title: Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes.
abstract: The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA.
authors.forename: Kevin V
authors.initials: KV
authors.lastname: Solomon
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA.
authors.forename: Charles H
authors.initials: CH
authors.lastname: Haitjema
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA.
authors.forename: John K
authors.initials: JK
authors.lastname: Henske
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA.
authors.forename: Sean P
authors.initials: SP
authors.lastname: Gilmore
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA.
authors.forename: Diego
authors.initials: D
authors.lastname: Borges-Rivera
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Lipzen
authors.affiliation: Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Heather M
authors.initials: HM
authors.lastname: Brewer
authors.affiliation: Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Samuel O
authors.initials: SO
authors.lastname: Purvine
authors.affiliation: Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Aaron T
authors.initials: AT
authors.lastname: Wright
authors.affiliation: Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK.
authors.forename: Michael K
authors.initials: MK
authors.lastname: Theodorou
authors.affiliation: U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA.
authors.forename: Dawn A
authors.initials: DA
authors.lastname: Thompson
authors.affiliation: Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA. momalley@engineering.ucsb.edu.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: O'Malley
mesh_terms: D000818:Animals; D001230:Aspergillus / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D001709:Biotechnology / Q000379:methods*; D044602:Cellulases / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D002482:Cellulose / Q000378:metabolism; D041981:Gastrointestinal Tract / Q000382:microbiology*; D060434:Herbivory; D022661:RNA, Untranslated / Q000235:genetics; D013379:Substrate Specificity; D014242:Trichoderma / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D014990:Xylans / Q000378:metabolism*
chemical_list: D022661:RNA, Untranslated; D014990:Xylans; D002482:Cellulose; D044602:Cellulases