Precision metabolic engineering: The design of responsive, selective, and controllable metabolic systems.

Metabolic engineering is generally focused on static optimization of cells to maximize production of a desired product, though recently dynamic metabolic engineering has explored how metabolic programs can be varied over time to improve titer. However, these are not the only types of applications where metabolic engineering could make a significant impact. Here, we discuss a new conceptual framework, termed "precision metabolic engineering," involving the design and engineering of systems that make different products in response to different signals. Rather than focusing on maximizing titer, these types of applications typically have three hallmarks: sensing signals that determine the desired metabolic target, completely directing metabolic flux in response to those signals, and producing sharp responses at specific signal thresholds. In this review, we will first discuss and provide examples of precision metabolic engineering. We will then discuss each of these hallmarks and identify which existing metabolic engineering methods can be applied to accomplish those tasks, as well as some of their shortcomings. Ultimately, precise control of metabolic systems has the potential to enable a host of new metabolic engineering and synthetic biology applications for any problem where flexibility of response to an external signal could be useful.

Precise metabolic engineering of carotenoid biosynthesis in Escherichia coli towards a low-cost biosensor.

Micronutrient deficiencies, including zinc deficiency, are responsible for hundreds of thousands of deaths annually. A key obstacle to allocating scarce treatment resources is the ability to measure population blood micronutrient status inexpensively and quickly enough to identify those who most need treatment. This paper develops a metabolically engineered strain of Escherichia coli to produce different colored pigments (violacein, lycopene, and ß-carotene) in response to different extracellular zinc levels, for eventual use in an inexpensive blood zinc diagnostic test. However, obtaining discrete color states in the carotenoid pathway required precise engineering of metabolism to prevent reaction at low zinc concentrations but allow complete reaction at higher concentrations, and all under the constraints of natural regulator limitations. Hence, the metabolic engineering challenge was not to improve titer, but to enable precise control of pathway state. A combination of gene dosage, post-transcriptional, and post-translational regulation was necessary to allow visible color change over physiologically relevant ranges representing a small fraction of the regulator's dynamic response range, with further tuning possible by modulation of precursor availability. As metabolic engineering expands its applications and develops more complex systems, tight control of system components will likely become increasingly necessary, and the approach presented here can be generalized to other natural sensing systems for precise control of pathway state.

Development of a Pigment-Based Whole-Cell Zinc Biosensor for Human Serum.

Deficiencies in vitamins and minerals (micronutrients) are a critical global health concern, in part due to logistical difficulties in assessing population micronutrient status. Whole-cell biosensors offer a unique opportunity to address this issue, with the potential to move sample analysis from centralized, resource-intensive clinics to minimal-resource, on-site measurement. Here, we present a proof-of-concept whole-cell biosensor in Escherichia coli for detecting zinc, a micronutrient for which deficiencies are a significant public health burden. Importantly, the whole-cell biosensor produces readouts (pigments) that are visible to the naked eye, mitigating the need for measurement equipment and thus increasing feasibility for sensor field-friendliness and affordability at a global scale. Two zinc-responsive promoter/transcription factor systems are used to differentially control production of three distinctly colored pigments in response to zinc levels in culture. We demonstrate strategies for tuning each zinc-responsive system to turn production of the different pigments on and off at different zinc levels, and we demonstrate production of three distinct color regimes over a concentration range relevant to human health. We also demonstrate the ability of the sensor cells to grow and produce pigment when cultured in human serum, the ultimate target matrix for assessing zinc nutritional status. Specifically, we present approaches to overcome innate immune responses that would otherwise hinder bacterial sensor survival, and we demonstrate production of multiple pigment regimes in human serum with different zinc levels. This work provides proof of principle for the development of low-cost, minimal-equipment, field-deployable biosensors for nutritional epidemiology applications.