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

OptSSeq: high-throughput sequencing readout of growth enrichment defines optimal gene expression elements for homoethanologenesis

Indro N. Ghosh; Robert Landick

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2016

The optimization of synthetic pathways is a central challenge in metabolic engineering. OptSSeq (Optimization by Selection and Sequencing) is one approach to this challenge. OptSSeq couples selection of optimal enzyme expression levels linked to cell growth rate with high-throughput sequencing to track enrichment of gene expression signals (promoters and ribosome-binding sites) from a combinatorial library. OptSSeq yields information on both optimal and suboptimal enzyme levels, and helps identify constraints that limit maximal product formation. Here we report a proof-of-concept implementation of OptSSeq using homoethanologenesis, a two-step pathway consisting of pyruvate decarboxylase (Pdc) and alcohol dehydrogenase (Adh) that converts pyruvate to ethanol and is naturally optimized in the bacterium Zymomonas mobilis. We used OptSSeq to determine optimal gene expression signals and enzyme levels for Z. mobilis Pdc, AdhA, and AdhB expressed in Escherichia coli. By varying both expression signals and gene order, we identified an optimal solution using only Pdc and AdhB. In contrast to current dogma, we discovered that the Fe2+-dependent AdhB is preferable to Zn2+-dependent AdhA for rapid growth in both E. coli and Z. mobilis. Finally, by comparing predictions of growth-linked metabolic flux to enzyme synthesis costs, we established that optimal E. coli homoethanologenesis was achieved by our best pdc-adhB expression cassette and that the remaining constraints lie in the E. coli metabolic network or inefficient Pdc or AdhB function in E. coli. OptSSeq is a general tool for synthetic biology to tune enzyme levels in any pathway whose optimal function can be linked to cell growth or survival.

PtMo bimetallic catalysts synthesized by controlled surface reactions for water gas shift

Canan Sener; Thejas S. Wesley; Ana C. Alba-Rubio; Mrunmayi D. Kumbhalkar; Sikander H. Hakim; Fabio H. Riberio; Jeffrey T. Miller; James A. Dumesic

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2016

Supported PtMo bimetallic catalysts were prepared by controlled surface reactions (CSR) and studied for water gas shift (WGS) at 543 K. Carbon and silica supports were used for the preparation of monometallic Pt catalysts, and Mo was deposited onto these catalysts by reaction with cycloheptatriene molybdenum tricarbonyl ((C7H8)Mo(CO)3). Catalysts were characterized by CO chemisorption, inductively coupled plasma-atomic emission spectroscopy (ICP-AES), STEM/EDS, and XAS analysis. We report that carbon-supported Pt nanoparticles are saturated with Mo species at a Mo:Pt atomic ratio of 0.32. Molybdenum has a strong promotional effect in these catalysts, increasing the TOF by up to a factor of more than 4000. Silica-supported catalysts were found to be more active, but the TOF promotional effect of Mo was smaller than for the carbon-supported catalysts at 15. EDS analyses and activity studies showed that the formation of bimetallic catalysts was therefore more efficient using the carbon support. The active sites for WGS are suggested to be at the interface between Pt atoms and Mo moieties that are possibly in an oxidized form.

Quantifying pretreatment degradation compounds in solution and accumulated by cells during solids and yeast recycling in the Rapid Bioconversion with Integrated recycling Technology process using AFEX™ corn stover

Cory Sarks; Alan Higbee; Jeff Piotrowski; Saisi Xue; Joshua J. Coon; Trey K. Sato; Mingjie Jin; Venkatesh Balan; Bruce E. Dale

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2016

Effects of degradation products (low molecular weight compounds produced during pretreatment) on the microbes used in the RaBIT (Rapid Bioconversion with Integrated recycling Technology) process that reduces enzyme usage up to 40% by efficient enzyme recycling were studied. Chemical genomic profiling was performed, showing no yeast response differences in hydrolysates produced during RaBIT enzymatic hydrolysis. Concentrations of degradation products in solution were quantified after different enzymatic hydrolysis cycles and fermentation cycles. Intracellular degradation product concentrations were also measured following fermentation. Degradation product concentrations in hydrolysate did not change between RaBIT enzymatic hydrolysis cycles; the cell population retained its ability to oxidize/reduce (detoxify) aldehydes over five RaBIT fermentation cycles; and degradation products accumulated within or on the cells as RaBIT fermentation cycles increased. Synthetic hydrolysate was used to confirm that pretreatment degradation products are the sole cause of decreased xylose consumption during RaBIT fermentations.

Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

Xing-Xing Shen; Xiaofan Zhou; Jacek Kominek; Cletus P. Kurtzman; Chris T. Hittinger; Antonis Rokas

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2016

Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

Selective hydrogenation of unsaturated carbon-carbon bonds in aromatic-containing platform molecules

Thomas J. Schwartz; Spencer D. Lyman; Ali H. Motagamwala; Max A. Mellmer; James A. Dumesic

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2016

The combination of chemical and biological catalysis enables the production from biomass of coumarin and dihydrocoumarin (DHC), opening new routes to the formation of fine chemicals and pharmaceutical building blocks. Each of these products requires the hydrogenation of 4-hydroxycoumarin (4HC) to 4-hydroxydihydrocoumarin (4HDHC), which, in turn, requires the reduction of an unsaturated C–C bond in the presence of an aromatic ring. Using in situ attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, we show that reaction at 348 K over monometallic Pd catalysts leads to the partial reduction of the aromatic ring in 4HC, obtaining 93% selectivity for C═C bond hydrogenation at 82% 4HC conversion and with a low turnover frequency (TOF). Decreasing the Pd dispersion from 70% to 6% not only leads to an increase in the rate of 4HC hydrogenation, but it also leads to an increase in the rate of overhydrogenation. However, the formation of bimetallic PdAu nanoparticles inhibits the overhydrogenation reaction while also doubling the TOF to a value of 6 ks–1 for 4HDHC production. A bimetallic PdAu catalyst supported on SiO2 leads to 97% selectivity for C═C bond hydrogenation at 86% 4HC conversion, while an acidic support such as amorphous silica–alumina can be used to produce DHC directly from 4HC.

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