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A, C, G? - The chemical evolution of a bacterial genome
25 August 2011
Commissariat a l'Energie Atomique (CEA)
An international team made up of researchers from the Institut für Biologie (Freie Universität, Berlin), the CEA (IG/Genoscope – Evry), the CNRS, the University of Evry, the Katholieke Universiteit (Leuven) and Heurisko (United States) has achieved a world-first by producing a viable bacterium in which one of the four DNA bases has been replaced by a synthetic analog compound. The advantage of the new bacterium is that it would eventually be dependent on this compound, which does not exist in nature, and would therefore be unable to compete or exchange genetic material with natural organisms.
This research result was published under the title ‘Chemical Evolution of a Bacterium’s Genome’ in the journal Angewandte Chemie International Edition on July 25, 2011.
All living organisms store their genetic information in their DNA, which consists of a string of bases forming what could be termed an ‘alphabet of life’. These bases, of which there are four, are better known by the letters A (adenine), T (thymine), G (guanine), and C (cytosine). The project was coordinated by Rupert Mutzel of the Institut für Biologie in Berlin, and Philippe Marlière of Heurisko USA Inc., with the researchers from the CEA and the University of Leuven handling the experimentation part. The aim was to completely replace the thymine in the genome of bacteria belonging to the Escherichia coli K12 strain, with 5-chlorouracil, a compound that is toxic to living organisms at high doses.
The researchers used a novel technique, developed by P. Marlière and R. Mutzel, that makes it possible to direct the evolution of organisms under strictly controlled conditions. This technique involves the use of an automated cell culture system (photo opposite), designed for the sustained cultivation of large populations of bacteria in the presence of a toxic chemical compound at sublethal concentrations. These culture conditions lead to the selection of genetic variants that are capable of tolerating higher concentrations of the toxic compound. The automated cell culture system responds to the appearance of these variants in the cell population by adjusting the composition of the culture medium to exert a constant selection pressure.
This continuous culture evolution protocol, carried out at the Genoscope, was applied to bacteria of the Escherichia coli K12 strain that are incapable of synthesizing the natural thymine base and therefore depend on the culture medium to provide it. After about 1000 cell generations produced under these culture conditions, i.e. in the presence of constantly small quantities of 5-chlorouracil and thymine, the descendants of the original strain proved capable of growing in the presence of 5-chlorouracil alone. DNA analysis on these bacteria showed that 5-chlorouracil had almost completely replaced the base T. Many mutations were also observed. The researchers now plan to focus on the role played by these mutations in the adaptation of the bacteria to the use of a halogenated base.
This radical change in the chemical makeup of a living organism is of great interest for fundamental research. Also, as P. Marlière puts it: “this work represents a significant step forward in xenobiology, which is an emerging branch of synthetic biology”. This recent discipline in the life sciences is aimed at designing non-natural organisms with optimized metabolic capabilities to produce alternative modes of synthesis. These could then be used to produce chemical compounds for various applications, particularly in the energy field. Synthetic organisms, such as those selected here, would have the advantage of relying entirely on compounds that cannot be found in nature to obtain their genetic material and proliferate. This means that, in time, they would be unable to compete or exchange genetic material with natural organisms, and would eventually die out for want of the xenobiotic they need to survive.
 Sublethal: less than lethal; which does not cause death
Automated cell culture system, Genoscope. ©C.Dupont/CEA
Cells of the E. Coli bacterium, dependent on thymine, one of the 4 basic building blocks of DNA. IG/CEA. Cells following adaptation to chlorouracil, a non-natural derivative of thymine. IG/CEA