Directed evolution can be done faster and more effectively

Artificial (or directed) evolution experiments were for a long time to me some kind of easy to understand concept. It's clear indeed, you take a gene (resembles a genotype), mutate it or part of it in preferentially random way, express it (to obtain a phenotype) and choose ones that match you criteria. This process you can do again and again until you exhaust your passion.

In a huge contrast to the theoretical concept, things become much more hazy once you start designing directed evolution setup (I have never done it myself). Here might come problems: size of the library (the bigger the better, if you can experimentally afford it), how much time you can spend on doing this exercise (otherwise, how long each evolutionary round will take) and you also be considering possible biases that comes from the experimental system you use. For instance, in vitro systems that normally compartmentalize a single gene and its protein product  are not self-sustaining (see my another post how researchers are trying to make this system sustainable). Whereas using in vivo evolution methods you'll be applying a selective pressure on a whole organism rather than only on you gene of interest so you might end up with more sophisticated pattern of unintentional selective pressures. The latter for instance affects the most advanced method 'phage-assisted continuous evolution' (PACE, to read about in Nature journal or on HHMI). It is great in terms of its ease. It relies on a phage M13 propagation (this makes very short turnover time) and its all happen in one constantly replenished medium (so it continuous!) Also, due to the fast phage proliferation it will let you pick even the most rare but very efficient mutants of you gene.

Here are the E.coli cell infected with M13 phage. It lacks one important protein (pIII) who's gene is on the extra plasmid (red circle). You transform this plasmid along with a plasmid bearing gene of interest (green circle) that will drive pIII expression and will result in maturation of infection-competent phage.

Again, this system is limited since the obtaining of you most precious active mutant is dependent on the phage replication who's biochemistry is totally irrelevant to you.

So, it took only two years to design another directed evolution system that almost fully lacks this drawback, though it has some others (will tell later about this). It's been published in recent issue of Nature biotechnology journal. So, instead of using phage as a 'machine' to amplify the protein mutants group of Professor Andrew Ellington (here is the link to his lab) simply coupled production of your gene to the synthesis of Taq DNA polymerase that we normally use in PCR (they call it 'compartmentalized partnered replication' CPR, don't get confused). The design looks very similar to the PACE:

The only difference is that your drive the expression of the enzyme only (not a phage). Next, you insert you cell into vesicles along with primers and simply do a PCR. Thus, PCR will occur on those vesicles containing larger number of Taq polymerase molecules. Again, similarly to the PACE we dealing with amplification that lets you to pick up the most rare mutants. The problem here that it is discontinuous. Although, authors consider this beneficial as it ads another leverage to evolutionary process. Also, production of your library is still dependent on an organism that means you will not be able to produce toxic to E.coli proteins (this might be an issue only if production of Taq-pol requires heaps of you protein).  Thinking of both systems,  I might be not right,  but they do not have negative selection that may a be a problem as well. Anyway, the CPR system due it simplicity might be used  for adjusting not only a single gene, but rather a whole circuit. A big step ahead for Synthetic Biology!