Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems

Abstract

Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues.

Figure 1

Sources of context effects and their connectivity. (A) Compositional context. , Physical composition: undesigned direct interaction between synthetic parts on the same molecule. , Functional composition: unexpected effects from module coupling, component titration or circuit “impedance”. (B) Host context. *, Parasitic interactions: undesirable interactions between synthetic and host endogenous components. , Host resources: synthetic devices often rely on host resources and machinery for functioning (R). Their production and partition can affect device activity. Alternatively, their depletion can affect host physiology, which can then affect the function of synthetic components. Also, host-specific variations of these endogenous components can be a source of context effects. , Host cell processes: synthetic devices are coupled to cellular fundamental processes such as replication, cell division and growth. (C) Environmental context. , Direct effects: environmental factors such as temperature and pH can directly impact part activity. , Host-mediated coupling: the environment defines the coupling circuit-host. For example, metabolic load can be sustainable or not in relation to the amount and quality of external nutrients.