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Genetic escape pods

Microbes share and preserve their genetic material by releasing bodies that resemble viruses into the environment

By | October 1, 2010

Packaging random snippets of DNA into virus-like capsules known as gene transfer agents, or GTAs, may be a key way for marine bacteria to exchange genetic information, a new linkurl:paper;http://www.sciencemag.org/cgi/content/abstract/330/6000/50 in __Science__ suggests.
Some GTAs resemble viruses that infect
bacteria such as Lambda phage

Image:Flickr/ACJ1
While this gene-swapping mechanism has been known for decades, the extent to which GTAs were relevant to microbes in the real world was unclear, having been observed in a limited number of species and almost exclusively inside microbiology labs. But a team of researchers, headed by University of South Florida marine microbiologist linkurl:John Paul,;http://www.marine.usf.edu/faculty/john-paul.shtml demonstrated that GTAs isolated from lab-grown bacteria conferred antibiotic resistance to a wide range of microbes naturally growing in the warm waters of the Gulf Coast, and at a much higher rate than expected. "This could represent a paradigm shift in how we view gene transfer in nature," said linkurl:Thaddeus Stanton,;http://www.ars.usda.gov/pandp/people/people.htm?personid=44895 a microbiologist at the US Department of Agriculture who was not involved in the study. "They've elevated the status of GTAs from laboratory anomalies or curiosities, to what I think are major players in microbial ecology and evolution." GTAs were first discovered in 1974 in the photosynthetic bacterium, __Rhodobacter capsulatus__, and immediately presented a puzzle to researchers: While they resembled bacteria-infecting viruses from the outside -- with small, protein heads and a short tail -- on they inside they contained random fragments of __Rhodobacter's__ own genome, instead of a viral genes. This led to the hypothesis that GTAs represented remnants of a viral genome that inserted itself into __Rhodobacter's__ ancestor millions of years ago and has since become defective -- seeding the bacterium's genome with genetic instructions to make the capsule and envelope. These genes are found not only in __Rhodobacter__, but in most members of the taxonomic class it belongs to, the α-proteobacteria. Typically, genes are conserved in an organism's genome because they confer some adaptive advantage, according to Lauren McDaniel, a postdoc in Paul's lab and first author of the paper. In fact, bacteria in a lab only make GTAs when they reach a point in their growth when crowding, stress, waste buildup, and low nutrient levels dramatically slow down their growth -- also known as stationary phase. "[GTAs] are functioning as little genetic escape pods," McDaniel said. When things look bad, bacteria may release a bevy of GTAs as a way to preserve pieces of their genetic legacy. To study how this can play out in a natural environment, McDaniel and her colleagues genetically modified two species of α-proteobacteria, __Roseovarius nubinhibens__ and __Reugeria mobilis__, to carry a set of antibiotic resistance genes. The researchers stressed these bacteria until they reached stationary phase, then they filtered out GTAs and added a cocktail of enzymes to chop up any free-floating DNA, resulting in a purified solution of GTAs. These GTAs were then added to water samples obtained from the Gulf of Mexico and from Florida estuaries and coral reefs that were teeming with bacteria -- especially α-proteobacteria. To test if antibiotic resistance genes were passed on to the natural bacteria via the GTAs, the samples were incubated in antibiotics, and the surviving colonies were sequenced. Because these GTAs package random pieces of DNA up to 1,000 base pairs long (barely enough to fit one gene), approximately 1 in 20,000 carried an antibiotic resistance gene, McDaniel said. Nevertheless, the researchers found that approximately 50 percent of the natural bacteria acquired antibiotic resistance in some of the experiments. "The results are really surprising," said linkurl:Tom Beatty,;http://www.microbiology.ubc.ca/beatty a microbiologist at the University of British Columbia who was not involved in the study. "It was generally thought that the frequencies of GTA-mediated gene transfer were much lower -- 10 to 100-fold lower." Equally surprising was that a variety of bacteria species successfully incorporated sequences from __Roseovarius__ and __Reugeria__ GTAs. Two of these, __Flavobacterium__ and __Flexibacter__, were not even α-proteobacteria at all, but belong to a different phyla. "I don't know of many horizontal gene transfers that can jump that far," Stanton said. Other species, completely unrelated to α-proteobacteria, have been found to produce GTAs as well. Stanton studies a species of Spirochete that causes swine dysentery. Spirochete GTAs don't carry any of the genes identified in __Rhodobacter__, __Roseovarius__ or __Reugeria__ GTAs. This suggests not only that a different virus was its source, but that the hijacking of defective viral genomes by bacteria to make GTAs may be a very common occurrence. "I've been predicting that GTAs are going to be a lot more common than we now appreciate," Stanton said L.D. McDaniel, et al., "High frequency of horizontal gene transfer in the Oceans," Science, 330:50, 2010.
**__Related stories:__***linkurl:Package delivery;http://www.the-scientist.com/article/display/57164/
[March 2010]*linkurl:Bacterial genes jump to host;http://www.the-scientist.com/news/display/53552/
[30th August 2007]*linkurl:A new breed of viral invasion;http://www.the-scientist.com/blog/display/56239/
[6th January 2010]
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Comments

Avatar of: anonymous poster

anonymous poster

Posts: 1

October 1, 2010

Why do we assume that the bacteria utilize acquired viral genomes to produce GTAs, rather than that the GTA mechanism was evolved first by bacteria to improve the survival of their own genomes (a primitive form of sex) and that viruses evolved by hijacking this process and diverting it to the transfer of a specific set of genes that result in the replication of additional copies of those genes?\n\nAlso "teaming" involves grouping with other players for a game and "teeming" indicates the presence of a large population.
Avatar of: anonymous poster

anonymous poster

Posts: 5

October 1, 2010

Do you remember transduction? How do you think it happens?
Avatar of: Cristina Luiggi

Cristina Luiggi

Posts: 5

October 1, 2010

Thanks for reading and for pointing out that embarrassing grammatical error. It's been corrected.\n\n- Cristina Luiggi
Avatar of: Gerald Hoff

Gerald Hoff

Posts: 1

October 1, 2010

As opposed to the hypothesis that this phenomenon is caused by ancient virus genes, might this not be the mechanism by which viruses originally evolved.
Avatar of: john toeppen

john toeppen

Posts: 52

October 1, 2010

Wow, this is cool. I agree with the ?phage evolution? post regarding this as a path for virus evolution and as an early version of sex. \n\nMore importantly, can we create synthetic versions that carry ?firmware updates? to reprogram existing cell genetics? How do these packets of genetic material get into the host cell? What do they do when they get there? What can we put into such packets? What sort of ?opener? do we need to get into different cells? \n

October 1, 2010

The first thing I thought of when I saw this article was "Hey, this is where viruses came from!" - but now I'm not so sure....\n\nConsider: while making particles to carry bits of your genome around may be regarded as a cool survival tactic, which could have given rise to an adventitious piece or two of genome which became selfish enough to be viruses, it's less cool if it was teh cell using the remnant of an integrated virus genome...or is it?\n\nI am afraid, like intracisternal A-particles and other retrovirus-like particles found in everything from mammals to yeasts, we will find it very difficult to say which came first - virus or virus-like particle.
Avatar of: Steven Pace

Steven Pace

Posts: 22

October 2, 2010

You could put oil eating bacteria into the water after an oil spill, but wouldn't it be simpler, and more effect to put the DNA into the water that would enable bacteria to eat the oil? The result would be an organism that can eat the oil, and is well adapted to the local environment. I have thought this for decades, but a better understanding of "jumping genes" possible makes this more practical.

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