Decoupling Isoprenoid Yield and Productivity via ATP Reduction
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Solution Overview
Problem
In biomanufacturing of isoprenoids, the inverse correlation between yield and productivity, known as rate-yield coupling, limits the ability to achieve high yield and high productivity simultaneously, as increasing oxygen and sugar uptake rates decrease isoprenoid yield, negating the cost benefits of increased productivity.
Innovation Solution
The method involves reducing ATP utilization in host cells through the use of ATP depleting agents, overexpression of ATP dissipation or uncoupling enzymes, and reducing carbon flux through the citric acid cycle, specifically using weak organic acids like benzoic acid, Saccharomyces cerevisiae SSB1, NADH oxidase, and alternative oxidase to decouple yield and productivity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If the rate of oxygen and sugar uptake is increased to improve productivity, then productivity increases, but yield decreases
Solution Approach 1:
The patent changes the metabolic parameters of the host cell by reducing ATP levels through various mechanisms (ATP-depleting agents, alternative oxidases, futile cycles). This parameter change decouples the inverse relationship between productivity and yield, allowing both to be optimized simultaneously without the traditional trade-off
Solution Approach 2:
The patent introduces intermediary substances and mechanisms (ATP-depleting agents like weak organic acids, alternative oxidase enzymes, futile cycle enzymes) that mediate between substrate uptake and product formation. These intermediaries alter the metabolic flow to reduce ATP utilization and break the rate-yield coupling
2Productivity
If ATP utilization is reduced to decouple yield and productivity, then both yield and productivity can be maximized, but additional process complexity is introduced
Solution Approach 1:
The patent employs self-service mechanisms where the host cell's own metabolic pathways are harnessed to reduce ATP utilization. Examples include expressing alternative oxidases that naturally bypass ATP-generating pathways, or introducing futile cycles that inherently consume ATP without requiring external control mechanisms
Solution Approach 2:
The patent simplifies the overall process by making a fundamental parameter change (reducing ATP levels) that cascades through the system to achieve decoupling, rather than implementing multiple complex control systems to manage the rate-yield relationship
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach allows for the simultaneous achievement of high yield and high productivity in isoprenoid production by reducing ATP levels and altering metabolic pathways, thereby breaking the rate-yield coupling, maximizing isoprenoid product output per cost of fermentation.
Implementation Method 1
reducing ATP utilization during fermentation by addition of one or more ATP depleting agents
Implementation Method 2
ATP utilization is reduced by over expression of one or more ATP dissipation enzymes
Implementation Method 3
one or more ATP uncoupling enzymes are selected from NADH oxidase (NOX)
Implementation Method 4
one or more ATP uncoupling enzymes are selected from alternative oxidase (AOX)
Implementation Method 5
ATP levels are reduced by expression of a futile cycle in the host cell
Implementation Method 6
reducing carbon flux through the citric acid cycle (TCA) in the host cell by inhibition of one or more TCA enzymes
Implementation Method 7
fermentation of a host cell that produces the non-catabolic compound
Data Source
AI summary
Provided herein are compositions and methods for uncoupling the yield and productivity of an isoprenoid compound produced in a host cell. In some embodiments, the yield and productivity are uncoupled by genetically modifying the host cell to reduce flux through the citric acid cycle (TCA). In other embodiments, the yield and productivity are uncoupled by reducing the levels of ATP in the host cell.