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

Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides

Wiliam G. Alexander; Jennifer H. Wisecaver; Antonis Rokas; Chris T. Hittinger

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2016

Horizontal gene transfer (HGT) among bacteria, archaea, and viruses is widespread, but the extent of transfers from these lineages into eukaryotic organisms is contentious. Here we systematically identify hundreds of genes that were likely acquired horizontally from a variety of sources by the early-diverging fungal phyla Microsporidia and Cryptomycota. Interestingly, the Microsporidia have acquired via HGT several genes involved in nucleic acid synthesis and salvage, such as those encoding thymidine kinase (TK), cytidylate kinase, and purine nucleotide phosphorylase. We show that these HGT-derived nucleic acid synthesis genes tend to function at the interface between the metabolic networks of the host and pathogen. Thus, these genes likely play vital roles in diversifying the useable nucleic acid components available to the intracellular parasite, often through the direct capture of resources from the host. Using an in vivo viability assay, we also demonstrate that one of these genes, TK, encodes an enzyme that is capable of activating known prodrugs to their active form, which suggests a possible treat- ment route for microsporidiosis. We further argue that interfacial genes with well-understood activities, especially those horizontally transferred from bacteria or viruses, could provide medical treat- ments for microsporidian infections.

Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate

Rebecca G. Ong; Alan Higbee; Scott Bottoms; Quinn Dickinson; Dan Xie; Scott A. Smith; Jose Serate; Edward Pohlmann; Arthur D. Jones; Joshua J. Coon; Trey K. Sato; Gregg R. Sanford; Dustin Eilert; Lawrence G. Oates; Jeff S. Piotrowski; Donna M. Bates; David Cavalier; Yaoping Zhang

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2016

Lactobacillus casei as a biocatalyst for biofuel production

Elena Vinay-Lara; Song Wang; Lina Bai; Ekkarat Phrommao; Jeff R. Broadbent; James L. Steele

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2016

Microbial fermentation of sugars from plant biomass to alcohols represents an alternative to petroleum-based fuels. The optimal biocatalyst for such fermentations needs to overcome hurdles such as high concentrations of alcohols and toxic compounds. Lactic acid bacteria, especially lactobacilli, have high innate alcohol tolerance and are remarkably adaptive to harsh environments. This study assessed the potential of five Lactobacillus casei strains as biocatalysts for alcohol production. L. casei 12A was selected based upon its innate alcohol tolerance, high transformation efficiency and ability to utilize plant-derived carbohydrates. A 12A derivative engineered to produce ethanol (L. casei E1) was compared to two other bacterial biocatalysts. Maximal growth rate, maximal optical density and ethanol production were determined under conditions similar to those present during alcohol production from lignocellulosic feedstocks. L. casei E1 exhibited higher innate alcohol tolerance, better growth in the presence of corn stover hydrolysate stressors, and resulted in higher ethanol yields.

Leveraging genetic background effects in Saccharomyces cerevisiae to improve lignocellulosic hydrolysate tolerance

Maria Sardi; Nikolay Rovinskiy; Yaoping Zhang; Audrey P. Gasch

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2016

A major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variation in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene over-expression in different yeast strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to implicate common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene over-expression in three different strains, we revealed the breadth of background-specific effects of gene-fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms. IMPORTANCE Recent studies on natural variation within Saccharomyces cerevisiae have uncovered substantial phenotypic diversity. Here, we take advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated cells' physiological state when exposed to this stress. We also explored strain-specific effects of gene overexpression to further implicate strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.

Leveraging genetic background effects in Saccharomyces cerevisiae to improve lignocellulosic hydrolysate tolerance

Maria Sardi; Nikolay Rovinskiy; Yaoping Zhang; Audrey P. Gasch

More Info

2016

A major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variation in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene over-expression in different yeast strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to implicate common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene over-expression in three different strains, we revealed the breadth of background-specific effects of gene-fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms. IMPORTANCE Recent studies on natural variation within Saccharomyces cerevisiae have uncovered substantial phenotypic diversity. Here, we take advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated cells' physiological state when exposed to this stress. We also explored strain-specific effects of gene overexpression to further implicate strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.

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