BMC Genomics 2005, 6:125 http://www.biomedcentral.com/1471-2164/6/125 Insects Basal chordate Animals γ-proteobacteria Vertebrates β-proteobacteria High G+C Gram+ Ascomycetes Fungi 1000 1000 1000 1000 996 984 1000 724 999 953 1000 1000 742 942 695 1000 1000 804 84910001000 1000 1000 High G+C Gram+ Actinoproteobacteria High G+C Gram+ γ-proteobacteria α-proteobacteria β-proteobacteria Basidiomycetes α-proteobacteria FUinguusrueal4phylogenetic distribution of the rTS gene Unusual phylogenetic distribution of the rTS gene. The sequences of the same set of proteins displayed in Fig. 2 were used to generate a neighbor-joining tree using ClustalX. The tree was displayed in TreeView program, while the taxonomic labels of the species were added manually afterward. In addition to the extension of the N-terminus as indicated in Fig. 2, adjustments to the currently annotated exon boundaries for a few rTS genes were necessarily made based on the best match between their genomic sequences and the human rTSγ protein sequence (see detailed modifications in supplemental materials). Bootstrap values that are over 700 (1000 trials) are shown at the nodes. which shows that suboptimal AUG codons can support translation via leaky scanning and reinitiation [14], the co-existence of protein products translated using different AUG codons in the same reading frame may not be a rare phenomena. In fact, the starting AUG codons for rTSγ and rTSβ are both qualified as optimal start codons according to recent studies of translation initiation in mammalian and plant genes [14-16], providing an explanation for the co-existence of rTSγ and rTSβ. A recent study suggests that many alternative splicing forms cause differential subcel- lular localization, especially in targeting either peroxi- somes or mitochondria [17], and our data serves as evidence supporting such a notion. An interesting subject for future studies will be to determine when the shorter rTSβ isoform appeared during evolution. Phylogenetic distribution and origin of rTS gene rTS is highly conserved, being found in a variety of spe- cies, ranging from bacteria to human. Unlike other eno- lase genes with a wider phylogenetic distribution, or the thymidylate synthase (TYMS) gene, which is ubiquitous in organisms from all three kingdoms and is highly con- served, rTS demonstrates an unusual phylogenetic distri- bution. As shown in Fig. 4, the presence of rTS is limited Page 7 of 10 (page number not for citation purposes)