Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power

Design, construction, and application of noncanonical redox cofactor infrastructures

Controlling the flow of carbon and reducing power in biological systems is a central theme in metabolic engineering. Often, trade-offs in pushing carbon flux through targeted pathways while operating in conditions agreeable to the host are required due to the central pools of the shared native redox cofactors NAD(P)/H. Noncanonical redox cofactors (NRCs) have emerged as promising tools to transform how engineers develop biotransformation systems. These new-to-Nature redox cofactors have been demonstrated to function orthogonally to the endogenous cofactors, support pathway thermodynamics optimization, and achieve product scopes previously difficult to reach due to endogenous pathway crosstalk. This review will discuss the development of NRC infrastructures, comprising NRC pools, cofactor reduction sources, and cofactor oxidation sinks, the (pool-source-sink) infrastructure.

Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor

Natural metabolism relies on chemical compartmentalization of two redox cofactors, NAD+ and NADP+, to orchestrate life-essential redox reaction directions. However, in whole cells the reliance on these canonical cofactors limits flexible control of redox reaction direction as these reactions are permanently tied to catabolism or anabolism. In cell-free systems, NADP+ is too expensive in large scale. We have previously reported the use of nicotinamide mononucleotide, (NMN+) as a low-cost, noncanonical redox cofactor capable of specific electron delivery to diverse chemistries. Here, we present Nox Ortho, an NMNH-specific water-forming oxidase, that completes the toolkit to modulate NMNH/NMN+ ratio. This work uncovers an enzyme design principle that succeeds in parallel engineering of six butanediol dehydrogenases as NMN(H)-orthogonal biocatalysts consistently with a 103 - 106 -fold cofactor specificity switch from NAD(P)+ to NMN+. We combine these to produce chiral-pure 2,3-butanediol (Bdo) isomers without interference from NAD(H) or NADP(H) in vitro and in E. coli cells. We establish that NMN(H) can be held at a distinct redox ratio on demand, decoupled from both NAD(H) and NADP(H) redox ratios in vitro and in vivo.

Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme's global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme's access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.