Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [100]
For now, synthetic biology is a craft practiced by artisans. It took Elowitz and his colleagues—some of the world’s top experts on E. coli and its genes—more than a year to produce blinking bacteria. And once they had their successes, it was very difficult for other scientists to improve their circuits or incorporate them into more elaborate ones. For one thing, a scientist would have to reconstruct the circuit. And the circuit might work only in a particular strain of E. coli. Scientists can keep track of E. coli strains only with elaborate pedigree charts, tracing the bacteria like royalty. Such are the challenges that make engineers despair.
Since 2001, Drew Endy and Thomas Knight of MIT have been building a catalog of standardized parts for synthetic biology. If you want to add a toggle switch to your particular circuit, you can search for it on the BioBricks Web site, download the DNA sequence, order the corresponding fragments of DNA from a biotech firm, and insert them in E. coli. With more than 160 parts in its inventory, BioBricks has not only made synthetic biology easier but has also begun to foster a community. Endy and Knight made BioBricks the basis of the annual synthetic biology competition for students. The students themselves add more parts to the registry, opening the way for future inventions.
But as synthetic biologists try to build more ambitious circuits, they may find a new obstacle in their path: E. coli itself. For all of the attention scientists have lavished on it, there is still much about the microbe they do not understand. Six hundred genes remain absolute mysteries. The microbe’s genetic network is particularly murky. Scientists can identify most of E. coli’s transcription factors, the proteins that grab DNA to switch genes on and off, but they know only about half their targets. And what synthetic biologists do understand about E. coli sometimes makes their hearts sink. Its circuits overlap with one another, forming tangles that no self-respecting engineer would ever design. It is very hard to predict how extra circuits will change the behavior of such a messy network.
Some synthetic biologists are trying to overcome E. coli’s mystery by taking it apart and rebuilding it from scratch. At Harvard University, for example, George Church and his colleagues have drawn up a list of 151 genes, which they think would be enough to keep an organism alive. Scientists understand these genes—which are drawn mostly from E. coli and its viruses—quite well. There should be relatively little mystery when they come together. Church hopes to create a genome with these essential genes. By combining it with a membrane and protein-building ribosomes, he hopes to create a living thing. Call it E. coli 2.0.
Meanwhile, at Rockefeller University, Albert Libchaber took an even simpler approach. He and his colleagues cooked up a solution of ribosomes and other molecules found in E. coli. Instead of a full genome, they engineered a small plasmid. They then added oily molecules from egg yolks, which form bubbles that scoop up the genes and molecules. These bubbles, Libchaber’s team found, could live—at least for a few hours. One of the genes Libchaber added to the plasmids encoded a pore protein. The protocells read the gene, built the proteins, and inserted them in the membrane. There they could allow amino acids and other small molecules to move into the protocell without letting the plasmid and other big molecules out. To track the production of new proteins, the scientists also added a gene from a firefly. The protocells gave off a cool green glow. Libchaber doesn’t call his creation a living thing. He prefers the term bioreactor. To go from bioreactor to life will take much more work. For one thing, Libchaber and his colleagues will need to add genes to allow