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Where bacteria get their genes

Bacteria acquired up to 90 percent of their genetic material from distantly related bacteria species, according to new research from The University of Arizona in Tucson.

The finding has important biomedical implications because such gene-swapping, or lateral gene transfer, is the way many pathogenic bacteria pick up antibiotic resistance or become more virulent.

"To maintain effective treatments and develop new antibiotics, it's important to monitor the rates and patterns of lateral gene transfer," said team member Howard Ochman, a UA professor of biochemistry and molecular biophysics and a member of UA's BIO5 Institute.

The research also solves a long-standing evolutionary puzzle. Many scientists have argued that drawing traditional family trees does not make sense for bacteria, because their genomes represent a mix of genetic material from their parental cells and from other species of bacteria.

Ochman and his colleagues' work shows that bacterial lineages can still be traced by considering only the "traditional" forms of genetic inheritance. The widespread exchange of genes does not blur the line of descent because the acquired genes get lost from the genome at a later point or, if they do persist, the bacteria then transmit them to their offspring.

Being able to classify bacteria is crucial for medicine, Ochman said. "If you go to the doctor with strep throat he can be pretty certain that it's the result of an infection with a species of Streptococcus and can therefore prescribe an appropriate antibiotic. If you couldn't classify bacteria because they have genes from all over, doctors wouldn't be able to do this."

The research report is published in the current issue of PLoS Biology, available on www.plosbiology.org. Ochman's coauthors are Nancy Moran, UA Regents' Professor of ecology and evolutionary biology and BIO5 member, and Emmanuelle Lerat, now at Universite Claude Bernard (Lyon, France) and Vincent Daubin, n ow at the Centre national de la recherche scientifique (CNRS) in France. The research was funded by the Department of Energy and the National Science Foundation.

Lateral gene transfer, unique to the bacterial world, has long been recognized as common. But until now scientists did not know which of a bacterium's genes came from lateral gene transfer and which had been inherited from its parent.

In their study, the scientists focused on the best-studied group of bacteria, the Gamma-Proteobacteria. It includes many human pathogens, including Salmonella, Shigella, pathogenic E. coli, and Pseudomonas.

Ochman's team compared the bacterial species by analyzing their genomic sequence data. The researchers then computed family trees, taking into account the acquired genes, and matched the trees to an established reference tree. For all genes, the match was about 95 percent. This showed that the widespread mechanism of lateral gene transfer does not interfere with the traditional approach of using family trees to infer relationships. Ochman's team found that only 205 genes of Gamma-Proteobacteria's approximately 7,205 genes are shared by all species. The vast majority of genes found in the group comes from lateral gene transfer. "Most of these occur in one or a few species only," Ochman said. "But these are the genes that make bacteria different from each other."

Most commonly, genes are transmitted by bacteriophages, viruses that specifically hijack bacteria cells. Like tiny syringes, phages inject their own genetic material into the host cell, forcing it to produce new phages. During such an event, genes from the bacterial genome can be incorporated into the newly made phages. They inject their newly modified genetic load into other bacteria. This way, bacteriophages act as shuttles, taking up DNA from one bacterium and dumping it into another. Bacteria can also make contact by tiny connection tubes through which they exchange pieces of DNA. They can also take up genetic material from the environment.

Ochman thinks the team's findings will stir new research in bacterial evolution. "It should be exciting to see whether gene transfer has been so widespread in other groups of bacteria, too."

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Emmanuelle Lerat, Vincent Daubin, Howard Ochman, Nancy A. Moran, Evolutionary Origins of Genomic Repertoires in Bacteria. PLoS Biology, May 2005, Volume 3, Issue 5, e130. http://www.plosbiology.org


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Source:University of Arizona


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