Synthetic biology: new engineering rules for an emerging discipline

Abstract

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

“…In another example of metabolic engineering, byproduct formation was minimized in E. coli during fermentation by disrupting the tricarboxylic acid cycle in order to reduce oxygen demand for NADH oxidation and eliminating pathways for NADH oxidation other than the electron transport system [ 43]. Other methods for cofactor balancing include overexpressing proteins to increase NADH [ 44] or NADPH [ 45] availability, interconverting NADH and NADPH [ 46], and changing the coenzyme specificity of specific proteins [ 47]. In silico genome-scale models have also been extended beyond gene deletion or overexpression strategies to include gene insertion strategies for redox balancing.…”

Synthetic biology – the state of play

“…Indeed the importance of engineering science to systems biology was clear recognised in the Inquiry into systems biology by the Academy of Medical Sciences and the Royal Academy of Engineering [UK] [25]. In this regard, the commonality of the two fields, in terms of basic methods, has been recognised in a number of books [26][27][28] -and [29] is an example of a paper which specifically addresses the issue of the application of engineering principles to synthetic biology.…”

The Conception of Life in Synthetic Biology

“…In other words, there is no difference between biological and mechanical processes, all of them are based 4 Rational design in the unnatural molecular biology approach could for instance be applied for the development of alternative genetic codes, to design HNA or GNA nucleotides (Schmidt 2010) or alternative nucleobases (Benner and Sismour 2005). on physical laws. Bioengineers on the other hand want to turn biology into an engineering discipline, they want to introduce engineering and a rational design into biotechnology (Andrianantoandro et al 2006;Heinemann and Panke 2006). Of course they agree with Descartes and La Mettrie in that the processes in living organisms are based on physical laws.…”

“…The bioengineering branch is driven by the aim of adapting the products of biotechnology to the layout of computers, especially in their organisation in a hierarchical structure made from standardised elements (Andrianantoandro et al 2006). It is therefore not surprising that the international synthetic biology competition, which largely follows the engineering approach, is called iGEM, with GEM standing for 'genetically engineered machines'.…”