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

Applications of constraint-based models for biochemical production

Cameron Cotten; Jennifer L. Reed

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2016

Biofuels are metabolic products, and knowledge of how metabolism operates is critical to understanding and improving biofuel production by microorganisms. Constraint-based metabolic modeling has been an important technique to broaden and deepen our knowledge of microbial metabolism and regulation. Genome-scale metabolic models enable global analysis of microbial metabolism by considering all metabolic reactions simultaneously. Genome-scale metabolic reconstructions are comprehensive listings of all the reactions, compounds, and genes that are involved in cellular metabolism for a particular organism. Constraint-based modeling methods use the information in metabolic reconstructions to predict intracellular fluxes and design strains for chemical and biofuel production. Recently, constraint-based modeling has been successful in designing a number of chemical production strains.

Comparative genomics of biotechnologically important yeasts

Robert Riley; Sajeet Haridas; Kenneth H. Wolfe; Mariana R. Lopes; Chris T. Hittinger; Markus Goker; Asaf A. Salamov; Jennifer H. Wisecaver; Tanya M. Long; Christopher H. Calvey; Andrea L. Aerts; Keriie W. Barry; Cindy Choi; Alicia Clum; Aisling Y. Coughlan; Shweta Deshpande; Alexander P. Douglass; Sara J. Hanson; Hans-Peter Klenk; Kurt M. LaButti; Alla Lapidus; Erika A. Lindquist; Anna M. Lipzen; Jan P. Meier-Kolthoff; Robin A. Ohm; Robert P. Otillar; Jasmyn L. Pangilinan; Yi Peng; Antonis Rokas; Carlos A. Rosa; Carmen Scheuner; Andriy A. Sibirny; Jason C. Slot; J. B. Stielow; Hui Sun; Cletus P. Kurtzman; Meredith Blackwell; Igor V. Grigoriev; Thomas W. Jeffries

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2016

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

Nicolas Bellora; Martin Moline; Marcia David-Palma; Marco A. Coelho; Chris T. Hittinger; Jose P. Sampaio; Paula Goncalves; Diego Libkind

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2016

BACKGROUND: The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed. RESULTS: Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cystofilobasidiales have the highest number of intron-containing genes and highest number of introns per gene. The Patagonian strain showed 4.4 % of nucleotide sequence divergence compared to the European strains which differed from each other by only 0.073 %. All known genes related to the synthesis of astaxanthin were annotated. A hitherto unknown gene cluster potentially responsible for photoprotection (mycosporines) was found in the newly sequenced P. rhodozyma strains but was absent in the non-mycosporinogenic strain CBS 6938. A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, genes involved in sexual reproduction were found and annotated. CONCLUSIONS: A draft genome sequence of the type strain of P. rhodozyma is now available, and comparison with that of the Patagonian population suggests the latter deserves to be assigned to a distinct variety. An unexpected genetic trait regarding high occurrence of introns in P. rhodozyma and other Cystofilobasidiales was revealed. New genomic insights into fungal homothallism were also provided. The genetic basis of several additional photoprotective and antioxidant strategies were described, indicating that P. rhodozyma is one of the fungi most well-equipped to cope with environmental oxidative stress, a factor that has probably contributed to shaping its genome.

Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus

David Peris; Quinn Langdon; Ryan V. Moriarty; Kayla Sylvester; Martin Bontrager; Guillaume Charron; Jean-Baptiste LeDuc; Christian R. Landry; Diego Libkind; Chris T. Hittinger

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2016

Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.

Different functions of phylogenetically distinct bacterial complex I isozymes

Melanie A. Spero; Joshua R. Brickner; Jordan T. Mollet; Tippapha Pisithkul; Daniel Amador-Noguez; Timothy J. Donohue

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2016

NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to the different electron transport chains of bacteria has only been tested in a few species. The discovery that individual bacteria contain phylogenetically distinct complex I enzymes begs the question of whether individual isozymes serve different functions. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an α-proteobacterium that contains well-characterized electron transport chains. We report that complex I function is central to R. sphaeroides energy metabolism, since a strain lacking both complex I isozymes grew more slowly via aerobic respiration and had anaerobic growth defects. Several observations also led us to conclude that the two complex I isozymes are not functionally redundant. For example, the complex I isozyme typically found in α-proteobacteria (referred to as complex IA) is required for photoheterotrophic growth on carbon sources whose catabolism is predicted to produce reduced quinone, while the isozyme that is commonly present in γ-proteobacteria (complex IE) is required for photoheterotrophic growth on carbon sources whose catabolism produces high levels of NADH. Additionally, complex IA is required to produce wild type levels of H2, while complex IE is dispensable for this process. We propose that these findings illustrate specific roles of complex I isozymes in either NADH synthesis (complex IA) or NADH oxidation (complex IE) during phototrophic growth. Unlike the singular role of complex I in mitochondrial aerobic respiration, we predict that the phylogenetically-distinct complex I isozymes found across bacterial species have evolved to enhance function in their respective electron transport chains

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