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. Danchin; Alfons 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

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 journal › Journal article › Research › peer-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 language	English
Journal	Nature Biotechnology
Volume	25
Issue number	2
Pages (from-to)	221-31
ISSN	1087-0156
Publication status	Published - 2007

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Pel, H. J., de Winde, J. H., Archer, D. B., Dyer, P. S., Hoffmann, G., Schaap, P. J., Turner, G., de Vries, R. P., Albang, R., Albermann, K., Andersen, M. R., Bendtsen, J. D., Benen, J. A. E., van den Berg, M., Breestraat, S., Caddick, M. X., Contreras, R., Cornell, M., Coutinho, P. M., ... 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",

volume = "25",

pages = "221--31",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "2",

}

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 journal › Journal article › Research › peer-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 -