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

Directed evolution reveals unexpected epistatic interactions that alter metabolic regulation and enable anaerobic xylose use by Saccharomyces cerevisiae

Trey K. Sato; Mary Tremaine; Lucas S. Parreiras; Alexander S. Herbert; Kevin S. Myers; Alan J. Higbee; Maria Sardi; Sean J. McIlwain; Irene M. Ong; Rebecca J. Breuer; Ragothaman Avanasi Narasimhan; Mick A. McGee; Quinn Dickinson; Alex La Reau; Dan Xie; Mingyuan Tian; Jeff S. Piotrowski; Jennifer L. Reed; Yaoping Zhang; Joshua J. Coon; Chris Todd Hittinger; Audrey P. Gasch; Robert Landick

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2016

Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes

Jennifer H. Wisecaver; William G. Alexander; Sean B. King; Chris Todd Hittinger; Antonis Rokas

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2016

Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide—a ubiquitous toxin whose antimicrobial properties many life forms exploit in competition and to defend against infection—to nitrate—a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family’s known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intra-bacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show are capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi poss­ess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Previous studies of cytotoxic aerolysins and antibacterial lysozymes also reported high rates of GD and HGT, raising the hypothesis that such single-protein metabolic modules might be frequent actors in host-microbe arms races due to their functional independence and propensity for GD and HGT.

Electron partitioning in anoxic phototrophic bacteria

Melanie A. Spero; Saheed Imam; Daniel R. Noguera; Timothy J. Donohue

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2016

Photosynthetic cells make major contributions to many important processes on this planet, including solar energy capture, nitrogen or carbon dioxide sequestration and production of useful biocommodities. The sheer number of photosynthetic cells also makes them significant contributors to global nutrient cycling, especially in aquatic ecosystems. For each of these activities, photosynthetic cells need efficient systems for production and distribution of reducing power among the myriad of cellular pathways that depend on reductant. This chapter focuses on the partitioning of reductant in purple nonsulfur photosynthetic bacteria. It summarizes known membrane and cytoplasmic enzymes and pathways that need the reductant produced via photochemical activity (quinol in these organisms). These observations illustrate that quinol is used to provide reducing power to a variety of crucial cellular processes (cellular biosynthesis, maintenance of a proton motive force) and key assimilatory pathways (carbon dioxide and nitrogen fixation), depending on the availability of nutrients. We also summarize data illustrating that cells use a variety of pathways to recycle excess reductant. Finally, we illustrate how recent use of genomic and computational approaches to the analysis of these and other photosynthetic organisms has provided testable predictions and considerable new insight into the partitioning of reductant among that is produced from solar energy capture.

Genome sequence and analysis of a stress-tolerant, wild-derived strain of Saccharomyces cerevisiae used in biofuels research

Sean J. McIlwain; David Peris; Maria Sardi; Oleg V. Moskvin; Fujie Zhan; Kevin S. Myers; Nicholas M. Riley; Alyssa Buzzell; Lucas S. Parreiras; Irene M. Ong; Robert Landick; Joshua J. Coon; Audrey P. Gasch; Trey K. Sato; Chris Todd Hittinger

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2016

The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.

Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora Hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov.

Mariana R. Lopes; Camila G. Morais; Jacek Kominek; Raquel M. Cadete; Marco A. Soares; Ana Paula T. Uetanabaro; Cesar Fonseca; Marc-Andre Lachance; Chris T. Hittinger; Carlos A. Rosa

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2016

Three novel D-xylose-fermenting yeast species of Spathaspora clade were recovered from rotting wood in regions of the Atlantic Rainforest ecosystem in Brazil. Differentiation of new species was based on analyses of the gene encoding the D1/D2 sequences of large subunit of rRNA and on 642 conserved, single-copy, orthologous genes from genome sequence assemblies from the newly described species and 15 closely-related Debaryomycetaceae/Metschnikowiaceae species. Spathaspora girioi sp. nov. produced unconjugated asci with a single elongated ascospore with curved ends; ascospore formation was not observed for the other two species. The three novel species ferment D-xylose with different efficiencies. Spathaspora hagerdaliae sp. nov. and Sp. girioi sp. nov. showed xylose reductase (XR) activity strictly dependent on NADPH, whereas Sp. gorwiae sp. nov. had XR activity that used both NADH and NADPH as co-factors. The genes that encode enzymes involved in D-xylose metabolism (XR, xylitol dehydrogenase and xylulokinase) were also identified for these novel species. The type strains are Sp. girioi sp. nov. UFMG-CM-Y302(T) (=CBS 13476), Sp. hagerdaliae f.a., sp. nov. UFMG-CM-Y303(T) (=CBS 13475) and Sp. gorwiae f.a., sp. nov. UFMG-CM-Y312(T) (=CBS 13472).

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