Horizontal Gene Transfer and Prokaryotic Genome Evolution

An early indication of the extent of prokaryotic horizontal gene transfer came from the multifactorial analysis of codon frequencies in portions of the Escherichia coli genome that revealed significant deviations from the general pattern of codon usage in approximately 15% of this bacterium's genes. Comparative analyses of archaeal genomes presented particularly striking evidence that strongly suggests massive horizontal gene exchange with bacteria. Genomic era revelations of the widespread contributions of horizontal gene transfer to the gene composition of prokaryotic genomes amounted to a major shift in one's understanding of evolution. This chapter discusses the methodology used to infer horizontal gene transfer events and also discusses examples of such transfers among prokaryotes with an emphasis on adaptive and biological implications that they entail. From a pragmatic perspective, phylogenetic analysis is time- and labor-consuming because it depends critically on correct sequence alignments and is hard to automate without compromising the robustness of the results. The term "surrogate methods" was coined to describe methods of detecting horizontally transferred genes based on their anomalous nucleotide composition. The acquisition of eukaryotic genes by bacteria may be of particular interest because of the possible role of such horizontally transferred genes in bacterial pathogenicity. Eukaryotes have vastly more complex signal transduction systems than most bacteria and archaea. Horizontal gene transfer, particularly between eukaryotes and bacteria, emphasizes the remarkable unity of molecular-biological mechanisms in all life forms.