title: Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila.
abstract: Myceliophthora thermophila is a thermophilic fungus whose genome encodes a wide range of carbohydrate-active enzymes (CAZymes) involved in plant biomass degradation. Such enzymes have potential applications in turning different kinds of lignocellulosic feedstock into sugar precursors for biofuels and chemicals. The present study examined and compared the transcriptomes and exoproteomes of M. thermophila during cultivation on different types of complex biomass to gain insight into how its secreted enzymatic machinery varies with different sources of lignocellulose. In the transcriptome analysis three monocot (barley, oat, triticale) and three dicot (alfalfa, canola, flax) plants were used whereas in the proteome analysis additional substrates, i.e. wood and corn stover pulps, were included. A core set of 59 genes encoding CAZymes was up-regulated in response to both monocot and dicot straws, including nine polysaccharide monooxygenases and GH10, but not GH11, xylanases. Genes encoding additional xylanolytic enzymes were up-regulated during growth on monocot straws, while genes encoding additional pectinolytic enzymes were up-regulated in response to dicot biomass. Exoproteome analysis was generally consistent with the conclusions drawn from transcriptome analysis, but additional CAZymes that accumulated to high levels were identified. Despite the wide variety of biomass sources tested some CAZy family members were not expressed under any condition. The results of this study provide a comprehensive view from both transcriptome and exoproteome levels, of how M. thermophila responds to a wide range of biomass sources using its genomic resources.
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: magdalena.kolbusz@concordia.ca.
authors.forename: Magdalena Anna
authors.initials: MA
authors.lastname: Kolbusz
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: marcos.difalco@concordia.ca.
authors.forename: Marcos
authors.initials: M
authors.lastname: Di Falco
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: nadeeza.ishmael@concordia.ca.
authors.forename: Nadeeza
authors.initials: N
authors.lastname: Ishmael
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: sandrine.marqueteau@concordia.ca.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Marqueteau
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: marie-claude.moisan@concordia.ca.
authors.forename: Marie-Claude
authors.initials: MC
authors.lastname: Moisan
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: Cassio.Baptista@nrc-cnrc.gc.ca.
authors.forename: Cassio da Silva
authors.initials: CDS
authors.lastname: Baptista
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: justin.powlowski@concordia.ca.
authors.forename: Justin
authors.initials: J
authors.lastname: Powlowski
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada. Electronic address: adrian.tsang@concordia.ca.
authors.forename: Adrian
authors.initials: A
authors.lastname: Tsang
mesh_terms: D018533:Biomass; D020869:Gene Expression Profiling; D006026:Glycoside Hydrolases / Q000235:genetics* / Q000378:metabolism*; D010944:Plants / Q000378:metabolism* / Q000382:microbiology; D020543:Proteome / Q000032:analysis*; D020037:Sordariales / Q000201:enzymology* / Q000235:genetics*
chemical_list: D020543:Proteome; D006026:Glycoside Hydrolases
keywords: Biomass degradation; Carbohydrate-active enzymes; Mass spectrometry; Myceliophthora thermophila; RNA-Seq