Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway

Kealan Exley,Soo Mei Chee,Richard Ian Kitney,Lorna Suckling,Christopher Robert Reynolds,Paul S. Freemont,Argyro Tsipa,David McClymont

doi:10.1186/s13036-019-0141-z

Kealan Exley, Soo Mei Chee + Show 6 more

Open Access

https://doi.org/10.1186/s13036-019-0141-z

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Abstract

BackgroundThe automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. The characterisation information held on datasheets can be used to determine whether a biological part meets the design requirements. To manage the design of genetic pathways, researchers have turned to modelling-based computer aided design software tools.ResultAn automated workflow has been developed for the design and build of heterologous metabolic pathways. In addition, to demonstrate the powers of electronic datasheets we have developed software which can transfer part information from a datasheet to the Design of Experiment software JMP. To this end we were able to use Design of Experiment software to rationally design and test randomised samples from the design space of a lycopene pathway in E. coli. This pathway was optimised by individually modulating the promoter strength, RBS strength, and gene order targets.ConclusionThe use of standardised and characterised biological parts will empower a design-oriented synthetic biology for the forward engineering of heterologous expression systems. A Design of Experiment approach streamlines the design-build-test cycle to achieve optimised solutions in biodesign. Developed automated workflows provide effective transfer of information between characterised information (in the form of datasheets) and DoE software.

Highlights

The automation of modular cloning methodologies permits the assembly of many genetic designs
The pipeline developed minimises human involvement by; (Step 1) linking data produced from characterisation experiments to datasheets (Fig. 1a), (Step 2) linking the data from datasheets to design tools (Fig. 1c), and (Step 3) linking genetic configurations from the design space to liquid-handling robotics for the assembly of intended genetic metabolic pathways (Fig. 1d)
To achieve a complete design-build framework, a link is required between characterised data of biological parts essential to build genetic pathways and the tools used to design these pathways, such as the Design of Experiment (DoE) software tool JMP

Summary

Introduction

The automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. One of the principal ideas behind synthetic biology is the utilisation of standardised biological parts for the assembly of genetic devices, circuits and pathways [1, 2]. As the field has developed, so too has the availability of standard parts; hastened by the arrival of cloning toolkits for DNA assembly [3, 4]. These toolkits are often designed for one-pot restriction-ligation based cloning of distinct parts, with many of the parts associated with characterisation data [4].

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