A model system of gene-enzyme nomenclature in the genome era applied to aromatic biosynthesis

Background: The accurate annotation of functional roles for newly sequenced genes of genomes is not a simple matter. Function is, of course, related to amino-acid sequence and to domain structure but not always in straightforward ways. Even where given functional roles have been identified experimentally, the application of an uneven and erratic nomenclature has generated confusion on the part of annotators and has produced errors that tend to become progressively compounded in database repositories. Results: The pathway that is deployed in nature for aromatic biosynthesis exemplifies an accumulation of chaotic nomenclature and a variety of annotation dilemmas. We view this pathway as one that is sufficiently complex to pose most of the common problems, and yet is one that at the same time is of a manageable size. A set of guidelines has been developed for naming genes of aromatic-pathway biosynthesis and the corresponding gene products, and we suggest that these can be generalized for application to other metabolic pathways. Conclusion: A system of nomenclature for aromatic biosynthesis is presented that is logical, consistent, and evolutionarily informative.