Interkingdom gene fusions.
BACKGROUND
Genome comparisons have revealed major lateral gene transfer between the three primary kingdoms of life - Bacteria, Archaea, and Eukarya. Another important evolutionary phenomenon involves the evolutionary mobility of protein domains that form versatile multidomain architectures. We were interested in investigating the possibility of a combination of these phenomena, with an invading gene merging with a pre-existing gene in the recipient genome.


RESULTS
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.


CONCLUSIONS
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.
Wolf
Y I
YI
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rockville Pike, Bethesda, MD 20894, USA.
Kondrashov
A S
AS
Koonin
E V
EV
D000123:Acetyltransferases; D000595:Amino Acid Sequence; D001105:Archaea / Q000235:genetics; D019843:Archaeal Proteins / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D004798:Enzymes / Q000235:genetics; D029968:Escherichia coli Proteins; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D005796:Genes / Q000235:genetics*; D016678:Genome; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016681:Genome, Fungal; D006867:Hydrolases / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D020543:Proteome / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004798:Enzymes; D029968:Escherichia coli Proteins; D005656:Fungal Proteins; D020543:Proteome; D000123:Acetyltransferases; C040285:pyruvate formate-lyase activating enzyme; D006867:Hydrolases; C111817:PHP protein, E coli