Shuffling bacterial metabolomes

The generation of bacterial genetic diversity through both vertical and horizontal gene transmission is well documented, but the relative contribution of each process has been a subject of much debate [1-7]. Now, because of the availability of many whole-genome sequences, biologists can perform unprecedented comparative analyses, looking at issues ranging from global genomic evolution to the roles of individual genes. A study published recently in Nature Genetics by Pál et al. [8] demonstrates how the powerful methodology of comparative genomics can be applied to the thorny issue of the evolution of bacterial metabolism.The work by Pál et al. [8] is the first large-scale analysis performed so far to elucidate the effect of horizontal gene transfer (HGT) on bacterial metabolic networks. The subject of the study was the model organism Escherichia coli K12, which has the best-characterized metabolism for a bacterium, several tools for in silico metabolic reconstruction, and an abundance of proteobacterial relatives whose genomes have been fully sequenced. Whether E. coli is typical of all, or even most, free-living bacteria will have to be determined in subsequent work, but there is no reason at present to believe otherwise. Pál et al. [8] identified HGT events by determining the presence and absence of genes by comparison with a phylogenetic tree of conserved proteins in 51 proteobacterial species. Unlike the model eukaryote Saccharomyces cerevisiae, the genome of E. coli K12 contains only a few duplicated genes for enzymes in metabolic pathways, and almost all these duplications appear to be ancient [8]. In fact, only one E. coli duplication event is predicted to have occurred since the divergence from the Salmonella lineage, whereas 15-32 genes are estimated to have been horizontally transferred during the same period. The likely reasons for this difference are the large number of mechanisms that facilitate gene transfer within and between bacteria (such as plasmids