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Development of an Integrated EMSL MS and NMR Metabolic Flux Analysis Capability In Support of Systems Biology: Test Application for Biofuels Production


EMSL Project ID
48535

Abstract

An important element in the production of biofuels is the metabolic engineering process required to maximize the production of renewable biofuel molecules from fermentable substrates. Biofuel production rates are, in simplest terms, the flux through the particular reaction creating the desired metabolite product, and understanding the level of production of a given metabolite requires understanding the integrated network response encompassing the entire genome of the host. Metabolic fluxes cannot be measured directly, and so must be inferred from other measurements. Much work has been done in the area of quantifying metabolic fluxes using stable isotope labeling and either nuclear magnetic resonance (NMR) or mass spectrometry (MS) detection methods. Metabolic flux analysis (MFA) then employs various formal mathematical approaches including stationary or quasi-steady state approaches as well as non-stationary or dynamic approaches. EMSL/PNNL presently lacks MFA capabilities commensurate with its stature as a world-class research facility. We do, however, possess state-of-the art instrumentation in both Mass Spectrometry and Nuclear Magnetic Resonance spectroscopy, which can generate the datasets needed for MFA. We therefore propose establishment of a new EMSL MFA capability to complement existing systems biology approaches in the context of a microbial biofuel production system. This will be accomplished by working in partnership with Dr. Wolfgang Wiechert and Dr. Katharina Noeh, the developers of 13CFLUX2 to implement their MFA platform at EMSL, and then, in a collaborative effort, to apply 13CFLUX2 to an existing EMSL User Project with Dr. Hector Garcia-Martin, as described herein. Establishing an EMSL base of MFA software and expertise that integrates into an overall complete systems biology platform will be crucial to fulfilling the Biosystem Dynamics and Design research goals of EMSL, to “understand intra- and intercellular complexes and dynamic processes in microbes, fungi and plant roots to advance systems biology for bioenergy and bio-renewables”.

Project Details

Start Date
2014-10-20
End Date
2016-09-30
Status
Closed

Team

Principal Investigator

Nancy Isern
Institution
Environmental Molecular Sciences Laboratory

Co-Investigator(s)

David Hoyt
Institution
Environmental Molecular Sciences Laboratory

Team Members

Evgeny Tishchenko
Institution
Agilent Technologies

Melanie Bukovec
Institution
Pacific Northwest National Laboratory

Sydney Dautel
Institution
Pacific Northwest National Laboratory

Patrick Reardon
Institution
Oregon State University

Mark Borkum
Institution
Pacific Northwest National Laboratory

Ronald Taylor
Institution
National Institutes of Health

Young-Mo Kim
Institution
Pacific Northwest National Laboratory

Eric Hill
Institution
Pacific Northwest National Laboratory

Thomas Metz
Institution
Pacific Northwest National Laboratory

Joshua Adkins
Institution
Pacific Northwest National Laboratory

Related Publications

Borkum MI, PN Reardon, RC Taylor, and NG Isern. 2017. "Modeling Framework for Isotopic Labeling of Heteronuclear Moieties." Journal of Cheminformatics 9(1):Article No. 14. doi:10.1186/s13321-017-0201-7
Reardon PN, C Marean-Reardon, MA Bukovec, BE Coggins, and NG Isern. 2016. "3D TOCSY-HSQC NMR for Metabolic Flux Analysis using Non-Uniform Sampling." Analytical Chemistry 88(5):2825-2831. doi:10.1021/acs.analchem.5b04535