Sludge Watch ==> Nature Magazine: Bacteria genes can flow into animal genes

[Maureen Reilly]

Sludgewatch Admin:

This is an extraordinary discovery.  Many of us already know that bacteria 
can swap DNA.
They can aquire virulence, antibiotic resistance.

But this story is about wholesale adoption of bacterial DNA into the DNA of 
fruitflies.  Bacteria conferring DNA to animals was thought to be rare.  
Apparently not.

Imagine what is happening in sewage treatment plants and digesters, as 
bacteria, viruses, and parasites duke it out in a survival-of-the-fittest 
contest.  Then we take these ... the most virulent and successfully armed 
bacteria, and spread them on our farm lands.

............................................................................



http://www.nature.com/news/2007/070827/full/070827-6.html

31 August 2007

Bacterial genome found within a fly's
DNA transfer from bacteria to animals is more common than thought.
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.

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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.

Visit our newsblog to read and post comments about this story.

* Correction: the article was amended to reflect the fact that 28 of 1206 
bacterial genes, rather than 28 of 45, were active in the flies studied.



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