Synthetic biology: putting synthesis into biology

Abstract

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself--encompassing many branches of science and across many scales of application. New DNA synthesis and assembly techniques have made routine customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery--a self-replicating organism--is being pursued at this moment. The aim of this article is to dissect and organize these various components of synthetic biology into a coherent picture.

Figure 1

Overview of synthetic biology. This scheme describes the relationship among the various methods used in synthetic biology and different applications of synthetic biology on different levels.

Figure 2

Synthesis of large DNA molecules in yeast. (a) Yeast homologous recombination mechanism. DNA fragments sharing an overlap region at 3^′‐ and 5^′‐ends with the neighboring DNA fragments can be assembled into a single larger DNA molecule. (b) Construction of a synthetic M. genitalium genome. Twenty‐five different overlapping DNA segments (blue arrows, 17–35 kb each) composing the genome were co‐transformed into yeast followed by assembly of the entire genome in a single step.

Figure 3

Analog‐to‐digital converter. (a) In this example system, the two toggle switches are initially ‘off’, i.e., repressor 2 and repressor 4 are expressed. Separately in a sensor array, repressor 1 has an input dependent promoter with a low input threshold. When input concentration rises above its threshold, repressor 1 is expressed, switching the state of toggle switch 1 to ‘on’. Using another input dependent promoter that has a higher threshold, switch 2 is toggled ‘on’ at a higher input concentration. (b) The corresponding digital response of the example gene switches.

Figure 4

Artemisinin biosynthetic pathway. The mevalonate‐based FPP biosynthetic pathway has been assembled from S. cerevisiae (HMG‐CoA synthase, hmgS; N‐terminally truncated HMG‐CoA reductase, thmgR; mevalonate kinase, mk; phosphomevalonate kinase, pmk; and mevalonate diphosphate decarboxylase, mpd) and E. coli (acetoacetyl‐CoA synthase, atoB; IPP isomerase, idi; and FPP synthase, ispA), and expressed in E. coli. The pathway is assembled in two operons, one is responsible for converting acetyl‐CoA to mevalonate, and the other is responsible for converting mevalonate to FPP. Further introduction of amorphadiene synthase (ads), oxidase (p450), and redox partner (cpr) allows the strain to convert FPP to artemisinic acid which can be chemically converted to artemisinin..

Figure 5

A synthetic predator–prey ecosystem. The system consists of two engineered bacterial populations that control each other's survival and death. CcdB is a cytotoxic protein that kills the cell and CcdA is its antidote. In the predator, CcdB is constitutively expressed, and will die off without an external signal. The antidote CcdA is expressed only when the predator receives signaling molecules (3OC6HSL) from the prey. At high enough prey concentration, the predator will survive. However, the prey also receives signaling molecules (3OC12HSL) from the predator. In the prey, CcdB is expressed in response to the predator signal. Therefore, in high enough predator concentration, the prey will die.