Just so genome stories: what does my neighbor tell me?

Discovery supposes either chance or inductive reasoning. We document here an approach to explore genome texts, where the neighborhoods of genes and gene products (in the genome, in phylogeny, in metabolic pathways, in codon usage bias, ‘‘in biblio’’. . .) were used to make inferences about the function of unknown genes. Examples are provided in the case of pyrimidine biosynthesis, showing that de novo DNA synthesis requires either mRNA or membrane turnover (or both). We further show that this approach indicated that uridylate kinase must be compartmentalized, and that this compartmentalization was likely to be associated to transcription termination at Rhoindependent terminators. Finally, this led us to explore links between secretion, translation and the architecture of the cell, pointing to a role of sulfur metabolism, methionine recycling and salvage in particular. D 2002 Elsevier Science B.V. All rights reserved.