High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA

Metabolic engineering uses enzymes to produce small molecules with industrial, pharmaceutical, and energy applications. However, efforts to optimize enzymatic pathways for commercial production are limited by the throughput of assays for quantifying metabolic intermediates and end products. We developed a multiplexed method for profiling CoA-dependent pathways that uses a cysteine-terminated peptide to covalently capture CoA-bound metabolites. Captured metabolites are then rapidly separated from the complex mixture by immobilization onto arrays of self-assembled monolayers and directly quantified by SAMDI mass spectrometry. We demonstrate the throughput of the assay by characterizing the cell-free synthesis of HMG-CoA, a key intermediate in the biosynthesis of isoprenoids, collecting over 10,000 individual spectra to map more than 800 unique reaction conditions. We anticipate that our rapid and robust analytical method will accelerate efforts to engineer metabolic pathways.

Using Microfluidics and Imaging SAMDI-MS To Characterize Reaction Kinetics

Microfluidic platforms have enabled the simplification of biochemical assays with a significant reduction in the use of reagents, yet the current methods available for analyzing reaction products can limit applications of these approaches. This paper demonstrates a simple microfluidic device that incorporates a functionalized self-assembled monolayer to measure the rate constant for a chemical reaction. The device mixes the reactants and allows them to selectively immobilize to the monolayer at the base of a microfluidic channel in a time-dependent manner as they flow down the channel. Imaging self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (iSAMDI-MS) is used to acquire a quantitative image representing the time-resolved progress of the reaction as it flowed through the channel. Knowledge of the surface immobilization chemistry and the fluid front characteristics allows for the determination of the chemical reaction rate constant. This approach widens the applicability of microfluidics for chemical reaction monitoring and establishes a label-free method for studying processes that occur within a dispersive regime.