Where Bacteria Get Their Genes

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Keywords
BIO5, EVOLUTION, GENOME, BACTERIA, GENOMICS, GENE TRANSFER, BACTERIOPHAGE, PATHOGENS, BIOMEDICAL, SALMONELLA, SHIGELLA, PATHOGENIC E. COLI, PSEUDOMONAS, FAMILY TREE, PHAGES 
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Bacteria acquired up to 90 percent of their genetic material from distantly related bacteria species, according to new research. The finding has important biomedical implications and solves a long-standing paradox in evolutionary biology.

Newswise — 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, now 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."

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

Related Web sites:

Howard Ochman
http://www.biochem.arizona.edu/dept/ppl/Profiles/ochman.htm

Nancy Moran
http://eebweb.arizona.edu/Faculty/Bios/moran.html

BIO5 Institute
http://www.bio5.org

    Newswise網(wǎng)4月6日消息，美國圖森市亞利桑那大學(xué)的一項(xiàng)新研究認(rèn)為,，細(xì)菌有90％的遺傳物質(zhì)來自它們的遠(yuǎn)親菌種,。該研究論文發(fā)表在2005年5月份第3卷第5期的《大眾科學(xué)圖書館生物卷》（PLoS Biology）上。

    該發(fā)現(xiàn)具有重大的生物醫(yī)學(xué)含義,，因?yàn)樵S多病原菌正是憑借這類基因交換（或稱橫向基因轉(zhuǎn)移）變得抗藥性更強(qiáng)或更為惡性,。

    研究小組成員、亞利桑那大學(xué)的生物化學(xué)及分子生物物理學(xué)教授霍華德· 奧克曼（Howard Ochman）說：“為了使治療有效并研制新的抗生素,，對(duì)橫向基因轉(zhuǎn)移的速度及方式的監(jiān)測是非常重要的,。”

    該研究還解決了很久以來的一個(gè)進(jìn)化難題。許多科學(xué)家曾經(jīng)認(rèn)為繪制傳統(tǒng)的細(xì)菌系譜圖是沒有意義的,，因?yàn)樗鼈兊幕蚪M是來自父母細(xì)胞及其它菌種的遺傳物質(zhì)的組合,。但奧克曼等人的研究表明，如果只考慮遺傳的“傳統(tǒng)”形式,，則還可以追蹤細(xì)菌系譜,。廣泛的基因交換不會(huì)模糊系譜，因?yàn)楹筇飓@得的基因會(huì)從基因組中丟失,，或者,，如果這些基因沒有丟失，則細(xì)菌會(huì)把它們遺傳給下一代,。

    奧克曼等人集中研究γ-變形菌,，包括沙門氏菌、志賀氏桿菌、病原性大腸桿菌,、假單胞菌等許多人類病菌,。他們通過分析菌種的基因組序列來比較這些菌種，然后用計(jì)算機(jī)做出系譜圖（考慮了后天獲得的基因）,，再將這些系譜圖與已知的參考系譜圖進(jìn)行匹配,。結(jié)果發(fā)現(xiàn)，所有基因的匹配率在95％左右,。這說明,，盡管橫向基因轉(zhuǎn)移廣泛存在，但這并不妨礙使用系譜圖來推斷基因關(guān)系,。他們還發(fā)現(xiàn),，在γ-變形菌的總共大約7,205種基因中，只有205種基因?yàn)樗芯N共有,。絕大部分基因來自橫向基因轉(zhuǎn)移。大部分基因都只出現(xiàn)在一或幾個(gè)菌種中,，但正是這些基因使細(xì)菌彼此區(qū)別開來,。

    橫向基因轉(zhuǎn)移為細(xì)菌世界獨(dú)有的普遍現(xiàn)象。但直到現(xiàn)在,，科學(xué)家還不知道細(xì)菌的基因哪一個(gè)來自橫向基因轉(zhuǎn)移,，哪一個(gè)來自父母遺傳。