Un génôme dans un autre

Bacterial genome found within a fly's

Ewen Callaway

Wolbachia bacteria (yellow) within the developing egg of a fruit fly (red). Science

Researchers have found a surprise hidden in the DNA of a fruitfly: what seems to be the entire genome of a parasitic bacterium called Wolbachia. Smaller bits of the promiscuous parasite's genetic material turned up in worms and wasps, too.

The size of the Wolbachia insertion in the fruitfly Drosophila ananassae - more than 1 million base pairs - has caught researchers by surprise. If bacterial DNA is so common in other creatures, they caution, researchers should be careful not to mistake it for contamination and accidentally throw it away when doing genome sequencing.

It has long been known that organisms can sop up foreign genes, the most usual example being bacteria swapping DNA with each other. DNA from mitochondria and chloroplasts - cell structures thought to have evolved from specialized bacteria - have also made their way into the genomes of multicellular eukaryotes (a category including plants and animals). And a worm parasite of plants has been found to contain a gene from nitrogen-fixing soil bacteria. But transfer of bacterial genes into animals has been thought rare.

The new work, published today in Science¹, suggests that gene flow from bacteria to animal hosts happens on a larger scale and more commonly than suspected.

The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. "You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."

Genome within a genome

One-fifth to three-quarters of all insect species are plagued by Wolbachia, which lives inside testes and ovaries and passes from one female generation to another through infected ova. To ensure its spread, Wolbachia can skew birth ratios towards females and even prevent infected males from successfully mating with disease-free females.

The bacterium's close association with egg cells means there's ample chance for bacterial DNA to get permanently sewn into a host's nuclear genome, says Dunning Hotopp, whose team expected to find just small stretches of parasite DNA in fruitflies. A Japanese team previously found a single Wolbachia gene in the adzuki bean beetle², and Dunning Hotopp and her colleagues expected to find much the same.

Instead, they found that the tropical fruitfly has sucked up the genome practically whole. The team looked at D. ananassae free of Wolbachia infection, and checked for 45 genes selected from across the bacterial genome. They found 44 of them. Because these test genes are so widely spread throughout Wolbachia DNA, this suggests that the rest of its genome is likely in fruitflies too.

Many of the Wolbachia genes were infiltrated by strands of insect DNA that jump around the genome, and so are unlikely to be functional. But at least 28 of the bacterium's 1206 genes are active in the flies, the researchers showed. They don't yet know whether these genes are producing proteins or what effect they might have. "It could be quite profound," says John Werren, a biologist at the University of Rochester, New York, and part of the team. If the genes weren't doing anything, he says, they would have been dropped or mutated away.

There's no telling when the insertion occurred, but because the sequences are unique to D. ananassae, it probably happened after the species split from other fruitflies.

The team found much shorter stretches of the Wolbachia genome in other insects, including several species of nematode worms, wasps and a mosquito - suggesting that this kind of DNA transfer is quite common.

Not trash

The work brings a note of caution for anyone doing genome sequencing, says Ulfar Bergthorsson, a geneticist at the University of New Mexico in Albuquerque.


Traditionally, when genomes are sequenced, computer programs toss out any bacterial genes from the final code, assuming that it is simple contamination. But the existence of wide-spread gene flow from bacteria to insects suggests that sequencers should be more careful, says Bergthorsson. "It's unwarranted to exclude bacteria-like genomes from sequences."

As yet more organisms get their DNA decoded, researchers are certain to find more genes that have seeped from bacteria into animals, says Werren, particularly in reptiles and amphibians. Finding bacterial genes in mammals, however, is unlikely, because no bacteria are known to infect their sperm and egg cells.

References

1. Dunning Hotopp, J. C., et al. Science doi:10.1126/science.1142490 (2007).
2. Kondo, N., et al. Proc. Nat. Acad. Sci. 99 14280-14285 (2002).