Figure 1

Biochemical pathway for phenylalanine and tyrosine biosynthesis. Small-molecule abbreviations: AGN, L-arogenate; CHA, chorismate; DAHP, 2-keto-3-deoxy-D-arabino-heptulosonate 7-P; DHQ, dehydroquinate; DHS, dehydroshikimate; E4P, erythrose-4-P; EPSP, enolpyruvylshikimate 3-P; HPP, 4-hydroxyphenylpyruvate; PEP, phosphoenolpyruvate; PHE, phenylalanine; PPA, prephenate; PPY, phenylpyruvate; SHK, shikimate; S3P, shikimate-3-P; TYR, tyrosine. Enzyme acronyms: [Aat], aromatic aminotransferase; [AroA], DAHP synthase; [AroB] DHQ synthase; [AroC], dehydroquinase; [AroD], SHK dehydrogenase; [AroE], SHK kinase; [AroF], EPSP synthase; [AroG], CHA synthase; [AroQ/AroR/AroH], CHA mutase; [PheA], prephenate dehydratase; [TyrA_c], prephenate (cyclohexadienyl) dehydrogenase; [*Aat], periplasmic aromatic aminotransferase; [*AroQ], periplasmic chorismate mutase; [*PheC], periplasmic cyclohexadienyl dehydratase. (In P. aeruginosa, the only organism so far shown to have *Aat, it belongs to the *Aat_Iβ grouping.) The flow route that progresses from PPA → AGN → TYR is shown in grey because this is a minor route in both P. aeruginosa and S. typhimurium. Different homology groups known so far that correspond with a given catalytic step are distinguished by Roman numeral subscripts, for example AroA_I or AroA_II. Subgroups within a homology group carry a further identifier, for example AroA_Iα or AroA_Iβ . As far as possible, these identifiers have been chosen to accommodate (within the constraints of logical naming) established precedents of naming. For example, the two homology groups of AroA were originally distinguished as class I or class II [50], and α and β subgroups for family-I DAHP synthases were defined recently [24]. AroC_I and AroC_II have been distinguished as biosynthetic or catabolic dehydroquinase, respectively, but this is a misnomer as many genomes use AroCII for aromatic amino acid biosynthesis (G.X. and R.A.J., unpublished data). Thus far, AroE_I is used exclusively in Bacteria, and AroE_II exclusively in Archaea [14]. The AroQ_Iα group of chorismate mutases has been so named to reflect previous reference to them as AroQ [22, 46]. Likewise, AroR_Iβreflects previous reference to it as AroR [32]. The α, β and γ subgrouping identifiers for Aat reflect the subgroupings within family-I aminotransferases defined by Jensen and Gu [3]. Color-coding is used to illustrate the substantial difference between P.aeruginosa and S. typhimurium in deployment of different homolog or analog proteins (numbers within boxes indicate the number of paralogs), chorismate mutase fusions (peg-and-hole matches) and periplasm-localized enzymes.