A highly efficient method for genetically engineering bacteria is reported online this week in Nature Methods. The efficiency gains make it possible to rapidly produce custom bacteria in which entire metabolic pathways have been redesigned for genetic studies or biotechnological applications.
One of the most effective ways to introduce many genetic changes is multiplex automated genome engineering (MAGE), in which short stretches of DNA are inserted one at a time into a bacterial chromosome over many iterations. The process is automated but is limited to very short changes-typically up to three bases of DNA sequence at any given location-and requires a lot of instrumentation.
Harris Wang, Duhee Bang and colleagues greatly improve on the efficiency of MAGE by selecting for changes at the site of interest and for an antibiotic resistance marker nearby. This co-selection enables them to insert 20 DNA bases at each site and increases the chances of producing multiple changes in each iteration.
Using co-selection MAGE (Cos-MAGE), the authors alter the promoters of 12 genes in the same metabolic pathway in only 4 days, enhancing production of the industrially relevant dye indigo and the anti-leukemia factor indirubin. The improved efficiency also makes it feasible for smaller laboratories lacking robotics to carry out genome-scale engineering.