Functional Synthetic Biology

Abstract

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.

Keywords: Collaboration; Design; Engineering; Reproducibility; Synthetic Biology.

Figure 1.

Abstraction layers in a function-centric view: system design focuses on biological functions, which are abstracted to produce ‘devices’ by adding a description of an interface, predicted range of behavior and operational context. Devices may then be combined to produce a multi-device system. This system may be described as having a function of its own at a ‘higher level,’ and the system may be abstracted as a new ‘higher-level’ device with a specified interface that does not depend on knowing all details of its implementation. Actually, building the system requires selecting sequences for each device and composing those sequences (e.g. via direct synthesis or assembly reactions) to form a complete implementation of the system. Each device may have multiple different options for how it can be implemented with ‘good enough’ parts, where parts are sequences with a specified interface for combining them to build composite sequences, which also may in turn be abstracted into higher-level parts.

Figure 2.

Other examples of functional devices: (A) the CrtYB enzyme catalyzes the production of beta-carotene from lycopene, (B) excision of a drop-out sequence using Cre recombinase targeting loxP sites, (C) constitutive expression of non-coding RNA using a U6 promoter and (D) CRISPR-based gene editing with constitutive expression of Cas9 and sgRNA. The ‘interface’ by which each device connects to other devices is shown in gray.

Figure 3.

Decoupling function and sequence enables the development of a collaborative ecosystem for distributing, using and improving biological devices. In this vision, (1) an expert curates a device and a set of parts that can implement the device, e.g. a green fluorescence reporter and a BioBricks-compatible coding sequence optimized for E. coli. The expert then (2) publishes the device and parts into a collection where they can be discovered by other synthetic biologists, e.g. version 1.0 of a collection of recommended fluorescent reporters. Synthetic biologists (3) obtain the device from the collection and put it to use in various contexts, e.g. as using the green fluorescence reporter as part of a small-molecule sensing system. Those practitioners may (4) contribute back ‘patches’ to improving the device, e.g. improved characterization data or adaption to another context such as adding an implementation with a MoClo-compatible part optimized for S. cerevisiae. These contributions are then (5) reviewed by either the original expert or others helping to maintain the collection, e.g. checking that the claimed MoClo-compatible part does in fact pass a compatibility check. The experts may similarly (6) contribute their own improvements to the collection as well. All of these improvements are then (7) made available when the collection is republished as a new version, e.g. version 1.1 of the collection of recommended fluorescent reporters. Finally, (8) the device users receive the benefits of these improvements by updating to the newest version, e.g. better predictions of fluorescence in E. coli and use of green fluorescent reporting in S. cerevisiae systems.

Figure 4.

Suggested roadmap of goals, from immediate to long-term, for achieving Functional Synthetic Biology. The first row describes software capabilities for describing behavior and using those descriptions to increase automation in design-related workflows. Next are goals related to increasing the predictability and flexibility of devices. The third row describes how reduction of technical risk (leveraging behavior descriptions and increased predictability and flexibility) will enable routine creation of incrementally larger systems across a growing range of organisms. The final row describes anticipated growth of a functional synthetic biology community building on and amplifying these goals.