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1. Yarrowia lipolytica: Safety assessment of an oleaginous yeast with a great industrial potential

Author

Groenewald, Marizeth, Boekhout, Teun, Neuveglise, Cecile, Gaillardin, Claude, van Dijck, Piet W. M., Wyss, Markus, Groenewald, Marizeth, Boekhout, Teun, Neuveglise, Cecile, Gaillardin, Claude, van Dijck, Piet W. M., and Wyss, Markus

Abstract

Yarrowia lipolytica has been developed as a production host for a large variety of biotechnological applications. Efficacy and safety studies have demonstrated the safe use of Yarrowia-derived products containing significant proportions of Yarrowia biomass (as for DuPont's eicosapentaenoic acid-rich oil) or with the yeast itself as the final product (as for British Petroleum's single-cell protein product). The natural occurrence of the species in food, particularly cheese, other dairy products and meat, is a further argument supporting its safety. The species causes rare opportunistic infections in severely immunocompromised or otherwise seriously ill people with other underlying diseases or conditions. The infections can be treated effectively by the use of regular antifungal drugs, and in some cases even disappeared spontaneously. Based on our assessment, we conclude that Y. lipolytica is a "safe-to-use" organism., Yarrowia lipolytica has been developed as a production host for a large variety of biotechnological applications. Efficacy and safety studies have demonstrated the safe use of Yarrowia-derived products containing significant proportions of Yarrowia biomass (as for DuPont's eicosapentaenoic acid-rich oil) or with the yeast itself as the final product (as for British Petroleum's single-cell protein product). The natural occurrence of the species in food, particularly cheese, other dairy products and meat, is a further argument supporting its safety. The species causes rare opportunistic infections in severely immunocompromised or otherwise seriously ill people with other underlying diseases or conditions. The infections can be treated effectively by the use of regular antifungal drugs, and in some cases even disappeared spontaneously. Based on our assessment, we conclude that Y. lipolytica is a "safe-to-use" organism.

Published
2014

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

Author

Pel, Herman J., de Winde, Johannes H., Archer, David B., Dyer, Paul S., Hofmann, Gerald, Schaap, Peter J., Turner, Geoffrey, de Vries, Ronald P., Albang, Richard, Albermann, Kaj, Andersen, Mikael R., Bendtsen, Jannick D., 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. M., 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, Rogier, Menke, Hildegard, Mortimer, Martin A., Nielsen, Jens, Oliver, Stephen G., Olsthoorn, Maurien, Pal, Karoly, van Peij, Noel N. M. E., Ram, Arthur F. J., Rinas, Ursula, Roubos, Johannes A., Sagt, Cees M. J., Schmoll, Monika, Sun, Jibin, Ussery, David, Varga, Janos, Vervecken, Wouter, de Vondervoort, Peter J. J. van, Wedler, Holger, Wosten, Han A. B., Zeng, An-Ping, van Ooyen, Albert J. J., Visser, Jaap, Stam, Hein, Pel, Herman J., de Winde, Johannes H., Archer, David B., Dyer, Paul S., Hofmann, Gerald, Schaap, Peter J., Turner, Geoffrey, de Vries, Ronald P., Albang, Richard, Albermann, Kaj, Andersen, Mikael R., Bendtsen, Jannick D., 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. M., 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, Rogier, Menke, Hildegard, Mortimer, Martin A., Nielsen, Jens, Oliver, Stephen G., Olsthoorn, Maurien, Pal, Karoly, van Peij, Noel N. M. E., Ram, Arthur F. J., Rinas, Ursula, Roubos, Johannes A., Sagt, Cees M. J., Schmoll, Monika, Sun, Jibin, Ussery, David, Varga, Janos, Vervecken, Wouter, de Vondervoort, Peter J. J. van, Wedler, Holger, Wosten, Han A. B., Zeng, An-Ping, van Ooyen, Albert J. J., Visser, Jaap, and Stam, Hein

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.

Published
2007

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

Author

Sub Molecular Microbiology, Molecular Microbiology, Pel, Herman J., de Winde, Johannes H., Archer, David B., Dyer, Paul S., Hofmann, Gerald, Schaap, Peter J., Turner, Geoffrey, de Vries, Ronald P., Albang, Richard, Albermann, Kaj, Andersen, Mikael R., Bendtsen, Jannick D., 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. M., 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, Rogier, Menke, Hildegard, Mortimer, Martin A., Nielsen, Jens, Oliver, Stephen G., Olsthoorn, Maurien, Pal, Karoly, van Peij, Noel N. M. E., Ram, Arthur F. J., Rinas, Ursula, Roubos, Johannes A., Sagt, Cees M. J., Schmoll, Monika, Sun, Jibin, Ussery, David, Varga, Janos, Vervecken, Wouter, de Vondervoort, Peter J. J. van, Wedler, Holger, Wosten, Han A. B., Zeng, An-Ping, van Ooyen, Albert J. J., Visser, Jaap, Stam, Hein, Sub Molecular Microbiology, Molecular Microbiology, Pel, Herman J., de Winde, Johannes H., Archer, David B., Dyer, Paul S., Hofmann, Gerald, Schaap, Peter J., Turner, Geoffrey, de Vries, Ronald P., Albang, Richard, Albermann, Kaj, Andersen, Mikael R., Bendtsen, Jannick D., 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. M., 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, Rogier, Menke, Hildegard, Mortimer, Martin A., Nielsen, Jens, Oliver, Stephen G., Olsthoorn, Maurien, Pal, Karoly, van Peij, Noel N. M. E., Ram, Arthur F. J., Rinas, Ursula, Roubos, Johannes A., Sagt, Cees M. J., Schmoll, Monika, Sun, Jibin, Ussery, David, Varga, Janos, Vervecken, Wouter, de Vondervoort, Peter J. J. van, Wedler, Holger, Wosten, Han A. B., Zeng, An-Ping, van Ooyen, Albert J. J., Visser, Jaap, and Stam, Hein

Published
2007

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

Author

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

Published
2007
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5. [sup31]P-Nuclear Magnetic Resonance and Freeze-Fracture Electron Microscopic Studies on Reconstituted Bacteriorhodopsin Vesicles.

Author

Van Dijck, Piet W. M., Nicolay, Klaas, Leunissen-Bijvelt, José, Van Dam, Karel, and Kaptein, Robert

Subjects
*NUCLEAR magnetic resonance, *GLUCOSE-6-phosphatase, *LECITHIN, *BACTERIORHODOPSIN, *ELECTRON microscopy, *FLUORESCENCE
Abstract

Bacteriorhodopsin has been reconstituted into egg-phosphatidylcholine vesicles by various methods. The resulting preparations have been analyzed on density gradients and by freeze-fracture electron microscopy. The homogeneity of the vesicle preparations and the light-induced intravesicular pH changes have been studied by 31P-NMR, using glucose 6-phosphate as pH probe. It is concluded that bacteriorhodopsin is incorporated in the inside-out mode in vesicles up to about 100 nm. Above this diameter, more or less random insertion takes place. [ABSTRACT FROM AUTHOR]

Published
1981
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6. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.

Author

Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, and Baker SE

Subjects
Base Sequence, Gene Expression Profiling, Gene Rearrangement genetics, Gene Transfer, Horizontal genetics, Genomics methods, Molecular Sequence Data, Polymorphism, Single Nucleotide genetics, Sequence Analysis, DNA, Species Specificity, Synteny genetics, Aspergillus niger genetics, Computational Biology methods, Evolution, Molecular, Genetic Variation, Genome, Fungal genetics, Phylogeny
Abstract

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.

Published
2011
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