Using high throughput data and dynamic flux balance modeling techniques to identify points of constraint in xylose utilization in Saccharomyces cerevisiae

Authors: HOHENSCHUH, WILLIAM - Oregon State University; Hector, Ronald - Ron; CHAPLEN, FRANK - Oregon State University; MURTHY, GANTI - Oregon State University

Submitted to: Systems Microbiology and Biomanufacturing
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2020
Publication Date: 6/30/2020
Citation: Hohenschuh, W., Hector, R.E., Chaplen, F., Murthy, G.S. 2021. Using high throughput data and dynamic flux balance modeling techniques to identify points of constraint in xylose utilization in Saccharomyces cerevisiae. Systems Microbiology and Biomanufacturing. 1: 58-75. https://doi.org/10.1007/s43393-020-00003-x.
DOI: https://doi.org/10.1007/s43393-020-00003-x

Interpretive Summary: Economically viable production of renewable, value-added chemicals from lignocellulosic biomass is limited by the rate and yield at which biomass-derived sugars can be converted to desired end products. Lignocellulosic biomass sugars are primarily glucose and xylose. Glucose is readily and efficiently utilized by brewer’s yeast (Saccharomyces cerevisiae); xylose utilization and product yield are significantly lower. Genome-scale dynamic flux balance modeling offers an opportunity to identify bottlenecks and to consider the interplay between different types of bottlenecks and changing culture conditions. This technique was used to identify a series of dynamic bottlenecks impacting xylose utilization and to suggest the highest value targets for future strain modification. The model developed suggests an increase ethanol production by 50% could be achieved with coproduction of another commercially valuable product, succinate. Alternative co-product production pathways were also identified as potential targets for manipulation to increase xylose conversion. A clear understanding of what bottlenecks occur when using xylose will benefit future strain development.

Technical Abstract: Several enzymes and cofactors have been identified as contributing to the slow utilization of xylose by xylose-fermenting strains of Saccharomyces cerevisiae. However, there has been no consensus on which of these possible bottlenecks are the most important to address. A previous strain characterization study from our lab suggested that insufficient NAD+'limits fermentation and may be the most important bottleneck affecting utilization of xylose for the production of ethanol. The development and validation of a genome scale dynamic flux balance model would help to verify the existence and extent of this and other metabolic bottlenecks and suggest solutions to guide future strain development thereby minimizing bottleneck impact on process economics.