title: Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus.
abstract: BACKGROUND
  White-rot basidiomycete fungi are potent degraders of plant biomass, with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. The Polyporale fungus Pycnoporus coccineus BRFM310 grows well on both coniferous and deciduous wood. In the present study, we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks and tested the effect of the secreted enzymes on lignocellulose deconstruction.
  
  
  RESULTS
  Transcriptomic and proteomic analyses revealed that P. coccineus grown separately on pine and aspen displayed similar sets of transcripts and enzymes implicated in lignin and polysaccharide degradation. In particular, the expression of lignin-targeting oxidoreductases, such as manganese peroxidases, increased upon cultivation on both woods. The sets of enzymes secreted during growth on both pine and aspen were more efficient in saccharide release from pine than from aspen, and characterization of the residual solids revealed polysaccharide conversion on both pine and aspen fiber surfaces.
  
  
  CONCLUSIONS
  The combined analysis of soluble sugars and solid residues showed the suitability of P. coccineus secreted enzymes for softwood degradation. Analyses of solubilized products and residual surface chemistries of enzyme-treated wood samples pointed to differences in fiber penetration by different P. coccineus secretomes. Accordingly, beyond the variety of CAZymes identified in P. coccineus genome, transcriptome and secretome, we discuss several parameters such as the abundance of manganese peroxidases and the potential role of cytochrome P450s and pectin degradation on the efficacy of fungi for softwood conversion.
authors.affiliation: Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; Polytech'Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada.
authors.forename: Marie
authors.initials: M
authors.lastname: Couturier
authors.affiliation: Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; Polytech'Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France.
authors.forename: David
authors.initials: D
authors.lastname: Navarro
authors.affiliation: INRA, UMR1319 Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, 78352 Jouy-En-Josas, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Chevret
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 13288 Marseille, France ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia ; INRA, USC 1408 AFMB, 13288 Marseille, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; Polytech'Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France.
authors.forename: François
authors.initials: F
authors.lastname: Piumi
authors.affiliation: CIB, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Ruiz-Dueñas
authors.affiliation: CIB, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.
authors.forename: Angel T
authors.initials: AT
authors.lastname: Martinez
authors.affiliation: US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Riley
authors.affiliation: US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Lipzen
authors.affiliation: Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; Polytech'Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France.
authors.forename: Jean-Guy
authors.initials: JG
authors.lastname: Berrin
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada.
authors.forename: Emma R
authors.initials: ER
authors.lastname: Master
authors.affiliation: Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France ; Polytech'Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques, 163 avenue de Luminy, 13288 Marseille, France.
authors.forename: Marie-Noëlle
authors.initials: MN
authors.lastname: Rosso
keywords: Carbohydrate-active enzymes; Lignin-active enzymes; Proteomics; Pycnoporus coccineus; ToF-SIMS; Transcriptomics; White-rot