title: The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger.
abstract: Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that the transcriptional response after 6h of exposure to wheat straw was very different from the response at 24h of exposure to the same substrate. For example, less than half of the genes encoding carbohydrate active enzymes that were induced after 24h of exposure to wheat straw, were also induced after 6h exposure. Importantly, over a third of the genes induced after 6h of exposure to wheat straw were also induced during 6h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. We show, using proteomics, that carbon-starved cultures indeed release CAZymes with predicted activity on plant polysaccharides. Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes.
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: jolanda.van_munster@nottingham.ac.uk.
authors.forename: Jolanda M
authors.initials: JM
authors.lastname: van Munster
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: paul.daly@nottingham.ac.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Daly
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: stephane.delmas@upmc.fr.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Delmas
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: steven.pullan@phe.gov.uk.
authors.forename: Steven T
authors.initials: ST
authors.lastname: Pullan
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK. Electronic address: martin.blythe@nottingham.ac.uk.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Blythe
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK. Electronic address: sunir.malla@nottingham.ac.uk.
authors.forename: Sunir
authors.initials: S
authors.lastname: Malla
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: matt.kokolski@nottingham.ac.uk.
authors.forename: Matthew
authors.initials: M
authors.lastname: Kokolski
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: emelie_noltorp@hotmail.com.
authors.forename: Emelie C M
authors.initials: ECM
authors.lastname: Noltorp
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: kristin.wennberg@telia.com.
authors.forename: Kristin
authors.initials: K
authors.lastname: Wennberg
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: richard.fetherston@hotmail.co.uk.
authors.forename: Richard
authors.initials: R
authors.lastname: Fetherston
authors.affiliation: Biological Mass Spectrometry Facility biOMICS, University of Sheffield, Brook Hill Road, Sheffield S3 7HF, UK. Electronic address: r.g.beniston@sheffield.ac.uk.
authors.forename: Richard
authors.initials: R
authors.lastname: Beniston
authors.affiliation: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK. Electronic address: xly20@cam.ac.uk.
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Yu
authors.affiliation: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK. Electronic address: pd101@cam.ac.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Dupree
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: david.archer@nottingham.ac.uk.
authors.forename: David B
authors.initials: DB
authors.lastname: Archer
mesh_terms: D001234:Aspergillus niger / Q000201:enzymology* / Q000378:metabolism*; D050260:Carbohydrate Metabolism; D002244:Carbon / Q000378:metabolism*; D005656:Fungal Proteins / Q000032:analysis; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D006026:Glycoside Hydrolases / Q000378:metabolism*; D018547:Plant Stems / Q000378:metabolism; D020543:Proteome / Q000032:analysis; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D020543:Proteome; D002244:Carbon; D006026:Glycoside Hydrolases
keywords: Aspergillus niger; CAZy enzymes; Carbon starvation; Inducer; Lignocellulose; Transcriptome