Space Invader DNA jumped across mammalian genomes

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Mammals like ourselves pass our genes ‘vertically’ from parent to child. But bacteria aren’t quite so limited; they have mastered the art of gene-swapping and regularly transfer DNA ‘horizontally’ from one cell to another. This “horizontal gene transfer” has been largely viewed as a trademark of single-celled organisms, with few examples among animals and plants. That is, until now.

A group of American researchers have discovered a group of genetic sequences that have clearly jumped around the genomes of several mammals, one reptile and one amphibian. It’s the most dramatic example yet that horizontal genetic transfer outside of the bacterial realm is more common than we thought, and has helped to shape the evolution of animals. Meet the Space Invaders, genetic hitchhikers coming soon to a genome near you.

John Pace from the University of Texas originally discovered the sequences he named Space Invaders (or SPIN elements) by looking at the genome of a small primate called a bushbaby. He was searching for transposons, a group of parasitic DNA sequences that can cut themselves out of genomes and jump to new locations of their own accord. One sequence in particular stood out and Pace searched for it in all other vertebrates whose full genomes have been sequenced.

To his surprise, he found a large number of matches among the DNA of seven very distantly related species – the green anole (a lizard), African clawed frog, little brown bat, mouse, rat, opossum and tenrec , a small animal that looks like a hedgehog but is more closely related to elephants, manatees and aardvarks.

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While these animals come from very diverse lineages, their SPIN sequences were incredibly similar; compare those of any two species and you’d get an average match of 96%. That is a remarkable resemblance; even genes for some of the most vital, unchanging proteins within the vertebrate repertoire aren’t that similar between different species.

The widespread but patchy distribution of SPIN sequences means that it is extremely unlikely that the seven species inherited these sequences from the same common ancestor. They each have close relatives with completely sequenced genomes that lack any SPINS; they’re in tenrecs but not elephants, in mice and rats but not squirrels, and in bushbabies but not macaques or humans.

There is more evidence. None of the SPIN elements (except for those in the rat and mouse) were found at the same locations in their respective genomes. And while the Space Invaders, like all transposons of their ilk, have characteristic sequences at their ends, theirs all differ in a small but consistent way – a single change to their sequence that always shows up in the same position and sets them apart from other transposons.

It’s strong evidence that they all of these species picked up their SPIN passengers independently. All the modern sequences are descended from a common ancestor, a transposon forefather that jumped across the genomes of all these species and left its descendents in its wake. They aren’t closely related to any other transposons so they don’t tell us the identity of the ‘Patient Zero’ species that was the source of the ancestral sequence, or how said sequence managed to jump into so many different vertebrates.

But Pace has some ideas on those fronts; he suggests that the Space Invaders may have infiltrated the genomes of vertebrates by stowing away aboard certain viruses. There is precedent for that – last year, scientists discovered a piece of DNA that hitched a ride from the genome of a carpet viper into that of a gerbil, by hitching a ride onboard a poxvirus that infected both species. And four of the species that harbour SPINs – bats, opossums, mice and rats – are rich reservoirs of poxviruses that could act as vehicles for mobile DNA.

Regardless of their origins, the SPINs have been busy in their new hosts. Each genome typically contains many copies of the full-length versions and even more shorter variants that do not have the ability to jump around themselves. Together, these short versions (known as MITEs) and the full-length originals can number in their thousands. The frog has 4,000 of them and the tenrec has around 99,000, making SPINs some of the most successful transposons known.  

In one case, within the genomes of mice and rats, a SPIN element appears to have given rise to a new gene. It’s not clear what it does, but it appears to be functional and dates back to the time before mice and rats diverged from each other. But for the most part, natural selection has turned a blind eye to these sequences, and they have simply drifted through evolutionary time, picking up the odd neutral mutation.

Based on this steady drift, Pace estimated that the majority of SPINs spread through the genomes of vertebrates  between 31 and 46 million years ago, with a possible second burst about 15 million years ago that affected the bat and opossum. That’s a very narrow period of time in evolutionary terms and during it, the elements managed to ‘infect’ the DNA of very unrelated species living in distant parts of the world. It was effectively a global pandemic that left lasting consequences.

Reference: J. K. Pace, C. Gilbert, M. S. Clark, C. Feschotte (2008). Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0806548105