In biology, fitness can be crudely measured by a simple method: counting. If a particular species is well represented in a particular ecosystem, one can conclude that evolution has treated them well, with circumstances allowing them to thrive. It’s a bit simplistic to declare evolutionary winners or losers, but a species that over-populates an island is certainly doing better than the another species that goes extinct.
The same logic can be applied to individual genes – if a particular gene is seen in many different species and environments, one can reason that it’s doing something right relative to genes that have fallen off the map. That was the approach taken by Ramy Aziz of the University of Chicago Computation Institute and collaborators in an unusual paper published earlier this year. Aziz and fellow researchers used the thousands of complete genomes now available to scientists and the new concept of “metagenomes” to take a kind of gene census. Their hunt produced a unique class of genes that is both more abundant and ubiquitous in nature than any other: the transposases.
Transposases are enzymes with a strange role. Like editors, their main job is cutting and pasting, though instead of working with text or video, transposases rearrange DNA. Their existence was first detected by the famed plant geneticist Barbara McClintock, who won the Nobel Prize for characterizing the “jumping genes” moved around by transposases in maize. This reshuffling of the genome can sometimes be harmful to a species, but it also creates increased diversity that can be evolutionarily advantageous, as diverse populations are more resistant to shifting environmental pressures.
Aziz and his colleagues didn’t go looking for tranposases when they organized their gene census. Their study sought to find the most abundant (how often it appears) and ubiquitous (how many species in which it appears) genes in nature, and they used 2,137 genomes from bacteria, viruses, animals, and plants for the search. Combining all those genomes and analyzing them with the computers at Argonne National Laboratory turned up a lot of transposases – 26,625 to be exact, almost 1 percent of all protein-encoding genes. On average, a genome contains more than 38 different transposases.
Simply pooling all the known complete genomes created a bias, as most of the bacteria and viruses that have been sequenced are those most relevant to humans for agricultural or medical reasons. So the team also used metagenomics, a broad sample of the genetic diversity present in a particular ecosystem such as ocean, soil, or even the human gut. In this data set, the transposases again were the most commonly found genes, and appeared in almost every ecosystem sampled, making them kings of the global genome.
“We demonstrate that these jumping genes are almost omnipresent in every ecosystem that contains nucleic acid-based life forms,” the authors write.
But why are transposases so successful in the arena of genetic competition? The authors point out that they are prime examples of “selfish genes,” as coined by Richard Dawkins, Francis Crick, and others. One can even think of transposases as particularly accomplished parasites inhabiting the genomes of everything from bacteria to humans, surviving by moving and replicating themselves at will. Yet for the organism they are parasites-with-benefits, with the ability to “induce advantageous rearrangements or enrich the host’s gene pool,” the authors write. Rather than being creeped out by these genomic invaders, perhaps they are deserving of a thank-you card.
“They may offer a selective advantage to the genomes and ecosystems that they ‘parasitize,'” the article concludes. “The diversification they induce in these genomes and ecosystems is arguably an essential way of maintaining, diversifying and evolving life on our planet.”
Aziz RK, Breitbart M, & Edwards RA (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic acids research, 38 (13), 4207-17 PMID: 20215432