of tryptophan synthase beta chains.; Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. Tryptophan limitation caused by production of INF-γ by the host and subsequent induction of indolamine dioxygenase is known to be a key aspect of the host-parasite interaction. The factors that accommodate the transition of different chlamydial species to the persistent (chronic) state of pathogenesis include marked differences in strategies deployed to obtain tryptophan from host resources. Chlamydophila psittaci appears to have a novel mechanism for intercepting an early intermediate of tryptophan catabolism and recycling it back to tryptophan.; The possible origin by lateral gene transfer (LGT) of both a block of trp-pathway genes in Xylella and the tryptophan supraoperon of Anabaena/Nostoc, which are redundant because they are already represented elsewhere in a genome, was evaluated. Support for origin of the low-GC block of genes in Xylella by LGT, but not of the gene block in Anabaena/Nostoc was obtained. |
