Genome sequencing and analysis of the versatile cell factory : Aspergillus niger: CBS 513.88 : Abstract : Nature Biotechnology

Nature Biotechnology 25, 221 - 231 (2007)
Published online: 28 January 2007 | doi:10.1038/nbt1282

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Herman J Pel¹, Johannes H de Winde^1,², David B Archer³, Paul S Dyer³, Gerald Hofmann⁴, Peter J Schaap⁵, Geoffrey Turner⁶, Ronald P de Vries⁷, Richard Albang⁸, Kaj Albermann⁸, Mikael R Andersen⁴, Jannick D Bendtsen⁹, Jacques A E Benen⁵, Marco van den Berg¹⁰, Stefaan Breestraat¹, Mark X Caddick¹¹, Roland Contreras¹², Michael Cornell¹³, Pedro M Coutinho¹⁴, Etienne G J Danchin¹⁴, Alfons J M Debets¹⁵, Peter Dekker¹, Piet W M van Dijck¹, Alard van Dijk¹, Lubbert Dijkhuizen^16,¹⁷, Arnold J M Driessen¹⁷, Christophe d'Enfert¹⁸, Steven Geysens¹², Coenie Goosen^16,¹⁷, Gert S P Groot¹, Piet W J de Groot¹⁹, Thomas Guillemette²⁰, Bernard Henrissat¹⁴, Marga Herweijer¹, Johannes P T W van den Hombergh¹, Cees A M J J van den Hondel²¹, Rene T J M van der Heijden²², Rachel M van der Kaaij^16,¹⁷, Frans M Klis¹⁹, Harrie J Kools⁵, Christian P Kubicek²³, Patricia A van Kuyk²¹, Jürgen Lauber²⁴, Xin Lu²⁵, Marc J E C van der Maarel¹⁶, Rogier Meulenberg¹, Hildegard Menke¹, Martin A Mortimer¹¹, Jens Nielsen⁴, Stephen G Oliver¹³, Maurien Olsthoorn¹, Karoly Pal^15,²⁶, Noël N M E van Peij¹, Arthur F J Ram²¹, Ursula Rinas²⁵, Johannes A Roubos¹, Cees M J Sagt¹, Monika Schmoll²³, Jibin Sun²⁵, David Ussery²⁷, Janos Varga^26,²⁸, Wouter Vervecken¹², Peter J J van de Vondervoort²¹, Holger Wedler²⁴, Han A B Wösten⁷, An-Ping Zeng²⁵, Albert J J van Ooyen¹, Jaap Visser²⁹ & Hein Stam¹

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

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DSM Food Specialties, PO Box 1, 2600 MA Delft, The Netherlands.
Kluyver Centre for Genomics of Industrial Fermentation, Department for Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
Center for Microbial Biotechnology, Technical University of Denmark, Building 223, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark.
Section Fungal Genomics, Laboratory of Microbiology, Wageningen University, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands.
Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
Microbiology, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Biomax Informatics AG, Lochhamer Str. 9, 82152 Martinsried, Germany.
CLC bio, Gustav Wieds Vej 10, 8000 Aarhus C, Denmark.
DSM Anti Infectives, PO Box 425, 2600 KA Delft, The Netherlands.
The University of Liverpool, School of Biological Sciences, Biosciences Bld., Crownstreet, Liverpool L69 7ZB, UK.
Ghent University and VIB, Dept. Molecular Biomedical Research, Unit of Fundamental and Applied Molecular Biology, Technologiepark 927, 9052 Gent, Belgium.
Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS. Universités Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille, France.
Laboratory of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands.
Centre for Carbohydrate Bioprocessing (CCB) TNO-RuG, PO Box 14, 9750 AA Haren, The Netherlands.
Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Materials Science Center Plus, University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands.
Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, 75724 Paris Cedex 15, France.
Swammerdam Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
Laboratoire de Microbiologie, UMR 77, Pathologie Végétale, Université d'Angers, 49045 Angers Cedex, France.
Institute of Biology Leiden, Leiden University, Molecular Microbiology, Wassenaarseweg 64 2333 AL Leiden, The Netherlands.
CMBI, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
Institute of Chemical Engineering, Research Area Gene Technology and Applied Biochemistry, Technical University Vienna, 1060 Vienna, Austria.
Qiagen Genomics Services, Qiagen GmbH., 40724 Hilden, Germany.
Helmholtz Center for Infection Research (former GBF-German Research Centre for Biotechnology), Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
Department of Microbiology, Faculty of Sciences, University of Szeged, PO Box 533, H-6701 Szeged, Hungary.
Center for Biological Sequence Analysis, BioCentrum-DTU, Building 301, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
Fungal Genetics and Technology Consultancy, PO Box 396, 6700 AJ Wageningen, The Netherlands.

Correspondence to: e-mail: hein.stam@dsm.com

Research abstract

Article abstract