title: Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics.
abstract: The filamentous fungus Aspergillus niger is widely exploited for industrial production of enzymes and organic acids. An integrated genomics approach was developed to determine cellular responses of A. niger to protein production in well-controlled fermentations. Different protein extraction methods in combination with automated sample processing and protein identification allowed quantitative analysis of 898 proteins. Three different enzyme overproducing strains were compared to their isogenic fungal host strains. Clear differences in response to the amount and nature of the overproduced enzymes were observed. The corresponding genes of the differentially expressed proteins were studied using transcriptomics. Genes that were up-regulated both at the proteome and transcriptome level were selected as leads for generic strain improvement. Up-regulated proteins included proteins involved in carbon and nitrogen metabolism as well as (oxidative) stress response, and proteins involved in protein folding and endoplasmic reticulum-associated degradation (ERAD). Reduction of protein degradation through the removal of the ERAD factor doaA combined with overexpression of the oligosaccharyl transferase sttC in A. niger overproducing beta-glucuronidase (GUS) strains indeed resulted in a small increase in GUS expression.
authors.affiliation: DSM Food Specialties, PO Box 1, NL-2600 MA Delft, The Netherlands.
authors.forename: Denise I
authors.initials: DI
authors.lastname: Jacobs
authors.forename: Maurien M A
authors.initials: MM
authors.lastname: Olsthoorn
authors.forename: Isabelle
authors.initials: I
authors.lastname: Maillet
authors.forename: Michiel
authors.initials: M
authors.lastname: Akeroyd
authors.forename: Stefaan
authors.initials: S
authors.lastname: Breestraat
authors.forename: Serge
authors.initials: S
authors.lastname: Donkers
authors.forename: Rob A M
authors.initials: RA
authors.lastname: van der Hoeven
authors.forename: Cees A M J J
authors.initials: CA
authors.lastname: van den Hondel
authors.forename: Rolf
authors.initials: R
authors.lastname: Kooistra
authors.forename: Thomas
authors.initials: T
authors.lastname: Lapointe
authors.forename: Hildegard
authors.initials: H
authors.lastname: Menke
authors.forename: Rogier
authors.initials: R
authors.lastname: Meulenberg
authors.forename: Marijke
authors.initials: M
authors.lastname: Misset
authors.forename: Wally H
authors.initials: WH
authors.lastname: Müller
authors.forename: Noël N M E
authors.initials: NN
authors.lastname: van Peij
authors.forename: Arthur
authors.initials: A
authors.lastname: Ram
authors.forename: Sabrina
authors.initials: S
authors.lastname: Rodriguez
authors.forename: Marc S
authors.initials: MS
authors.lastname: Roelofs
authors.forename: Johannes A
authors.initials: JA
authors.lastname: Roubos
authors.forename: Marcel W E M
authors.initials: MW
authors.lastname: van Tilborg
authors.forename: Arie J
authors.initials: AJ
authors.lastname: Verkleij
authors.forename: Herman J
authors.initials: HJ
authors.lastname: Pel
authors.forename: Hein
authors.initials: H
authors.lastname: Stam
authors.forename: Cees M J
authors.initials: CM
authors.lastname: Sagt
mesh_terms: D001234:Aspergillus niger / Q000235:genetics* / Q000378:metabolism*; D005656:Fungal Proteins / Q000096:biosynthesis* / Q000235:genetics*; D020869:Gene Expression Profiling; D023281:Genomics; D005966:Glucuronidase / Q000096:biosynthesis / Q000235:genetics; D007218:Industrial Microbiology; D020543:Proteome / Q000032:analysis
chemical_list: D005656:Fungal Proteins; D020543:Proteome; D005966:Glucuronidase