So far, there have been two primary routes to reengineering an organism's genome. The first is to start with an existing form of life and tweak it a bit, eliminating a few genes and adding in some others. The second is to start from scratch, building a new genome up from short stretches of DNA made with a machine. There are advantages to each approach, but a paper in Science provides a third option: wholesale editing of entire genomes.
Making a collection of individual tweaks gives you fine control over the properties of an organism, but can be time-consuming. Individual genes may have to be deleted or replaced, additional ones can be added to the genome, and others may be hosted on smaller pieces of DNA that are maintained by the organism in question. It can be technically challenging to perform this long series of modifications, and it's certainly time consuming. The alternative, building a genome from scratch, can allow you to make a series of extensive modifications as part of a single process. But at the moment, it only works on extremely simple organisms that don't have any of the complex biochemical pathways we're likely to want to reengineer.
The new approach provides something that's a bit in between the two, allowing researchers to edit DNA sequences scattered around the genome, allowing wide-scale modification of genomes as complex as the one carried by E. coli.
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