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United States Department of Agriculture

Agricultural Research Service

2007 Annual Report

1a.Objectives (from AD-416)
The overall objective of this project is to elucidate genomic mechanisms of detoxification and tolerance of ethanologenic yeast to biomass conversion inhibitors furfural and 5-hydroxymethylfurfural (HMF), and thereafter to genome-wise manipulate and engineer more robust strains for low-cost biomass conversion to ethanol. This study will identify and characterize genes involved in pathways relevant to detoxification, biotransformation, and tolerance to furfural and HMF involved in biomass conversion to ethanol; and elucidate regulatory mechanisms of major gene interactions in relevant pathways involved in furfural and HMF detoxification and tolerance using computational prediction and mathematical modeling.

1b.Approach (from AD-416)
We plan to study genomic regulatory mechanisms of inhibitor detoxification by yeast during ethanol production from dilute acid-hydrolyzed biomass. We propose to characterize the genomic transcriptional profiling of wild-type and several improved, more inhibitor-tolerant strains in response to furfural and 5-hydroxymethylfurfural (HMF) supplied in a defined culture medium. To accomplish this, yeast cells will be sampled in a time-course study to isolate total RNA and conduct microarray experiments using two-color microarray with spiking universal external RNA quality controls. Inhibitor and inhibitor-conversion products, glucose consumption, ethanol production, and other byproducts generated during the fermentation process will also be monitored during the time-course study to establish metabolic profiles for wild-type and more tolerant strains involved in detoxification of biomass conversion inhibitors. Based on data from culture time-course studies, we will propose computational models to predict the behavior of the gene function and expression of natural and genetically engineered networks under furfural and HMF stress. A dynamic mathematical model using difference equations and estimate parameters will be applied and tested for its ability to describe gene regulatory network behavior. Based on these approaches, we will form testable hypotheses to explain molecular and genomic mechanisms of yeast detoxification and tolerance to furfural and HMF.

3.Progress Report
This report documents accomplishments under an Assistance Type Cooperative Agreement between Agricultural Research Services (ARS) and New Mexico State University (NMSU). Additional details of research can be found in the parent project 3620-41000-123-00D entitled "Genomics and Engineering of Stress-tolerant Microbes for Lower Cost Production of Biofuels and Bioproducts." This research will generate computational models to predict ethanologenic yeast gene expression involved in inhibitor tolerance and detoxification. In collaboration with NMSU, we developed computational modeling to infer gene regulatory networks involved in 5-hydroxymethylfurfural stress response for ethanologenic yeast Saccharomyces cerevisiae. The Authorized Departmental Officer's Designated Representative has been keeping a close working relationship and monitoring activities by regular conference calls and frequent e-mail communications. As a joint effort, we published our research [Song M.J. and Liu, Z.L. 2007. A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast) in Lecture Notes Bioinfomatics 4532:77-95. Currently, we are continuing to pursue our research objectives outlined in this project.

Last Modified: 11/30/2015
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