Re: News: One Species' Genome Discovered Inside Another's.

In message <1188579335.505881.310010@xxxxxxxxxxxxxxxxxxxxxxxxxxx>, SJAB1958 <balfres@xxxxxxxxxxx> writes
On 31 Aug, 13:34, Ye Old One <use...@xxxxxxxxx> wrote:
August 30, 2007
One Species' Genome Discovered Inside Another's

http://www.rochester.edu/news/show.php?id=2963

Bacterial to Animal Gene Transfers Now Shown to be Widespread, with
Implications for Evolution and Control of Diseases and Pests

Scientists at the University of Rochester and the J. Craig Venter
Institute have discovered a copy of the genome of a bacterial parasite
residing inside the genome of its host species.

The research, reported in today's Science, also shows that lateral
gene transfer-the movement of genes between unrelated species-may
happen much more frequently between bacteria and multicellular
organisms than scientists previously believed, posing dramatic
implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire
new genes and functions extremely quickly, says Jack Werren, a
principle investigator of the study. If such genes provide new
abilities in species that cause or transmit disease, they could
provide new targets for fighting these diseases.

The results also have serious repercussions for genome-sequencing
projects. Bacterial DNA is routinely discarded when scientists are
assembling invertebrate genomes, yet these genes may very well be part
of the organism's genome, and might even be responsible for
functioning traits.

"This study establishes the widespread occurrence and high frequency
of a process that we would have dismissed as science fiction until
just a few years ago," says W. Ford Doolittle, Canada Research Chair
in Comparative Microbial Genomics at Dalhousie University, who is not
connected to the study. "This is stunning evidence for increased
frequency of gene transfer."

"It didn't seem possible at first," says Werren, professor of biology
at the University of Rochester and a world-leading authority on the
parasite, called Wolbachia. "This parasite has implanted itself inside
the cells of 70 percent of the world's invertebrates, coevolving with
them. And now, we've found at least one species where the parasite's
entire or nearly entire genome has been absorbed and integrated into
the host's. The host's genes actually hold the coding information for
a completely separate species."

Wolbachia may be the most prolific parasite in the world-a "pandemic,"
as Werren calls it. The bacterium invades a member of a species, most
often an insect, and eventually makes its way into the host's eggs or
sperm. Once there, the Wolbachia is ensured passage to the next
generation of its host, and any genetic exchanges between it and the
host also are much more likely to be passed on.

Since Wolbachia typically live within the reproductive organs of their
hosts, Werren reasoned that gene exchanges between the two would
frequently pass on to subsequent generations. Based on this and an
earlier discovery of a Wolbachia gene in a beetle by the Fukatsu team
at the University of Tokyo, Japan, the researchers in Werren's lab and
collaborators at J. Craig Venter Institute (JCVI) decided to
systematically screen invertebrates. Julie Dunning-Hotopp at JCVI
found evidence that some of the Wolbachia genes seemed to be fused to
the genes of the fruitfly, Drosophila ananassae, as if they were part
of the same genome.

Michael Clark, a research associate at Rochester then brought a colony
of ananassae into Werren's lab to look into the mystery. To isolate
the fly's genome from the parasite's, Clark fed the flies a simple
antibiotic, killing the Wolbachia. To confirm the ananassae flies were
indeed cured of the wolbachia, Clark tested a few samples of DNA for
the presence of several Wolbachia genes.

To his dismay, he found them.

"For several months, I thought I was just failing," says Clark. "I
kept administering antibiotics, but every single Wolbachia gene I
tested for was still there. I started thinking maybe the strain had
grown antibiotic resistance. After months of this I finally went back
and looked at the tissue again, and there was no Wolbachia there at
all."

Clark had cured the fly of the parasite, but a copy of the parasite's
genome was still present in the fly's genome. Clark was able to see
that Wolbachia genes were present on the second chromosome of the
insect.

Clark confirmed that the Wolbachia genes are inherited like "normal"
insect genes in the chromosomes, and Dunning-Hotopp showed that some
of the genes are "transcribed" in uninfected flies, meaning that
copies of the gene sequence are made in cells that could be used to
make Wolbachia proteins.

Werren doesn't believe that the Wolbachia "intentionally" insert their
genes into the hosts. Rather, it is a consequence of cells routinely
repairing their damaged DNA. As cells go about their regular business,
they can accidentally absorb bits of DNA into their nuclei, often
sewing those foreign genes into their own DNA. But integrating an
entire genome was definitely an unexpected find.

Werren and Clark are now looking further into the huge insert found
in the fruitfly, and whether it is providing a benefit. "The chance
that a chunk of DNA of this magnitude is totally neutral, I think, is
pretty small, so the implication is that it has imparted of some
selective advantage to the host," says Werren. "The question is, are
these foreign genes providing new functions for the host? This is
something we need to figure out."

Evolutionary biologists will certainly take note of this discovery,
but scientists conducting genome-sequencing projects around the world
also may have to readjust their thinking.

Before this study, geneticists knew of examples where genes from a
parasite had crossed into the host, but such an event was considered a
rare anomaly except in very simple organisms. Bacterial DNA is very
conspicuous in its structure, so if scientists sequencing a nematode
genome, for example, come across bacterial DNA, they would likely
discard it, reasonably assuming that it was merely
contamination-perhaps a bit of bacteria in the gut of the animal, or
on its skin.

But those genes may not be contamination. They may very well be in the
host's own genome. This is exactly what happened with the original
sequencing of the genome of the anannassae fruitfly-the huge Wolbachia
insert was discarded from the final assembly, despite the fact that it
is part of the fly's genome.

In the early days of the Human Genome Project, some studies appeared
to show bacterial DNA residing in our own genome, but those were shown
indeed to be caused by contamination. Wolbachia is not known to infect
any vertebrates such as humans.

"Such transfers have happened before in the distant past" notes
Werren. "In our very own cells and those of nearly all plants and
animals are mitochondria, special structures responsible for
generating most of our cells' supply of chemical energy. These were
once bacteria that lived inside cells, much like Wolbachia does today.
Mitochondria still retain their own, albeit tiny, DNA, and most of the
genes moved into the nucleus in the very distant past. Like wolbachia,
they have passively exchanged DNA with their host cells. It's possible
wolbachia may follow in the path of mitochondria, eventually becoming
a necessary and useful part of a cell.

"In a way, wolbachia could be the next mitochondria," says Werren. "A
hundred million years from now, everyone may have a wolbachia
organelle."

"Well, not us," he laughs. "We'll be long gone, but wolbachia will
still be around."

This research was funded by the National Science Foundation's
Frontiers in Integrative Biological Research program, which supports
large, integrative projects addressing major questions in biology.

--
Bob.

This is nothing new, bacterial and viral DNA have been found in other
species for a lot longer.


It's not even greatly new with respect to Wolbachia. There's a paper about a partial Wolbachia genome being found integrated into the host genome from 2002.

* Kondo et al, Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect, PNAS 99(22): 14280-14285 (2002)

The novelty, as far as I can tell, is that this time it's a complete (or nearly so) Wolbachia genome.
--
alias Ernest Major

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