Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations

Based on sequence similarity and the clustering, fusion, and phylogenetic distribution of genes, several functional predictions emerged from this analysis. For bacteria, these included the existence of novel GTP cyclohydrolase I and folylpolyglutamate synthase gene families, and of a trifunctional p-aminobenzoate synthesis gene. For plants and bacteria, the predictions comprised the identities of a 'missing' folate synthesis gene (folQ) and of a folate transporter, and the absence from plants of a folate salvage enzyme. Genetic and biochemical tests bore out these predictions.For bacteria, these results demonstrate that much can be learnt from comparative genomics, even for well-explored primary metabolic pathways. For plants, the findings particularly illustrate the potential for rapid functional assignment of unknown genes that have prokaryotic homologs, by analyzing which genes are associated with the latter. More generally, our data indicate how combined genomic analysis of both plants and prokaryotes can be more powerful than isolated examination of either group alone.Folates are tripartite molecules comprising pterin, p-aminobenzoate (pABA), and glutamate moieties to which one-carbon units at various oxidation levels can be attached at the N5 and N10 positions (Figure 1). In natural folates the pterin ring is in the dihydro or tetrahydro state, and a short, γ-linked polyglutamyl tail of up to about eight residues is usually attached to the first glutamate.Tetrahydrofolates serve as cofactors in one-carbon transfer reactions during the synthesis of purines, formylmethionyl-tRNA, thymidylate, pantothenate, glycine, serine, and methionine [1] (Figure 2). Most folate-dependent enzymes strongly prefer polyglutamates to monoglutamates, but the opposite is usually true of folate transporters so that polyglutamylation is generally considered to favor folate retention within cells and subcellular compartments [2,3].Plants, fungi, certain protists, and most bacteria mak