Conversion

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GLBRC's Conversion Research Area

Conversion

Research team achieves concentrated stream of sugars, cost savings

GLBRC Conversion research aims to increase the quantity, diversity, and efficiency of energy products derived from plant biomass. Researchers focus on improving biological and chemical methods to convert plant material into advanced biofuels or valuable chemicals that can replace petroleum. Basic research discoveries that enhance the efficiency and sustainability of biomass conversion can break down barriers to developing economically viable biofuels technologies.

Conversion Leadership

Scientific Director, Conversion Lead

Landick is an expert on structure, function and regulation of RNA polymerase, the central engine of gene expression. His work spans disciplines from single-molecule biochemistry to genome-scale mechanisms of gene regulation, and includes devising the first single-molecule observation of nucleic...

Conversion Lead

Hegg’s research team focuses on the variety of ways that nature uses metals to activate and/or produce small molecules such as O2, H2, NO, and H2O2.  In pursuit of this goal, his lab utilizes a combination of mechanistic enzymology, molecular...

Project Overview

Stacks of petri dishes in the Currie Lab

Within the Conversion group, researchers apply a combination of synthetic biology, directed evolution, systems biology, and computational modeling approaches to accelerate the rate and yield of microbial conversion of biomass to fuels. Microbial efforts focus on well-established models and biofuel-producing organisms to identify key genes and pathways that may illuminate opportunities for strain improvement. Chemical routes focus on direct catalytic conversion of biomass-derived sugars and lignin into liquid transportation fuels and/or high-value chemicals.

Specific Conversion projects fall in three categories:

  • Engineering microbe strains to enhance stress tolerance and improve conversion efficiency of sugars to biofuels
  • Developing flexible routes to biofuel production that can be adapted to diverse biomass feedstocks
  • Producing light-driven and lignin-derived advanced biofuels, and using catalytic conversion to convert biomass to biofuels and value-added chemicals

 

Conversion Publications

Measurement of intrinsic catalytic activity of Pt monometallic and Pt-MoOx interfacial sites over visible light enhanced PtMoOx/SiO2 catalyst in reverse water gas shift reaction

Insoo Ro; Canan Sener; Thomas M. Stadelman; Madelyn R. Ball; Juan M. Venegas; Samuel P. Burt; I. Hermans; James A. Dumesic; George W. Huber

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2016

Supported Pt-Mo catalysts were prepared with different Mo contents by a controlled surface reaction (CSR) method and studied for the reverse water gas shift (RWGS) reaction under dark and visible light irradiation conditions. Characterization results from Raman spectroscopy, scanning transmission electron microscopy (STEM), CO chemisorption, and inductively coupled plasma-absorption emission spectroscopy (ICP-AES) indicate that selective Mo deposition onto Pt was achieved at low Mo loading (Mo/Pt ratio

Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain

Quinn Dickinson; Scott Bottoms; Li Hinchman; Sean McIlwain; Sheena Li; Chad L. Myers; Charles Boone; Joshua J. Coon; Alexander Hebert; Trey K. Sato; Robert Landick; Jeff S. Piotrowski

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2016

Background
Imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property for strain engineering. To enable rational engineering, we used chemical genomic profiling to understand the effects of IILs on S. cerevisiae.

Results
We found that IILs likely target mitochondria as their chemical genomic profiles closely resembled that of the mitochondrial membrane disrupting agent valinomycin. Further, several deletions of genes encoding mitochondrial proteins exhibited increased sensitivity to IIL. High-throughput chemical proteomics confirmed effects of IILs on mitochondrial protein levels. IILs induced abnormal mitochondrial morphology, as well as altered polarization of mitochondrial membrane potential similar to valinomycin. Deletion of the putative serine/threonine kinase PTK2 thought to activate the plasma-membrane proton efflux pump Pma1p conferred a significant IIL-fitness advantage. Conversely, overexpression of PMA1 conferred sensitivity to IILs, suggesting that hydrogen ion efflux may be coupled to influx of the toxic imidazolium cation. PTK2 deletion conferred resistance to multiple IILs, including [EMIM]Cl, [BMIM]Cl, and [EMIM]Ac. An engineered, xylose-converting ptk2∆ S. cerevisiae (Y133-IIL) strain consumed glucose and xylose faster and produced more ethanol in the presence of 1 % [BMIM]Cl than the wild-type PTK2 strain. We propose a model of IIL toxicity and resistance.

Conclusions
This work demonstrates the utility of chemical genomics-guided biodesign for development of superior microbial biocatalysts for the ever-changing landscape of fermentation inhibitors.

Methodology for the experimental measurement of vapor-liquid equilibrium distillation curves using a modified ASTM D86 setup

Alison M. Ferris; David A. Rothamer

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2016

A method has been developed to determine experimental equilibrium distillation curves using a modified ASTM D86 distillation apparatus.The method determines accurate equilibrium initial boiling points and accounts for the dynamic holdup inherent in distillation curves measured in accordance with the ASTM D86 standard.In this work, the ASTM D86 distillation setup has been modified to simultaneously measure liquid and vapor temperature using two resistance temperature detectors (RTDs) and a data acquisition system has been employed to record temperature data at one-second time intervals for the duration of each distillation.Additionally, the time for each volume recovery point is recorded.The method presented here uses the time-resolved liquid temperature data to identify the true initial boiling point (IBP) of four fuel mixtures of known composition; the IBPs are within 2 °C of the calculated equilibrium values.The time-resolved volume recovery information and the identified initial boiling point time are used to construct a volume evaporated versus time curve.The measured temperatures determined at the corresponding volume evaporated increments provide an experimental equilibrium distillation curve (EEDC). The EEDCs for the four fuel mixtures of known composition match the calculated equilibrium curves within a few degrees Celsius; a maximum mean absolute error of 2.2 ± 1.4 °C was observed.The dynamic holdup (volume difference between volume evaporated and volume recovered) associated with a distillation is found to correlate with the initial boiling point of the fuel being distilled and the temperature of the condenser bath used in the experiment.The method was also applied to measure EEDCs for a gasoline fuel and a diesel fuel, where the compositions were unknown, to investigate the differences between the EEDCs and the ASTM D86 distillation curves.The results highlight the large errors incurred when using ASTM D86 results to approximate equilibrium distillation curves.

Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling

Jonathan A. Stefely; Nicolas W. Kwiecien; Elyse C. Freiberger; Alicia L. Richards; Adam Jochem; Matthew J.P. Rush; Arne Ulbrich; Kyle P. Robinson; Paul D. Hutchins; Michael T. Veling; Xiao Guo; Zachary A. Kemmerer; Kyle J. Connors; Edna A. Trujillo; Jacob Sokol; Harald Marx; Michael S. Westphall; Alexander S. Hebert; David J. Pagliarini;

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2016

Mitochondria are complex organelles linked to diverse human diseases, often through incompletely characterized proteins and pathways. Here, toward systematically defining functions for poorly characterized mitochondrial proteins, we used mass spectrometry to map proteome, lipidome, and metabolome alterations across 174 single gene deletion yeast strains; 144 of these genes have human homologs, and 60 are associated with disease. We generated a dataset with over 3.5 million biomolecule measurements and developed a data analysis and visualization approach to enable biological hypothesis generation. Our multi-omic analysis reveals functionally-predictive molecule covariance networks, correlations between related genes, gene-specific perturbations, and a universal respiration deficiency response—each of which provides a foundation for numerous biological investigations. Here, we leveraged a subset of our data to elucidate uncharacterized features of mitochondrial coenzyme Q (CoQ) biosynthesis—an essential pathway disrupted in many human diseases. Our analyses link seven new proteins to this pathway, including Hfd1p and its human homolog ALDH3A1. Collectively, our results provide molecular insight into mitochondrial biology and establish a widely applicable approach for multi-omic analysis of diagnostic phenotypes and protein functions.

Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network

Meihua Christina Kuang; Paul D. Hutchins; Jason D. Russell; Joshua J. Coon; Chris Todd Hittinger

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2016

The evolutionary mechanisms leading to duplicate gene retention are well understood, but the long-term impacts of paralog differentiation on the regulation of metabolism remain underappreciated. Here we experimentally dissect the functions of two pairs of ancient paralogs of the GALactose sugar utilization network in two yeast species. We show that the Saccharomyces uvarum network is more active, even as over-induction is prevented by a second co-repressor that the model yeast Saccharomyces cerevisiae lacks. Surprisingly, removal of this repression system leads to a strong growth arrest, likely due to overly rapid galactose catabolism and metabolic overload. Alternative sugars, such as fructose, circumvent metabolic control systems and exacerbate this phenotype. We further show that S. cerevisiae experiences homologous metabolic constraints that are subtler due to how the paralogs have diversified. These results show how the functional differentiation of paralogs continues to s

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