A general strategy to construct small molecule biosensors in eukaryotes

Feng, Justin; Jester, Benjamin W.; Tinberg, Christine E.; Mandell, Daniel J.; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J.; Rios, Xavier; Medford, June I.; Church, George M.; Fields, Stanley; Baker, David

doi:10.7554/elife.10606

Cited by 156 publications

(168 citation statements)

References 61 publications

Supporting

Mentioning

165

Contrasting

Order By: Relevance

“…While riboswitches can work well for targets that aptamers can be created for, protein-based biochemical activities are generally out of the scope of detection of such RNA-based parts, and translating these tools in mammalian systems often results in diminished performance 17 . Outside of these somewhat general strategies, a host of other synthetic biology parts have been developed for highly specialized activities 2,21 . Therefore, there is a need for a general method to transduce endogenous chemical and biochemical information into DNA or RNA for subsequent storage or integration with engineered regulatory systems.…”

mentioning

confidence: 99%

Evolution of a split RNA polymerase as a versatile biosensor platform

2017

View full text Add to dashboard Cite

Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies often suffer from a lack of signal-to-noise, requirements for extensive optimization for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE). We then applied the resulting “activity-responsive RNAP” (AR) system to create light and small molecule activated biosensors, demonstrating the “plug-and-play” nature of the platform. Finally, we validated that ARs can interrogate multidimensional protein-protein interactions and trigger RNA nanostructure production, protein synthesis, and gene knockdown in mammalian systems, illustrating the versatility of ARs in synthetic biology applications.

show abstract

mentioning

confidence: 99%

Evolution of a split RNA polymerase as a versatile biosensor platform

2017

View full text Add to dashboard Cite

show abstract

“…For example, Feng and colleagues developed eukaryotic biosensors based on protein lifetime that could be applied to biofuel-related molecules [45]. In this approach, a library of mutagenized LBDs fused to a reporter are screened for high signal in the presence of ligand, due to conditional protein stabilization, and low signal in the absence of ligand, due to degradation by the proteasome.…”

Section: Discussionmentioning

confidence: 99%

Biofuel metabolic engineering with biosensors

Morgan

Nadler

Yokoo

et al. 2016

Current Opinion in Chemical Biology

View full text Add to dashboard Cite

Metabolic engineering offers the potential to renewably produce important classes of chemicals, particularly biofuels, at an industrial scale. DNA synthesis and editing techniques can generate large pathway libraries, yet identifying the best variants is slow and cumbersome. Traditionally, analytical methods like chromatography and mass spectrometry have been used to evaluate pathway variants, but such techniques cannot be performed with high throughput. Biosensors - genetically encoded components that actuate a cellular output in response to a change in metabolite concentration - are therefore a promising tool for rapid and high-throughput evaluation of candidate pathway variants. Applying biosensors can also dynamically tune pathways in response to metabolic changes, improving balance and productivity. Here, we describe the major classes of biosensors and briefly highlight recent progress in applying them to biofuel-related metabolic pathway engineering.

show abstract

“…The rational creation of uniRapR not only offers a powerful means for targeted activation of many pathways to study signaling in living organisms but also exemplifies the strength of computational protein design. The more recent work by Feng et al [49] attempts to provide a general methodology to develop biosensors for a broad range of molecules in eukaryotes. In this method, the ligand-binding domain is fused to either a fluorescent protein or a transcriptional activator and the key feature is that the protein is destabilized by mutation so that the fusion accumulates only in cells containing the target ligand.…”

Section: Engineering Of Bioswitches Via Domain Fusionmentioning

confidence: 99%

Engineering Biomolecular Switches for Dynamic Metabolic Control

Zhou

Zeng

2016

Synthetic Biology – Metabolic Engineering

View full text Add to dashboard Cite

Living organisms have been exploited as production hosts for a large variety of compounds. To improve the efficiency of bioproduction, metabolic pathways in an organism are usually manipulated by various genetic modifications. However, bottlenecks during the conversion of substrate to a desired product may result from cellular regulations at different levels. Dynamic regulation of metabolic pathways according to the need of cultivation process is therefore essential for developing effective bioprocesses, but represents a major challenge in metabolic engineering and synthetic biology. To this end, switchable biomolecules which can sense the intracellular concentrations of metabolites with different response types and dynamic ranges are of great interest. This chapter summarizes recent progress in the development of biomolecular switches and their applications for improvement of bioproduction via dynamic control of metabolic fluxes. Further studies of bioswitches and their applications in industrial strain development are also discussed.

show abstract

A general strategy to construct small molecule biosensors in eukaryotes

Cited by 156 publications

References 61 publications

Evolution of a split RNA polymerase as a versatile biosensor platform

Evolution of a split RNA polymerase as a versatile biosensor platform

Biofuel metabolic engineering with biosensors

Engineering Biomolecular Switches for Dynamic Metabolic Control

Contact Info

Product

Resources

About