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Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins

van Leeuwen, H.C. (author), Roelofs, D. (author), Corver, J. (author), Hensbergen, P. (author)

Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and...

article 2021

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The fate of chicory root pulp polysaccharides during fermentation in the TNO in vitro model of the colon (TIM-2)

Ramasamy, U.S. (author), Venema, K. (author), Gruppen, H. (author), Schols, H.A. (author)

The aim of this study was to monitor cell wall polysaccharide (CWPs) utilization during fermentation by the human colonic microbiota in the TNO in vitro model of the colon (TIM-2). Chicory root pulp (CRP) and treated (ensiled) CRP (ECRP) containing four times more soluble pectin than CRP, were fermented in the model. After the adaptation phase...

article 2014

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Effect of soluble and insoluble fibers within the in vitro fermentation of chicory root pulp by human gut bacteria

Ramasamy, U.S. (author), Venema, K. (author), Schols, H.A. (author), Gruppen, H. (author)

The aim of this research was to study the in vitro fermentation of chicory root pulp (CRP) and ensiled CRP (ECRP) using human fecal inoculum. Analysis of carbohydrate levels in fermentation digests showed that 51% of all CRP carbohydrates were utilized after 24 h of fermentation. For ECRP, having the same cell wall polysaccharide composition as...

article 2014

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Moisture transport in coated wood

van Meel, P.A. (author), Erich, S.J.F. (author), Huinink, H.P. (author), Kopinga, K. (author), DE Jong, J. (author), Adan, O.C.G. (author)

Moisture accumulation inside wood causes favorable conditions for decay. Application of a coating alters the moisture sorption of wood and prevents accumulation of moisture. This paper presents the results of a nuclear magnetic resonance (NMR) study on the influence of a coating on the moisture absorption of wood. NMR allows to determine both...

article 2011

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Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles

Yuan, X.-L. (author), van der Kaaij, R.M. (author), van den Hondel, C.A.M.J.J. (author), Punt, P.J. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author)

The filamentous ascomycete Aspergillus niger is well known for its ability to produce a large variety of enzymes for the degradation of plant polysaccharide material. A major carbon and energy source for this soil fungus is starch, which can be degraded by the concerted action of α-amylase, glucoamylase and α-glucosidase enzymes, members of the...

article 2008

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A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis

Damveld, R.A. (author), Franken, A. (author), Arentshorst, M. (author), Punt, P.J. (author), Klis, F.M. (author), van den Hondel, C.A.M.J.J. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author)

To identify cell wall biosynthetic genes in filamentous fungi and thus potential targets for the discovery of new antifungals, we developed a novel screening method for cell wall mutants. It is based on our earlier observation that the Aspergillus niger agsA gene, which encodes a putative a-glucan synthase, is strongly induced in response to...

article 2008

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Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored α-glucanotransferase enzymes of Aspergillus niger

van der Kaaij, R.M. (author), Yuan, X.L. (author), Franken, A. (author), Ram, A.F.J. (author), Punt, P.J. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Kwaliteit van Leven (author)

In the genome sequence of Aspergillus niger CBS 513.88, three genes were identified with high similarity to fungal α-amylases. The protein sequences derived from these genes were different in two ways from all described fungal α-amylases: they were predicted to be glycosylphosphatidylinositol anchored, and some highly conserved amino acids of...

article 2007

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Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes

van der Kaaij, R.M. (author), Janeček, Š. (author), van der Maarel, M.J.E.C. (author), Dijkhuizen, L. (author), TNO Kwaliteit van Leven (author)

Currently known fungal α-amylases are well-characterized extracellular enzymes that are classified into glycoside hydrolase subfamily GH13_1. This study describes the identification, and phylogenetic and biochemical analysis of novel intracellular fungal α-amylases. The phylogenetic analysis shows that they cluster in the recently identified...

article 2007

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The Aspergillus niger MADS-box transcription factor RlmA is required for cell wall reinforcement in response to cell wall stress

Damveld, R.A. (author), Arentshorst, M. (author), Franken, A. (author), van Kuyk, P.A. (author), Klis, F.M. (author), van den Hondel, C.A.M.J.J. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven (author)

In Aspergillus niger, the genes coding for glutamine:fructose-6-phosphate amidotransferase (gfaA) and α-1,3-glucan synthase (agsA) are induced in response to cell wall stress. In silico analysis of the promoter region of the two genes revealed the presence of putative DNA binding sites for transcription factors involved in stress responses,...

article 2005

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Time-lapse tracking of barley androgenesis reveals position-determined cell death within pro-embryos

Maraschin, S.D.F. (author), Vennik, M. (author), Lamers, G.E.M. (author), Spaink, H.P. (author), Wang, M. (author)

Following abiotic stress to induce barley (Hordeum vulgare L.) androgenesis, the development of 794 enlarged microspores in culture was monitored by time-lapse tracking. In total, 11% of the microspores tracked developed into embryo-like structures (type-I pathway), 36% formed multicellular structures (type-II pathway) and 53% of the microspores...

article 2005

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Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization

te Biesebeke, R. (author), Levin, A. (author), Sagt, C. (author), Bartels, J. (author), Goosen, T. (author), Ram, A. (author), van den Hondel, C. (author), Punt, P. (author), TNO Kwaliteit van Leven (author)

Aspergillus oryzae requires polarized growth for colonization of solid substrates, and this growth phenotype differs from that seen in liquid medium. Various experimental approaches were used to identify genes that are differentially expressed when A. oryzae is grown on wheat kernels and in a wheat-based liquid medium. Hybridization of A. oryzae...

article 2005

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Expression of agsA, one of five 1,3-α-d-glucan synthase-encoding genes in Aspergillus niger, is induced in response to cell wall stress

Damveld, R.A. (author), van Kuyk, P.A. (author), Arentshorst, M. (author), Klis, F.M. (author), van den Hondel, C.A.M.J.J. (author), Ram, A.F.J. (author), TNO Kwaliteit van Leven TNO Voeding (author)

1,3-α-d-Glucan is an important component of the cell wall of filamentous fungi. We have identified a family of five 1,3-α-d-glucan synthase-encoding genes in Aspergillus niger. The agsA gene was sequenced and the predicted protein sequence indicated that the overall domain structure of 1,3-α-d-glucan synthases is conserved in fungi. Using RT-PCR...

article 2005

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The cell wall stress response in Aspergillus niger involves increased expression of the glutamine: Fructose-6-phosphate amidotransferase-encoding gene (gfaA) and increased deposition of chitin in the cell wall

Ram, A.F.J. (author), Arentshorst, M. (author), Damveld, R.A. (author), van Kuyk, P.A. (author), Klis, F.M. (author), van den Hondel, C.A.M.J.J. (author), TNO Voeding (author)

Perturbation of cell wall synthesis in Saccharomyces cerevisiae, either by mutations in cell wall synthesis-related genes or by adding compounds that interfere with normal cell wall assembly, triggers a compensatory response to ensure cell wall integrity. This response includes an increase in chitin levels in the cell wall. Here it is shown that...

article 2004

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Horseradish peroxidase-catalyzed oligomerization of ferulic acid on a template of a tyrosine-containing tripeptide

Centraal Instituut voor Voedingsonderzoek TNO TNO Voeding (author), Oudgenoeg, G. (author), Dirksen, E. (author), Ingemann, S. (author), Hilhorst, R. (author), Gruppen, H. (author), Boeriu, C.G. (author), Piersma, S.R. (author), van Berkel, W.J.H. (author), Laane, C. (author), Voragen, A.G.J. (author)

Ferulic acid (FA) is an abundantly present phenolic constituent of plant cell walls. Kinetically controlled incubation of FA and the tripeptide Gly-Tyr-Gly (GYG) with horseradish peroxidase and H2O2 yielded a range of new cross-linked products. Two predominant series of hetero-oligomers of FA linked by dehydrogenation to the peptidyl tyrosine...

article 2002

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One repeat of the cell wall binding domain is sufficient for anchoring the Lactobacillus acidophilus surface layer protein

Smit, E. (author), Pouwels, P.H. (author)

The N-terminal repeat (SAC1) of the S-protein of Lactobacillus acidophilus bound efficiently and specifically to cell wall fragments (CWFs) when fused to green fluorescent protein, whereas the C-terminal repeat (SAC2) did not. Treatment of CWFs with hydrofluoric acid, but not phenol, prevented binding. Apparently, SAC1 is necessary and...

article 2002

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The S-layer protein of Lactobacillus acidophilus ATCC 4356: Identification and characterisation of domains responsible for S-protein assembly and cell wall binding

Smit, E. (author), Oling, F. (author), Demel, R. (author), Martinez, B. (author), Pouwels, P.H. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

Lactobacillus acidophilus, like many other bacteria, harbors a surface layer consisting of a protein (SA-protein) of 43 kDa. SA-protein could be readily extracted and crystallized in vitro into large crystalline patches on lipid monolayers with a net negative charge but not on lipids with a net neutral charge. Reconstruction of the S-layer from...

article 2001

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Glucoamylasegreen fluorescent protein fusions to monitor protein secretion in Aspergillus niger

TNO Voeding (author), Gordon, C.L. (author), Khalaj, V. (author), Ram, A.F.J. (author), Archer, D.B. (author), Brookman, J.L. (author), Trinci, A.P.J. (author), Jeenes, D.J. (author), Doonan, J.H. (author), Wells, B. (author), Punt, P.J. (author), van den Hondel, C.A.M.J.J. (author), Robson, G.D. (author)

A glucoamylase::green fluorescent protein fusion (GLA::sGFP) was constructed which allows the green fluorescent protein to be used as an in vivo reporter of protein secretion in Aspergillus niger. Two secretory fusions were designed for secretion of GLA::sGFP which employed slightly different lengths of the glucoamylase protein (GLA499 and...

article 2000

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Localization of synthesis of β1,6-glucan in Saccharomyces cerevisiae

Montijn, R.C. (author), Vink, E. (author), Müller, W.H. (author), Verkleij, A.J. (author), van den Ende, H. (author), Henrissat, B. (author), Klis, F.M. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

β1,6-Glucan is a key component of the yeast cell wall, interconnecting cell wall proteins, β1,3-glucan, and chitin. It has been postulated that the synthesis of β1,6-glucan begins in the endoplasmic reticulum with the formation of protein-bound primer structures and that these primer structures are extended in the Golgi complex by two putative...

article 1999

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Spatial and temporal regulation of DNA fragmentation in the aleurone of germinating barley

Wang, M. (author), Oppedijk, B.J. (author), Caspers, M.P.M. (author), Lamers, G.E.M. (author), Boot, M.J. (author), Geerlings, D.N.G. (author), Bakhuizen, B. (author), Meijer, A.H. (author), van Duijn, B. (author), Centraal Instituut voor Voedingsonderzoek TNO (author)

During germination of barley grains, the appearance of DNA fragmentation started in aleurone cells near the embryo and extended to the distal end in a time-dependent manner. DNA fragmentation was demonstrated to occur only after the expression of α-amylase mRNA in the aleurone layer. In addition, cell wall degradation started in cells near the...

article 1998

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Immune responses and side effects of five different oil-based adjuvants in mice

Leenaars, M. (author), Koedam, M.A. (author), Hendriksen, C.F.M. (author), Claassen, E. (author), TNO Preventie en Gezondheid (author)

In this study, five different oil based adjuvants were compared to assess efficacy and side effects. Mice were injected subcutaneously (s.c.) or intraperitoneally (i.p.) with a weak immunogen (synthetic peptide) emulsified in Freund's adjuvant (FA), Specol, RIBI, TiterMax or Montanide ISA50. Efficacy of adjuvants was evaluated based on their...

article 1998