An article published online at the Nature web site on November 24 (Chou et al., 2014) presents a fascinating study of examples in which bacterial genes have found their way to a number of distinct eukaryotic lineages including ticks and mites, gastropod (e.g., snails and slugs) and bivalve mollusks (e.g. clams and oysters), and choanoflagellates (a subset of ptotozoans). Type VI secretion amidase effector (Tae) molecules (encoded by tae genes) can kill rival bacteria by degrading their cells walls when delivered into those competing cells. The eukaryotes cited above all have “domesticated amidase effectors” (dae) genes, all of which are extremely similar to one of the four extant bacterial tae genes. Of the four tae genes found in bacterial species, three have been transferred to one or another eukaryotic genome.
The authors document several lines of evidence to support their conclusion that dae genes in the lineage encompassing ticks and mites are functional and contributing to fitness. First, they find that the dae genes in ticks and mites and in mollusks have ratios of non-synonymous to synonymous (dN/dS) mutations that are indicative of purifying selection, i.e. selection against codon changes implying a useful function of the current nucleotide sequences. For the ticks and mites, 21% of the codons of the genes that were subjected to analysis showed dN/dS values supportive of purifying selection. In the case of mollusks, the percentage of such codons was even higher (40%).
A second key observation was that most of the Dae proteins in eukaryotic organisms have eukaryotic secretion (Sec) signals. This amino acid sequence motif facilitates the process by which a protein is transferred from the intracellular space to the extracellular space. If the proteins Dae lacked such secretion signals, it might be more plausible to argue that the genes may have bacterial origins but were not functional in their new eukaryotic hosts.
Third, the authors acquired evidence for expression of the dae genes in a species of ameba. They also found previously published evidence for dae gene expression in a species of lancelet, a small marine organism.
Fourth, several examples of eukaryotic Dae proteins from tick, ameba, and lancelet species were tested for the ability to enzymatically degrade peptidoglycan, a major component in bacterial cell walls. The authors found that all the Dae proteins tested generated the expected the peptidoglycan degradation products consistent with the anticipated enzymatic activity.
Fifth, Chou et al. did not find any evidence for transfer of bacterial housekeeping amidases to eukaryotic species. They speculated that bacterial effector proteins transferred to target cells via Type VI secretion systems might be especially effectively maintained in eukaryotic genomes. Whether or why this might be the case relative to other potentially fitness-enhancing bacterial genes remains unclear.
Of particular relevance to the clinical sphere, the Dae2 protein found in the deer tick (Ixodes scapularis) that serves as a vector for the Lyme disease bacillus, Borrelia burgdorferi, exhibited peptidoglycan-degrading activity against B. burgdorferi and other bacteria. Since a Dae2 mutant without amidase activity was not lytic against permeabilized E. coli and Bacillus subtilis (for which peptidoglycan is accessible on the cell surface even without permeabilization), the authors concluded that Dae2 is effective as an anti-bacterial agent by virtue of amidase activity. Of key importance, the authors show that decreasing expression of the dae2 gene in I. scapularis ticks is associated with higher loads of B. burgdorferi, suggesting, in conjunction with other evidence, that the Dae2 protein is used by the tick to control the load of spirochetes.
Chou et al. also argue that in order to be effective in killing most bacteria in vivo, secretion of Dae2 would need to be accompanied by secretion of molecules that can cause breaches in the bacterial outer membrane thereby allowing the Dae2 molecules access to the peptidoglycan in the cell wall. The only exceptions would be microbes for which the peptidoglycan is accessible on the surface of the cell.
The transfer of amidase-encoding genes from bacteria to eukaryotic organisms is not the first instance of such trans-kingdom horizontal gene transfer (HGT). For example, the authors cite an already described case of transfer of bacterial cysteine synthase genes to mites and the lineage including butterflies and moths (Lepidoptera). What is of special note in the transfers of both cysteine synthase and amidase genes is that, unlike in some other cases, the evidence supports the inference that these transferred genes actually benefit their new hosts.
These results point to larger implications. First, although HGT from bacteria to eukaryotes is certainly less common and presumably less consequential for evolution than inter-bacterial HGT, it does occur and can likely be evolutionarily meaningful. Thus genomes are best regarded as somewhat fluid entities, not the static repositories of information associated with such phrases as “the human genome,” as if human genomes were all fundamentally identical. Second, the assumption that all of the genes in a given genome are homogeneous with respect to their evolutionary origins is not necessarily reliable. Third, reflecting the previous point, the “tree” or “net”metaphor for the relationships among all living beings probably should be replaced by a “web” metaphor (Doolittle, 1999) to indicate the possibility of multiple genomic ancestors, with different ancestors for different genes or groups of genes in a single genome.
Much additional investigation will be required to fully gauge the extent of trans-kingdom HGT and the magnitude of the effects on recipient eukaryote evolution. The impact of this mechanism on medicine also remains to be more completely delineated.
Chou S, Daugherty MD, Peterson SB, … Mougous JD. Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature. 2014 Nov 24; doi:10.1038/nature13965.
Doolittle WF. Phylogenetic classification and the universal tree. Science. 1999 Jun 25;284(5423):2124-9. PubMed PMID: 10381871.