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

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.Electronic supplementary materialThe online version of this article (10.1186/s13036-019-0141-z) contains supplementary material, which is available to authorized users.

DNA-BOT: A low-cost, automated DNA assembly platform for synthetic biology

“…We previously developed the Biopart Assembly Standard for Idempotent Cloning (BASIC) method and standard to enable highly accurate multi-part DNA assembly at both manual bench and fully automated Biofoundry scale 5,6 . BASIC defines a single biopart storage format with prefix and suffix sequences flanking each part and provides a method for highly accurate linker-based DNA assembly.…”

“…BASIC provides this high accuracy and efficiency through long linker overhangs, guiding the assembly of linker-ligated parts. Currently, BASIC and alternative DNA assembly methods have only been automated using expensive infrastructure, limiting community access to the benefits automated DNA assembly brings to research and applications in biology 6,[8][9][10][11] .…”

Beyond natural: synthetic expansions of botanical form and function

“…While biologists typically learn to vary a single parameter at a time, the combined influence of factors may be nonlinear, therefore obtaining an optimal configuration requires optimising multiple factors in combination. The use of statistical experiment design, also known as design of experiments (DoE), has therefore been applied in synthetic biology to understand the relative importance and influence of multiple factors on the desired outcome while reducing the overall number of experiments (Exley et al , 2019). DoE mathematically defines relationships between influencing factors and applies statistics to infer an experimental design by which only the necessary combinations (rather than every possible combination) need to be tested to obtain the equation.…”

“…DoE mathematically defines relationships between influencing factors and applies statistics to infer an experimental design by which only the necessary combinations (rather than every possible combination) need to be tested to obtain the equation. Following a history of use in bioprocess engineering it has been adopted into synthetic biology to, for example, optimise metabolic pathways (Brown et al , 2018; Exley et al , 2019).…”

Modular Engineering of Biomass Degradation Pathways

“…Several tools have been built for the development and assessment of modular pathways. Initial work, such as the BioBrick framework [160,161], focused on assembly standards that could then lead to standard characterization [162][163][164]. This standardization of methods, materials, and parts seeks to enable the rapid development of modular parts through the division of labor and characterization across the bioengineering field.…”