Genetic escape pods

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 saidL.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]

Genetic escape pods

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