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

Herman J. Pel, Johannes H. de Winde, David B. Archer, Paul S. Dyer, Gerald Hoffmann, Peter J. Schaap, Geoffrey Turner, Ronald P. de Vries, Richard Albang, Kaj Albermann, Mikael Rørdam Andersen, Jannick Dyrløv Bendtsen, Jacques A. E. Benen, Marco van den Berg, Stefaan Breestraat, Mark X. Caddick, Roland Contreras, Michael Cornell, Pedro M. Coutinho, Etienne G. J. DanchinAlfons J. M. Debets, Peter Dekker, Piet W. van Dijck, Alard van Dijk, Lubbert Dijkhuizen, Arnold J. M. Driessen, Christophe d'Enfert, Steven Geysens, Coenie Goosen, Gert S. P. Groot, Piet W. J. de Groot, Thomas Guillemette, Bernard Henrissat, Marga Herweijer, Johannes P. T. W. van den Hombergh, Cees A. M. J. J. van den Hondel, Rene T. J. M. van der Heijden, Rachel M. van der Kaaij, Frans M. Klis, Harrie J. Kools, Christian P. Kubicek, Patricia A. van Kuyk, Juergen Lauber, Xin Lu, Marc J. E. C. van der Maarel, Roiger Meulenberg, Hildegard Menke, Martin A. Mortimer, Jens Nielsen, Stephen G. Oliver, Maurien Olsthoorn, Karoly Pal, Noel N. M. E. van Peij, Arthur F. Ram, Ursula Rinas, Johannes A. Roubos, Cees M. J. Sagt, Monika Schmoll, Jibin Sun, David Ussery, Janos Varga, Wouter Vervecken, Peter J. J. van de Vondervoort, Holger Wedler, Han A. B. Wosten, An-Ping Zeng, Albert J. J. van Ooyen, Jaap Visser, Hein Stam

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    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.
    Original languageEnglish
    JournalNature Biotechnology
    Volume25
    Issue number2
    Pages (from-to)221-31
    ISSN1087-0156
    Publication statusPublished - 2007

    Cite this

    Pel, H. J., de Winde, J. H., Archer, D. B., Dyer, P. S., Hoffmann, G., Schaap, P. J., ... Stam, H. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology, 25(2), 221-31.
    Pel, Herman J. ; de Winde, Johannes H. ; Archer, David B. ; Dyer, Paul S. ; Hoffmann, Gerald ; Schaap, Peter J. ; Turner, Geoffrey ; de Vries, Ronald P. ; Albang, Richard ; Albermann, Kaj ; Andersen, Mikael Rørdam ; Bendtsen, Jannick Dyrløv ; Benen, Jacques A. E. ; van den Berg, Marco ; Breestraat, Stefaan ; Caddick, Mark X. ; Contreras, Roland ; Cornell, Michael ; Coutinho, Pedro M. ; Danchin, Etienne G. J. ; Debets, Alfons J. M. ; Dekker, Peter ; van Dijck, Piet W. ; van Dijk, Alard ; Dijkhuizen, Lubbert ; Driessen, Arnold J. M. ; d'Enfert, Christophe ; Geysens, Steven ; Goosen, Coenie ; Groot, Gert S. P. ; de Groot, Piet W. J. ; Guillemette, Thomas ; Henrissat, Bernard ; Herweijer, Marga ; van den Hombergh, Johannes P. T. W. ; van den Hondel, Cees A. M. J. J. ; van der Heijden, Rene T. J. M. ; van der Kaaij, Rachel M. ; Klis, Frans M. ; Kools, Harrie J. ; Kubicek, Christian P. ; van Kuyk, Patricia A. ; Lauber, Juergen ; Lu, Xin ; van der Maarel, Marc J. E. C. ; Meulenberg, Roiger ; Menke, Hildegard ; Mortimer, Martin A. ; Nielsen, Jens ; Oliver, Stephen G. ; Olsthoorn, Maurien ; Pal, Karoly ; van Peij, Noel N. M. E. ; Ram, Arthur F. ; Rinas, Ursula ; Roubos, Johannes A. ; Sagt, Cees M. J. ; Schmoll, Monika ; Sun, Jibin ; Ussery, David ; Varga, Janos ; Vervecken, Wouter ; van de Vondervoort, Peter J. J. ; Wedler, Holger ; Wosten, Han A. B. ; Zeng, An-Ping ; van Ooyen, Albert J. J. ; Visser, Jaap ; Stam, Hein. / Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. In: Nature Biotechnology. 2007 ; Vol. 25, No. 2. pp. 221-31.
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    title = "Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88",
    abstract = "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.",
    author = "Pel, {Herman J.} and {de Winde}, {Johannes H.} and Archer, {David B.} and Dyer, {Paul S.} and Gerald Hoffmann and Schaap, {Peter J.} and Geoffrey Turner and {de Vries}, {Ronald P.} and Richard Albang and Kaj Albermann and Andersen, {Mikael R{\o}rdam} and Bendtsen, {Jannick Dyrl{\o}v} and Benen, {Jacques A. E.} and {van den Berg}, Marco and Stefaan Breestraat and Caddick, {Mark X.} and Roland Contreras and Michael Cornell and Coutinho, {Pedro M.} and Danchin, {Etienne G. J.} and Debets, {Alfons J. M.} and Peter Dekker and {van Dijck}, {Piet W.} and {van Dijk}, Alard and Lubbert Dijkhuizen and Driessen, {Arnold J. M.} and Christophe d'Enfert and Steven Geysens and Coenie Goosen and Groot, {Gert S. P.} and {de Groot}, {Piet W. J.} and Thomas Guillemette and Bernard Henrissat and Marga Herweijer and {van den Hombergh}, {Johannes P. T. W.} and {van den Hondel}, {Cees A. M. J. J.} and {van der Heijden}, {Rene T. J. M.} and {van der Kaaij}, {Rachel M.} and Klis, {Frans M.} and Kools, {Harrie J.} and Kubicek, {Christian P.} and {van Kuyk}, {Patricia A.} and Juergen Lauber and Xin Lu and {van der Maarel}, {Marc J. E. C.} and Roiger Meulenberg and Hildegard Menke and Mortimer, {Martin A.} and Jens Nielsen and Oliver, {Stephen G.} and Maurien Olsthoorn and Karoly Pal and {van Peij}, {Noel N. M. E.} and Ram, {Arthur F.} and Ursula Rinas and Roubos, {Johannes A.} and Sagt, {Cees M. J.} and Monika Schmoll and Jibin Sun and David Ussery and Janos Varga and Wouter Vervecken and {van de Vondervoort}, {Peter J. J.} and Holger Wedler and Wosten, {Han A. B.} and An-Ping Zeng and {van Ooyen}, {Albert J. J.} and Jaap Visser and Hein Stam",
    year = "2007",
    language = "English",
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    journal = "Nature Biotechnology",
    issn = "1087-0156",
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    Pel, HJ, de Winde, JH, Archer, DB, Dyer, PS, Hoffmann, G, Schaap, PJ, Turner, G, de Vries, RP, Albang, R, Albermann, K, Andersen, MR, Bendtsen, JD, Benen, JAE, van den Berg, M, Breestraat, S, Caddick, MX, Contreras, R, Cornell, M, Coutinho, PM, Danchin, EGJ, Debets, AJM, Dekker, P, van Dijck, PW, van Dijk, A, Dijkhuizen, L, Driessen, AJM, d'Enfert, C, Geysens, S, Goosen, C, Groot, GSP, de Groot, PWJ, Guillemette, T, Henrissat, B, Herweijer, M, van den Hombergh, JPTW, van den Hondel, CAMJJ, van der Heijden, RTJM, van der Kaaij, RM, Klis, FM, Kools, HJ, Kubicek, CP, van Kuyk, PA, Lauber, J, Lu, X, van der Maarel, MJEC, Meulenberg, R, Menke, H, Mortimer, MA, Nielsen, J, Oliver, SG, Olsthoorn, M, Pal, K, van Peij, NNME, Ram, AF, Rinas, U, Roubos, JA, Sagt, CMJ, Schmoll, M, Sun, J, Ussery, D, Varga, J, Vervecken, W, van de Vondervoort, PJJ, Wedler, H, Wosten, HAB, Zeng, A-P, van Ooyen, AJJ, Visser, J & Stam, H 2007, 'Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88', Nature Biotechnology, vol. 25, no. 2, pp. 221-31.

    Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. / Pel, Herman J.; de Winde, Johannes H.; Archer, David B.; Dyer, Paul S.; Hoffmann, Gerald; Schaap, Peter J.; Turner, Geoffrey; de Vries, Ronald P.; Albang, Richard; Albermann, Kaj; Andersen, Mikael Rørdam; Bendtsen, Jannick Dyrløv; Benen, Jacques A. E.; van den Berg, Marco; Breestraat, Stefaan; Caddick, Mark X.; Contreras, Roland; Cornell, Michael; Coutinho, Pedro M.; Danchin, Etienne G. J.; Debets, Alfons J. M.; Dekker, Peter; van Dijck, Piet W.; van Dijk, Alard; Dijkhuizen, Lubbert; Driessen, Arnold J. M.; d'Enfert, Christophe; Geysens, Steven; Goosen, Coenie; Groot, Gert S. P.; de Groot, Piet W. J.; Guillemette, Thomas; Henrissat, Bernard; Herweijer, Marga; van den Hombergh, Johannes P. T. W.; van den Hondel, Cees A. M. J. J.; van der Heijden, Rene T. J. M.; van der Kaaij, Rachel M.; Klis, Frans M.; Kools, Harrie J.; Kubicek, Christian P.; van Kuyk, Patricia A.; Lauber, Juergen; Lu, Xin; van der Maarel, Marc J. E. C.; Meulenberg, Roiger; Menke, Hildegard; Mortimer, Martin A.; Nielsen, Jens; Oliver, Stephen G.; Olsthoorn, Maurien; Pal, Karoly; van Peij, Noel N. M. E.; Ram, Arthur F.; Rinas, Ursula; Roubos, Johannes A.; Sagt, Cees M. J.; Schmoll, Monika; Sun, Jibin; Ussery, David; Varga, Janos; Vervecken, Wouter; van de Vondervoort, Peter J. J.; Wedler, Holger; Wosten, Han A. B.; Zeng, An-Ping; van Ooyen, Albert J. J.; Visser, Jaap; Stam, Hein.

    In: Nature Biotechnology, Vol. 25, No. 2, 2007, p. 221-31.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

    AU - Pel, Herman J.

    AU - de Winde, Johannes H.

    AU - Archer, David B.

    AU - Dyer, Paul S.

    AU - Hoffmann, Gerald

    AU - Schaap, Peter J.

    AU - Turner, Geoffrey

    AU - de Vries, Ronald P.

    AU - Albang, Richard

    AU - Albermann, Kaj

    AU - Andersen, Mikael Rørdam

    AU - Bendtsen, Jannick Dyrløv

    AU - Benen, Jacques A. E.

    AU - van den Berg, Marco

    AU - Breestraat, Stefaan

    AU - Caddick, Mark X.

    AU - Contreras, Roland

    AU - Cornell, Michael

    AU - Coutinho, Pedro M.

    AU - Danchin, Etienne G. J.

    AU - Debets, Alfons J. M.

    AU - Dekker, Peter

    AU - van Dijck, Piet W.

    AU - van Dijk, Alard

    AU - Dijkhuizen, Lubbert

    AU - Driessen, Arnold J. M.

    AU - d'Enfert, Christophe

    AU - Geysens, Steven

    AU - Goosen, Coenie

    AU - Groot, Gert S. P.

    AU - de Groot, Piet W. J.

    AU - Guillemette, Thomas

    AU - Henrissat, Bernard

    AU - Herweijer, Marga

    AU - van den Hombergh, Johannes P. T. W.

    AU - van den Hondel, Cees A. M. J. J.

    AU - van der Heijden, Rene T. J. M.

    AU - van der Kaaij, Rachel M.

    AU - Klis, Frans M.

    AU - Kools, Harrie J.

    AU - Kubicek, Christian P.

    AU - van Kuyk, Patricia A.

    AU - Lauber, Juergen

    AU - Lu, Xin

    AU - van der Maarel, Marc J. E. C.

    AU - Meulenberg, Roiger

    AU - Menke, Hildegard

    AU - Mortimer, Martin A.

    AU - Nielsen, Jens

    AU - Oliver, Stephen G.

    AU - Olsthoorn, Maurien

    AU - Pal, Karoly

    AU - van Peij, Noel N. M. E.

    AU - Ram, Arthur F.

    AU - Rinas, Ursula

    AU - Roubos, Johannes A.

    AU - Sagt, Cees M. J.

    AU - Schmoll, Monika

    AU - Sun, Jibin

    AU - Ussery, David

    AU - Varga, Janos

    AU - Vervecken, Wouter

    AU - van de Vondervoort, Peter J. J.

    AU - Wedler, Holger

    AU - Wosten, Han A. B.

    AU - Zeng, An-Ping

    AU - van Ooyen, Albert J. J.

    AU - Visser, Jaap

    AU - Stam, Hein

    PY - 2007

    Y1 - 2007

    N2 - 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.

    AB - 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.

    M3 - Journal article

    VL - 25

    SP - 221

    EP - 231

    JO - Nature Biotechnology

    JF - Nature Biotechnology

    SN - 1087-0156

    IS - 2

    ER -

    Pel HJ, de Winde JH, Archer DB, Dyer PS, Hoffmann G, Schaap PJ et al. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology. 2007;25(2):221-31.