P. J. Schaap

Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member (2009)

Narayanan, B., Niu, W., Joosten, H-J., Li, Z., Kuipers, R.K., Schaap, P.J., ...

The Aspergillus niger genome contains four genes that encode proteins exhibiting greater than 30% amino acid sequence identity to the confirmed oxaloacetate acetyl hydrolase (OAH), an enzyme that...

Correlated mutation analyses on super-family alignments reveal functionally important residues (Online first) (2009)

Kuipers, R.K., Joosten, H-J., Verwiel, E., Paans, S., Akerboom, J., ...

Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the...

Correlated mutation analyses on super-family alignments reveal functionally important residues (2009)

Kuipers, R.K., Joosten, H-J., Verwiel, E., Paans, J., Akerboom, J., ...

Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the...

Correlated mutation analyses on super-family alignments reveal functionally important residues. (2009)

Kuipers, R.K.P., Joosten, H-J., Verwiel, E., Paans, S., Vriend, G., ...

Correlated mutation analyses (CMA) on multiple sequence alignments are widely used for the prediction of the function of amino acids. The accuracy of CMA-based predictions is mainly determined by the...

3DM: From Data to Medicine (2008)

Henk-jan Joosten, Promotor Prof, J. A. Berg, Hoogleraar Genomics, Co-promotor Dr, P. J. Schaap, ...

Dr. R. van Schaik

Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method (2008)

Joosten, H-J., Han, Y., Niu, W., Vervoort, J.J.M., Dunaway-Mariano, D., Schaap, P.J.

Aspergillus niger produces oxalic acid through the hydrolysis of oxaloacetate, catalyzed by the cytoplasmic enzyme oxaloacetate acetylhydrolase (OAH). The A. niger genome encodes four additional open...

An evolutionary conserved d-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation (2008)

Martens-Uzunova, E.S., Schaap, P.J.

Transcriptome analysis of Aspergillus niger transfer cultures grown on galacturonic acid media identified a highly correlating cluster of four strongly induced hypothetical genes linked with a subset...

Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method (2008)

Joosten, H-J., Han, Y., Niu, W.L., Vervoort, J.J.M., Dunaway-Mariano, D., Schaap, P.J.

Aspergillus niger produces oxalic acid through the hydrolysis of oxaloacetate, catalyzed by the cytoplasmic enzyme oxaloacetate acetylhydrolase (OAH). The A. niger genome encodes four additional open...

Identification of a gatekeeper residue that prevents dehydrogenases to act as oxidases (Online first) (2008)

Leferink, N.G.H., Fraaije, M.W., Joosten, H-J., Schaap, P.J., Mattevi, A.

The oxygen reactivity of flavoproteins is poorly understood. Here we show that a single Ala to Gly substitution in L-galactono-1,4-lactone dehydrogenase (GALDH) turns the enzyme into a catalytically...

Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi (2007)

Han, Y., Joosten, H-J., Niu, W., Zhao, Z., Mariano, P.S., McCalman, M., ...

Oxalate secretion by fungi is known to be associated with fungal pathogenesis. In addition, oxalate toxicity is a concern for the commercial application of fungi in the food and drug industries....

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. (2007)

Pel, H.J., Archer, D.B., Dyer, P.S., Hofmann, G., Schaap, P.J., ...

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...

Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi (2007)

Han, Y., Joosten, H.J., Niu, W., Zhao, Z., Mariano, P.S., McCalman, M., ...

Oxalate secretion by fungi is known to be associated with fungal pathogenesis. In addition, oxalate toxicity is a concern for the commercial application of fungi in the food and drug industries....

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 (2007)

Pel, H.J., Winde, J.H. De, Archer, D.B., Dyer, P.S., Hofmann, G., Schaap, P.J., ...

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 (2007)

Pel, H.J., Archer, D.B., Schaap, P.J., Benen, J.A.E., Debets, A.J.M., ...

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 (2007)

Pel, H.J., Winde, J.H. De, Archer, D.B., Dyer, P.S., Hofmann, G., Schaap, P.J., ...

A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation (2006)

Martens-Uzunova, E.S., Zandleven, J.S., Benen, J.A.E., Awad, H., Kools, H.J., Beldman, G., ...

The fungus Aspergillus niger is an industrial producer of pectin degrading enzymes. The recent solving of the genomic sequence of A. niger allowed an inventory of the entire genome of the fungus for...

A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation (2006)

Martens-Uzunova, E.S., Zandleven, J.S., Benen, J.A.E., Awad, H., Kools, H.J., Beldman, G., ...

The fungus Aspergillus niger is an industrial producer of pectindegrading enzymes. The recent solving of the genomic sequence of A. niger allowed an inventory of the entire genome of the fungus for...

Characterisation of the Aspergilllus niger dapB gene, which encodes a novel fungal type IV dipeptidyl aminopeptidase (2005)

Jalving, R., Godefrooij, J., Schaap, P.J.

We have cloned the Aspergillus niger dapB gene. Analysis of its nucleotide sequence and the corresponding protein sequence indicates that the gene encodes a type IV dipeptidyl aminopeptidase (DPP...

Characterisation of Aspergillus niger prolyl aminopeptidase (2005)

Basten, E.J.W., Schaap, P.J.

We have cloned a gene (papA) that encodes a prolyl aminopeptidase from Aspergillus niger. Homologous genes are present in the genomes of the Eurotiales A. nidulans, A. fumigatus and Talaromyces...

Aminopeptidase C of Aspergillus niger is a Novel Phenylalanine Aminopeptidase (2003)

Basten, E.J.W., Dekker, P.J.T., Schaap, P.J.

Analysis of the extracellular proteome of Agaricus bisporus (2003)

Straatsma, G., Schaap, P.J.

Lignin degradation by Agaricus bisporus accounts for a 30% increase in bioavailable holocellulose during cultivation on compost (2003)

Ten Have, R., Wijngaard, H., Straatsma, G., Schaap, P.J.

The common mushroom Agaricus bisporus is a non-white rot saphrophytic fungus that can degrade lignin to free and utilize holocellulose embedded in fermented straw as present in compost. A new method...

Cloning of a prolidase gene from Aspergillus nidulans and characterisation of its product (2002)

Jalving, R., Bron, P., Kester, H.C.M., Visser, J., Schaap, P.J.

Using EST sequence information available from the filamentous fungus Aspergillus nidulans as a starting point, we have cloned the prolidase-encoding gene, designated pepP. Introduction of multiple...

Lysine aminopeptidase of Aspergillus niger (2001)

Visser, J., Schaap, P.J.

Conserved regions within the M1 family of metallo-aminopeptidases have been used to clone a zinc aminopeptidase from the industrially used fungus Aspergillus niger. The derived amino acid sequence of...

The glutamine synthetase from the edible mushroom Agaricus bisporus (2000)

Baars, J.J.P., Schaap, P.J., ...

Different temporal and spatial expression of two hydrophobin-encoding genes of the edible mushroom Agaricus bisporus (1999)

Roeven, R.T.P., Visser, J., Schaap, P.J.

NAD+-dependent glutamate dehydrogenase of the edible mushroom Agarisuc bisporus: biochemical and molecular characterization (1999)

Muller, Y., Baars, J.J.P., ...

Abr1, a transposon-like element in the genome of the cultivated mushroom Agaricus bisporus (Lange) Imbach (1999)

Sonnenberg, A.S.M., Baars, J.J.P., Mikosch, T.S.P., Schaap, P.J.

Nuclear and nucleolar localization of Saccharomyces cerevisiae ribosomal proteins S22 and S25 (1999)

Timmers, A.C.J., Stuger, R., Schaap, P.J., Raue, H.A.

An endo-1,4-beta-xylanase encoding gene from Agaricus bisporus is regulated by compost specific factors. (1998)

Basten, E.J.W., Sonnenberg, A.S.M., Visser, J., Schaap, P.J.

Biochemical and molecular aspects of growth and fruiting of the edible mushroom Agaricus bisporus. (1998)

Visser, J., Schaap, P.J.

Isolation and characterisation of genes that are specifically expressed at high levels during fruit body development of the edible mushroom Agaricus bisporus. (1998)

Roeven, R.T.P., Visser, J., Schaap, P.J.

Compost specific factors determine expression of an endo-1,4-beta-xylanase encoding gene from Agaricus bisporus. (1998)

Schaap, P.J., Sonnenberg, A.S.M., Visser, J.

Isolation of developmentally regulated genes from the edible mushroom Agaricus bisporus. (1997)

Schaap, P.J., Visser, J.

Molecular characterization of glnA encoding glutamine synthetase from the edible mushroom Agaricus bisporus. (1997)

Müller, Y., Vogels, G.D., Visser, J., ...

The Agaricus bisporus pruA gene encodes a cytosolic delta1-pyrroline-5-carboxylate dehydrogenase which is expressed in fruit bodies but not in gill tissue. (1997)

Schaap, P.J., Müller, Y., Sonnenberg, A.S.M., Visser, J.

Cloning and characterization of two rhamnogalacturonan hydrolase genes from Aspergillus niger. (1997)

Suykerbuyk, M.E.G., Kester, H.C.M., Schaap, P.J., Stam, H., Musters, W., Visser, J.

Molecular characterization of the glnA gene encoding glutamine synthetase from the edible mushroom Agaricus bisporus (1997)

Schaap, P.J., Visser, J., Vogels, G.D., Muller, Y., ...

The Agaricus bisporus hypA gene encodes a hydrophobin and specifically accumulates in peel tissue of mushroom caps during fruit body development. (1996)

Schaap, P.J., Sonnenberg, A.S.M., Visser, J.

Isolation of expressed sequence tags of Agaricus bisporus and their assignment to chromosomes. (1996)

Sonnenberg, A.S.M., Schaap, P.J., Baars, J.J.P., Visser, J.

Nucleotide sequence and expression of the gene encoding NADP+-dependent glutamate dehydrogenase (gdhA) from Agaricus bisporus. (1996)

Schaap, P.J., Müller, Y., Baars, J.J.P., Sonnenberg, A.S.M., ...

Identification of regulatory mutants of Aspergillus aculeatus affected in rhamnogalacturonan hydrolase expression. (1996)

Suykerbuyk, M.E.G., Schaap, P.J., Visser, J.

Cloning, sequence and expression of the gene coding for rhamnogalacturonase (RHG) of Aspergillus aculeatus: a novel pectinolytic enzyme. (1996)

Suykerbuyk, M.E.G., Schaap, P.J., Stam, H., Muster, W., Visser, J.

Nucleotide sequence and expression of the gene encoding NADP(+) dependent glutamate dehydrogenase (gdhA) from Agaricus bisporus (1996)

Visser, J., Sonnenberg, A.S.M., Baars, J.J.P., Muller, Y., ...

Molecular cloning and sequence of the cytoplasmic ribosomal protein S15a gene from Agaricus bisporus. (1995)

Schaap, P.J., Müller, Y., Visser, J.

Cloning, sequence and expression of the gene coding for rhamnogalacturonase (RHG) of Aspergillus aculeatus; a novel pectinolytic enzyme. (1995)

Suykerbuyk, M.E.G., Schaap, P.J., Stam, H., Musters, W., Visser, J.

Molecular characterization of genes involved in carbon metabolism and ammonium assimilation of the button mushroom Agaricus bisporus. (1995)

Schaap, P.J., Müller, Y., Baars, J.J.P., Sonnenberg, A.S.M., ...

Isolation and characterization of genes involved in growth and maintenance of fruit bodies of Agaricus bisporus. (1995)

Schaap, P.J., Visser, J.

A codon usage table for Agaricus bisporus. (1994)

Schaap, P.J., Müller, Y., Thurston, C.F., Sonnenberg, A.S.M., Visser, J., ...

Cloning and expression of DNA encoding a ripening from a polypeptide having sulfhydryl oxidase activity. (1993)

Maat, J., Musters, W., Stam, H., Schaap, P.J., Visser, J., ...

The invention relates to recombinant DNA technology for the production of an enzyme having sulfhydryl oxidase ("SOX") activity. This SOX-enzyme can be used where the oxidation of free sulfhydryl...

Induction of glucose oxidase, catalase and lactonase in Asperillus niger. (1993)

Witteveen, C.F.B., ...

Isolation of expressed sequence tags of Agaricus bisporus and their assignment to chromosomes.

Sonnenberg, A S, De Groot, P W, Schaap, P J, Baars, J J, Visser, J, Van Griensven, L J

The genome of the cultivated basidiomycete Agaricus bisporus Horst U1 and of its homokaryotic parents has been characterized by using an optimized method of pulsed-field gel electrophoresis....

The Agaricus bisporus pruA gene encodes a cytosolic delta 1-pyrroline-5-carboxylate dehydrogenase which is expressed in fruit bodies but not in gill tissue.

Schaap, P J, Müller, Y, Sonnenberg, A S, Van Griensven, L J, Visser, J

A fortuitously cloned 3'-truncated cDNA encoding the Agaricus bisporus delta 1-pyrroline-5-carboxylate dehydrogenase was used to characterize the complete gene. The gene would encode a cytosolic...

Cloning and characterization of two rhamnogalacturonan hydrolase genes from Aspergillus niger.

Suykerbuyk, M E, Kester, H C, Schaap, P J, Stam, H, Musters, W, Visser, J

A rhamnogalacturonan hydrolase gene of Aspergillus aculeatus was used as a probe for the cloning of two rhamnogalacturonan hydrolase genes of Aspergillus niger. The corresponding proteins,...

Isolation of expressed sequence tags of Agaricus bisporus and their assignment to chromosomes.

Sonnenberg, A S, De Groot, P W, Schaap, P J, Baars, J J, Visser, J, Van Griensven, L J

The genome of the cultivated basidiomycete Agaricus bisporus Horst U1 and of its homokaryotic parents has been characterized by using an optimized method of pulsed-field gel electrophoresis....

The Agaricus bisporus pruA gene encodes a cytosolic delta 1-pyrroline-5-carboxylate dehydrogenase which is expressed in fruit bodies but not in gill tissue.

Schaap, P J, Müller, Y, Sonnenberg, A S, Van Griensven, L J, Visser, J

A fortuitously cloned 3'-truncated cDNA encoding the Agaricus bisporus delta 1-pyrroline-5-carboxylate dehydrogenase was used to characterize the complete gene. The gene would encode a cytosolic...

Cloning and characterization of two rhamnogalacturonan hydrolase genes from Aspergillus niger.

Suykerbuyk, M E, Kester, H C, Schaap, P J, Stam, H, Musters, W, Visser, J

A rhamnogalacturonan hydrolase gene of Aspergillus aculeatus was used as a probe for the cloning of two rhamnogalacturonan hydrolase genes of Aspergillus niger. The corresponding proteins,...