title: Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.
abstract: Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.
authors.affiliation: Department of Genetics, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Dana J
authors.initials: DJ
authors.lastname: Wohlbach
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.forename: Trey K
authors.initials: TK
authors.lastname: Sato
authors.forename: Katlyn M
authors.initials: KM
authors.lastname: Potts
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.forename: Kurt M
authors.initials: KM
authors.lastname: Labutti
authors.forename: Hui
authors.initials: H
authors.lastname: Sun
authors.forename: Alicia
authors.initials: A
authors.lastname: Clum
authors.forename: Jasmyn L
authors.initials: JL
authors.lastname: Pangilinan
authors.forename: Erika A
authors.initials: EA
authors.lastname: Lindquist
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Mingjie
authors.initials: M
authors.lastname: Jin
authors.forename: Christa
authors.initials: C
authors.lastname: Gunawan
authors.forename: Venkatesh
authors.initials: V
authors.lastname: Balan
authors.forename: Bruce E
authors.initials: BE
authors.lastname: Dale
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Jeffries
authors.forename: Robert
authors.initials: R
authors.lastname: Zinkel
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.forename: Audrey P
authors.initials: AP
authors.lastname: Gasch
mesh_terms: D056804:Biofuels / Q000382:microbiology*; D002175:Candida / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D005285:Fermentation / Q000235:genetics*; D005658:Fungi / Q000235:genetics*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005838:Genotype; D010641:Phenotype; D010802:Phylogeny; D013045:Species Specificity; D014994:Xylose / Q000378:metabolism*
chemical_list: D056804:Biofuels; D014994:Xylose