Where Bacteria Get Their Genes
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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网4月6日消息,美国图森市亚利桑那大学的一项新研究认为,细菌有90%的遗传物质来自它们的远亲菌种。该研究论文发表在2005年5月份第3卷第5期的《大众科学图书馆生物卷》(PLoS Biology)上。
该发现具有重大的生物医学含义,因为许多病原菌正是凭借这类基因交换(或称横向基因转移)变得抗药性更强或更为恶性。
研究小组成员、亚利桑那大学的生物化学及分子生物物理学教授霍华德· 奥克曼(Howard Ochman)说:“为了使治疗有效并研制新的抗生素,对横向基因转移的速度及方式的监测是非常重要的。”
该研究还解决了很久以来的一个进化难题。许多科学家曾经认为绘制传统的细菌系谱图是没有意义的,因为它们的基因组是来自父母细胞及其它菌种的遗传物质的组合。但奥克曼等人的研究表明,如果只考虑遗传的“传统”形式,则还可以追踪细菌系谱。广泛的基因交换不会模糊系谱,因为后天获得的基因会从基因组中丢失,或者,如果这些基因没有丢失,则细菌会把它们遗传给下一代。
奥克曼等人集中研究γ-变形菌,包括沙门氏菌、志贺氏杆菌、病原性大肠杆菌、假单胞菌等许多人类病菌。他们通过分析菌种的基因组序列来比较这些菌种,然后用计算机做出系谱图(考虑了后天获得的基因),再将这些系谱图与已知的参考系谱图进行匹配。结果发现,所有基因的匹配率在95%左右。这说明,尽管横向基因转移广泛存在,但这并不妨碍使用系谱图来推断基因关系。他们还发现,在γ-变形菌的总共大约7,205种基因中,只有205种基因为所有菌种共有。绝大部分基因来自横向基因转移。大部分基因都只出现在一或几个菌种中,但正是这些基因使细菌彼此区别开来。
横向基因转移为细菌世界独有的普遍现象。但直到现在,科学家还不知道细菌的基因哪一个来自横向基因转移,哪一个来自父母遗传。