Understanding Biological Design from Synthetic Circuits

REVIEWS MODELLING Synthetic biology: understanding biological design from synthetic circuits Shankar Mukherji* and Alexander van Oudenaarden‡ Abstract | An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems — from synthetic promoters to the control of cell–cell interactions — has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics. 10–12 Modularity One of the most astounding findings of the Human potential clinical applications . In this Review, however, A property of a system such Genome Project was that our genome contains as many we focus on how synthetic circuits help us to under- that it can be broken down into genes as that of Drosophila melanogaster. This finding stand how natural biological systems are genetically discrete subparts that perform begged the question: how do you get one organism to assembled and how they operate in organisms from specific tasks independently of look like a fly and another like a human with the same microbes to mammalian cells. In this light, synthetic the other subparts. number of genes? One possibility is that the rich rep- circuits have been crucial as simplified test beds in Bioremediation ertoire of non-protein-coding sequences found in the which to refine our ideas of how similarly structured The treatment of pollution with genomes of complex organisms adds many new parts natural networks function, and they have served as microorganisms. with which to generate complexity1. However, a decade tools for controlling natural networks. We highlight of research has put forward the rather different idea that the contribution of synthetic biology to the generation instead of looking at the length of the parts list as the of increasingly quantitative descriptions of gene expres- determinant of organismal complexity, we should look sion and signal transduction, to uncovering the diversity at how those parts fit together2,3. From this perspective, of behaviours that can arise from positive and negative complexity arises from novel combinations of pre-existing feedback systems, and to advances in the rational con- proteins, and the ability to evolve new phenotypes rests trol of spatial organization and cell–cell interactions. on the modularity of biological parts. We pay particular attention to recent progress in using In addition to natural examples of modularity3, synthetic systems to uncover novel aspects of cell biol- strong evidence to support this post-genomic view of ogy, such as how cells decide to undergo apoptosis and biology has come from the synthesis of new biological the molecular basis for communication between the *Harvard-MIT Division of systems. Rational synthesis of biological systems can endoplasmic reticulum and mitochondria. We aim to Health Sciences and Technology, Massachusetts hint at the natural history of how a particular system show that synthetic biological approaches have given 4,5 Institute of Technology, came to acquire its properties . More often, however, us many insights into how the simple building blocks Cambridge, Massachusetts we use synthetic circuits to explore, in a hands-on that underlie complex natural systems work, in addition 02139, USA. fashion, the set of design principles that determine the to basic tools with which to quantitatively characterize ‡Department of Physics and Department of Biology, structure and operation of biological systems. natural phenomena, both of which are crucial for the Massachusetts Institute of The core aim of synthetic biology is to develop and field to progress towards the analysis and complete Technology, Cambridge, apply engineering tools to control cellular behaviour by control of natural circuits. Massachusetts 02139, USA. using precisely characterized parts, such as cis-regulatory Correspondence to A.v.O. elements, to achieve desired functions. An important Quantitative descriptions of gene expression e-mail: [email protected] doi:10.1038/nrg2697 direction, for example, has been to engineer cells with The first step in assembling a biological circuit is to 6 Published online practical applications in the areas of bioremediation , gather the component parts. In cells, circuits are accom- 10 November 2009 biosensing7 and biofuel production8,9, or even with plished by gene expression, and so a great deal of effort NATURE REVIEWS | GENETICS VOLUME 10 | DECEMBER 2009 | 859 © 2009 Macmillan Publishers Limited. All rights reserved REVIEWS Gene expression Synthetic biology tool Natural phenomenon Transcriptional regulation. The earliest contributions subprocess analysed of synthetic biology to understanding natural biological Transcription Inducible promoter • Stochastic gene expression processes include detailed, quantitative measurements • Gene regulation function of transcriptional regulation, which build on a founda- tion laid 50 years ago in the groundbreaking work of Promoter library • Genomic positioning of researchers such as Jacob and Monod13. Synthetic con- TF sites transfer function Distal Core Proximal • Weak TF–DNA interactions structs have been used to map out the • TF–TF interactions that relates the input concentrations of transcription factors (TFs)14,15 and inducers16 to the output concentrations of reporter genes14,17,18, single mRNA molecules19,20 or single proteins21. Many of these constructs have also been used to measure the mean output of the transcriptional process and the higher-order moments (such as the variance) in organisms ranging from Escherichia coli and Bacillus subtilis to mammalian cells. Single-molecule studies in these model organisms have directly estab- lished that mRNA and proteins are produced in bursts of activity22. A key question in the study of transcriptional regulation is how the architecture of promoters affects transcriptional activity. For example, below we describe several studies that have shown how the number and genomic positions of TF binding sites affect transcrip- AraC LacI LuxR TetR tional activity. Given the combinatorial control of gene expression, it is also crucial to study how multiple TFs Post-transcription RBS accessibility Stochastic gene interact with DNA and with each other to tune mRNA or -translation CR expression production. Endogenous promoters use all of these AUG parameters to specify either a desired transcription rate RBS or a Boolean function, such as an AND gate that allows Aptamer Cell cycle progression transcription to occur only when all TF binding sites in the promoter are occupied. Promoter library studies in bacteria and eukaryotes. The experimental breakthrough that allowed quantita- Translation Inducible protease Enzyme kinetics tive measurements of the transcriptional power of different promoter architectures was the use of combinatorial clpX promoter libraries23. Libraries of promoters that drive Figure 1 | Controlling the flow of information from DNA toNa proteinsture Revie usingws | Genetics reporter proteins, such as luciferase or fluorescent synthetic elements. The diagram shows the transcriptional and post-transcriptional proteins, allow for an unbiased measurement of tran- processes in gene expression that can be manipulated by synthetic biology tools, scriptional activity over the space of possible promoters with some example applications. The differences in shading reflect variations — such an unbiased method can be used to ascertain in the strength of the input from the four regulators (for example, dark pink rules that describe the responsiveness of a promoter to represents strong input, and light pink represents weak input). CR, complementary TFs. Earlier work used randomly mutated promoters region to the RBS; RBS, ribosome binding site; TF, transcription factor. to draw inferences about the functional subparts of the Promoter library diagram is reproduced, with permission, from REF. 24 (2007) Macmillan Publishers Ltd. All rights reserved. RBS accessibility diagram is promoter, such as the TATA box; by contrast, the con- reproduced, with permission, from REF. 38 (2004) Macmillan Publishers Ltd. struction of combinatorial promoter libraries involves All rights reserved. Aptamer diagram is reproduced, with permission, from REF. 34 identifying specific operator sites that bind TFs and ran- (2001) Elsevier. domly ligating them together in a way that shuffles their relative positions and copy numbers (FIG. 1). The studies highlighted below have combined such promoter libraries and modelling to show that the strength of a promoter in synthetic biology has gone into investigating the rules is determined largely by the position of TF binding sites surrounding the expression of genes, particularly the with respect to key promoter elements, such as the TATA processes of transcription and translation. The precise box, and with respect to each other. Motif measurements afforded by artificially constructed sys- The simplest case is to understand how the posi- A subcircuit that is embedded tems allow us to transform qualitative notions of tran- tioning of a single operator affects the expression of a in a larger network and that is

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