Directed evolution: new parts and optimized function

Abstract

Constructing novel biological systems that function in a robust and predictable manner requires better methods for discovering new functional molecules and for optimizing their assembly in novel biological contexts. By enabling functional diversification and optimization in the absence of detailed mechanistic understanding, directed evolution is a powerful complement to 'rational' engineering approaches. Aided by clever selection schemes, directed evolution has generated new parts for genetic circuits, cell-cell communication systems, and non-natural metabolic pathways in bacteria.

Figure 1

Synthetic gene circuits frequently do not function as designed due to mismatches in component properties. Mathematical modeling combined with directed evolution can rapidly tune circuit performance. For example, the sensitivities of two transcription factors to individual inputs can be tuned to generate a functional AND gate from a non-functional circuit.

Figure 2

Directed evolution can be used to generate novel metabolic routes to useful chemicals. A phosphoenolpyruvate (PEP)-independent route (shown in black) to the key intermediate, 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP), was engineered by using directed evolution to enhance a weak DAHP-synthesizing activity present in 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase [23•]. The original route using DAHP synthase is shown in gray.