Interkingdom gene fusions

Complete genomes of fifteen bacteria, four archaea and one eukaryote were searched for interkingdom gene fusions (IKFs); that is, genes coding for proteins that apparently consist of domains originating from different primary kingdoms. Phylogenetic analysis supported 37 cases of IKF, each of which includes a 'native' domain and a horizontally acquired 'alien' domain. IKFs could have evolved via lateral transfer of a gene coding for the alien domain (or a larger protein containing this domain) followed by recombination with a native gene. For several IKFs, this scenario is supported by the presence of a gene coding for a second, stand-alone version of the alien domain in the recipient genome. Among the genomes investigated, the greatest number of IKFs has been detected in Mycobacterium tuberculosis, where they are almost always accompanied by a stand-alone alien domain. For most of the IKF cases detected in other genomes, the stand-alone counterpart is missing.The results of comparative genome analysis show that IKF formation is a real, but relatively rare, evolutionary phenomenon. We hypothesize that IKFs are formed primarily via the proposed two-stage mechanism, but other than in the Actinomycetes, in which IKF generation seems to be an active, ongoing process, most of the stand-alone intermediates have been eliminated, perhaps because of functional redundancy.Comparative genome analysis has revealed major lateral gene transfer between the three primary kingdoms of life, Bacteria, Archaea, and Eukarya [1,2,3,4]. The best recognized form of lateral gene flux is the transfer of numerous genes from mitochondria and chloroplasts to eukaryotic nuclear genomes [5]. Far beyond that, however, the role of lateral gene exchange, along with lineage-specific gene loss, as one of the principal factors of evolution, at least among prokaryotes, is obvious from the fact that the great majority of conserved families of orthologous genes show a 'patchy' phyletic distribution [6,7].