Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Elucidation of the 4-hydroxyacetophenone catabolic pathway in Pseudomonas fluorescens ACB
    Moonen, M.J.H. ; Kamerbeek, N.M. ; Westphal, A.H. ; Boeren, J.A. ; Janssen, D.B. ; Fraaije, M.W. ; Berkel, W.J.H. van - \ 2008
    Journal of Bacteriology 190 (2008). - ISSN 0021-9193 - p. 5190 - 5198.
    meta-cleavage pathway - cleaving catecholic dioxygenase - baeyer-villiger monooxygenase - candida-parapsilosis cbs604 - plasmid-encoded degradation - sp strain b13 - crystal-structure - gene-cluster - p-nitrophenol - hydroxyquinol 1,2-dioxygenase
    The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to -ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of an 15-kb DNA fragment showed the presence of fourteen open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE) and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the yci1 family (hapH) and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12 and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron (II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence it is proposed that the hapC and hapD gene products are involved in the ring-cleavage of hydroquinone.
    Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts
    Berkel, W.J.H. van; Kamerbeek, N.M. ; Fraaije, M.W. - \ 2006
    Journal of Biotechnology 124 (2006)4. - ISSN 0168-1656 - p. 670 - 689.
    baeyer-villiger monooxygenases - flavin-containing monooxygenase - vanillyl-alcohol oxidase - para-hydroxybenzoate hydroxylase - encoding nitrilotriacetate monooxygenase - p-hydroxyphenylacetate 3-hydroxylase - bacillus-thermoglucosidasius a7 - tryptophan 7-halo
    During the last decades a large number of flavin-dependent monooxygenases have been isolated and studied. This has revealed that flavoprotein monooxygenases are able to catalyze a remarkable wide variety of oxidative reactions such as regioselective hydroxylations and enantioselective sulfoxidations. These oxidation reactions are often difficult, if not impossible, to be achieved using chemical approaches. Analysis of the available genome sequences has indicated that many more flavoprotein monooxygenases exist and await biocatalytic exploration. Based on the known biochemical properties of a number of flavoprotein monooxygenases and sequence and structural analyses, flavoprotein monooxygenases can be classified into six distinct flavoprotein monooxygenase subclasses. This review provides an inventory of known flavoprotein monooxygenases belonging to these different enzyme subclasses. Furthermore, the biocatalytic potential of a selected number of flavoprotein monooxygenases is highlighted
    Coenzyme binding is beneficial for the stability of 4 hydroxyacetophenone monooxygenase
    Heuvel, R.H.H. van den; Tahallah, N. ; Kamerbeek, N.M. ; Fraaije, M.W. ; Berkel, W.J.H. van; Janssen, D.B. ; Heck, A. - \ 2005
    Journal of Biological Chemistry 280 (2005)37. - ISSN 0021-9258 - p. 32115 - 32121.
    baeyer-villiger monooxygenases - ionization mass-spectrometry - vanillyl-alcohol oxidase - electrospray-ionization - escherichia-coli - methylenetetrahydrofolate reductase - cyclohexanone monooxygenase - synthetic applications - protein complexes - specificity
    The NADPH-dependent dimeric flavoenzyme 4-hydroxyacetophenone monooxygenase (HAPMO) catalyzes Baeyer-Villiger oxidations of a wide range of ketones, thereby generating esters or lactones. In the current work, we probed HAPMO-coenzyme complexes present during the enzyme catalytic cycle with the aim to gain mechanistic insight. Moreover, we investigated the structural role of the nicotinamide coenzyme. For these studies, we used (i) wild type HAPMO, (ii) the R339A variant, which is active but has a low affinity toward NADPH, and (iii) the R440A variant, which is inactive but has a high affinity toward NADPH. Electrospray ionization mass spectrometry was used as the primary tool to directly observe noncovalent protein-coenzyme complexes in real time. These analyzes showed for the first time that the nicotinamide coenzyme remains bound to HAPMO during the entire catalytic cycle of the NADPH oxidase reaction. This may also have implications for other homologous Baeyer-Villiger monooxygenases. Together with the observations that NADP+ only weakly interacts with oxidized enzyme and that HAPMO is mainly in the reduced form during catalysis, we concluded that NADP+ interacts tightly with the reduced form of HAPMO. We also demonstrated that the association with the coenzyme is crucial for enzyme stability. The interaction with the coenzyme analog 3-aminopyridine adenine dinucleotide phosphate (AADP+) strongly enhanced the thermal stability of wild type HAPMO. This coenzyme-induced stabilization may also be important for related enzymes.
    Baeyer-Villiger monooxygenases, an emerging family of flavin-dependent biocatalysts
    Kamerbeek, N.M. ; Janssen, D.B. ; Berkel, W.J.H. van; Fraaije, M.W. - \ 2003
    Advanced Synthesis and Catalysis 345 (2003)6-7. - ISSN 1615-4150 - p. 667 - 678.
    p-hydroxybenzoate hydroxylase - rna differential display - cyclohexanone monooxygenase - escherichia-coli - gene-cluster - steroid monooxygenase - formate dehydrogenase - coenzyme specificity - acinetobacter sp - pseudomonas sp
    Baeyer-Villiger monooxygenases (BVMOs) are flavoenzymes that catalyze a remarkably wide variety of oxidative reactions such as regio- and enantioselective Baeyer-Villiger oxidations and sulfoxidations. Several of these conversions are difficult to achieve using chemical approaches. Due to their selectivity and catalytic efficiency, BVMOs are highly valuable biocatalysts for the synthesis of a broad range of fine chemicals. For a long time, only one member of this class of flavin-containing biocatalysts had been cloned and overexpressed which has limited their application for synthetic processes. Recently a number of new genes that encode BVMOs have been sequenced and overexpressed. In this paper the biocatalytic properties of recently cloned BVMOs are reviewed. Furthermore, the potential for obtaining novel BVMOs from sequenced genomes will be discussed.
    Reductive genome evolution in Buchnera aphidicola
    Ham, R.C.H.J. van; Kamerbeek, J. ; Palacios, C. ; Rausell, C. ; Abascal, F. ; Bastolla, U. ; Fernandez, J.M. ; Jimenez, L. ; Postigo, M. ; Silva, F.J. ; Tamames, J. ; Viguera, E. ; Latorre, A. ; Valencia, A. ; Moran, F. ; Moya, A. - \ 2003
    Proceedings of the National Academy of Sciences of the United States of America 100 (2003)2. - ISSN 0027-8424 - p. 581 - 586.
    replication fork - endosymbiotic bacteria - model proteins - sequence - aphids - genes - symbionts - selection - growth - aps
    We have sequenced the genome of the intracellular symbiont Buchnera aphidicola from the aphid Baizongia pistacea. This strain diverged 80-150 million years ago from the common ancestor of two previously sequenced Buchnera strains. Here, a field-collected, nonclonal sample of insects was used as source material for laboratory procedures. As a consequence, the genome assembly unveiled intrapopulational variation, consisting of 1,200 polymorphic sites. Comparison of the 618-kb (kbp) genome with the two other Buchnera genomes revealed a nearly perfect gene-order conservation, indicating that the onset of genomic stasis coincided closely with establishment of the symbiosis with aphids, 200 million years ago. Extensive genome reduction also predates the synchronous diversification of Buchnera and its host; but, at a slower rate, gene loss continues among the extant lineages. A computational study of protein folding predicts that proteins in Buchnera, as well as proteins of other intracellular bacteria, are generally characterized by smaller folding efficiency compared with proteins of free living bacteria. These and other degenerative genomic features are discussed in light of compensatory processes and theoretical predictions on the long-term evolutionary fate of symbionts like Buchnera
    The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes
    Gil, R. ; Silva, F.J. ; Zientz, E. ; Delmotte, F. ; Gonzalez-Candelas, F. ; Latorre, A. ; Rausell, C. ; Kamerbeek, J. ; Gadau, J. ; Hölldobler, B. ; Ham, R.C.H.J. van; Gross, R. ; Moya, A. - \ 2003
    Proceedings of the National Academy of Sciences of the United States of America 100 (2003)16. - ISSN 0027-8424 - p. 9388 - 9393.
    escherichia-coli k-12 - endosymbiotic bacteria - phylogenetic analysis - gene-cluster - evolution - proteins - buchnera - replication - selection - aphids
    Bacterial symbioses are widespread among insects, probably being one of the key factors of their evolutionary success. We present the complete genome sequence of Blochmannia floridanus, the primary endosymbiont of carpenter ants. Although these ants feed on a complex diet, this symbiosis very likely has a nutritional basis: Blochmannia is able to supply nitrogen and sulfur compounds to the host while it takes advantage of the host metabolic machinery. Remarkably, these bacteria lack all known genes involved in replication initiation (dnaA, priA, and recA). The phylogenetic analysis of a set of conserved protein-coding genes shows that Bl. floridanus is phylogenetically related to Buchnera aphidicola and Wigglesworthia glossinidia, the other endosymbiotic bacteria whose complete genomes have been sequenced so far. Comparative analysis of the five known genomes from insect endosymbiotic bacteria reveals they share only 313 genes, a number that may be close to the minimum gene set necessary to sustain endosymbiotic life
    Substrate specificity of 4-hydroxyacetophenone monooxygenase
    Fraaije, M.W. ; Kamerbeek, N.M. ; Berkel, W.J.H. van; Janssen, D.B. - \ 2002
    In: Applied Biocatalysis : 7th annual meeting of the working party Biotransformations, Zurich, 2002
    Identification of a Baeyer-Villiger monooxygenase sequence motif
    Fraaije, M.W. ; Kamerbeek, N.M. ; Berkel, W.J.H. van; Janssen, D.B. - \ 2002
    FEBS Letters 518 (2002). - ISSN 0014-5793 - p. 43 - 47.
    4-Hydroxyacetophenone monooxygenase from Pseudomonas fluorescens ACB A novel flavoprotein catalyzing Baeyer-Villiger oxidation of aromatic compounds
    Kamerbeek, N.M. ; Moonen, M.J. ; Ven, J.G. van der; Berkel, W.J.H. van; Fraaije, M.W. ; Janssen, D.B. - \ 2001
    European Journal of Biochemistry 268 (2001)9. - ISSN 0014-2956 - p. 2547 - 2557.
    A novel flavoprotein that catalyses the NADPH-dependent oxidation of 4-hydroxyacetophenone to 4-hydroxyphenyl acetate, was purified to homogeneity from Pseudomonas fluorescens ACB. Characterization of the purified enzyme showed that 4-hydroxyacetophenone monooxygenase (HAPMO) is a homodimer of 140 kDa with each subunit containing a noncovalently bound FAD molecule. HAPMO displays a tight coupling between NADPH oxidation and substrate oxygenation. Besides 4-hydroxyacetophenone a wide range of other acetophenones are readily converted via a Baeyer-Villiger rearrangement reaction into the corresponding phenyl acetates. The P. fluorescens HAPMO gene (hapE) was characterized. It encoded a 640 amino-acid protein with a deduced mass of 71 884 Da. Except for an N-terminal extension of 135 residues, the sequence of HAPMO shares significant similarity with two known types of Baeyer-Villiger monooxygenases: cyclohexanone monooxygenase (27-33␜equence identity) and steroid monooxygenase (33␜equence identity). The HAPMO sequence contains several sequence motifs indicative for the presence of two Rossman fold domains involved in FAD and NADPH binding. The functional role of a recently identified flavoprotein sequence motif (ATG) was explored by site-directed mutagenesis. Replacement of the strictly conserved glycine (G490) resulted in a dramatic effect on catalysis. From a kinetic analysis of the G490A mutant it is concluded that the observed sequence motif serves a structural function which is of importance for NADPH binding.
    Wie de woning past trekke er in: een case-studie naar woningtoewijzing via plaatsingsbeleid en aanbodsystemen.
    Kamerbeek, A. - \ 1992
    Vakgroep Huishoudstudies, LUW - 63 p.
    Het bloembollenonderzoek in Groot-Brittannie : verslag van een studiereis van 7 tot 22 Mei 1973
    Kamerbeek, G.A. ; Schenk, P.K. ; Timmer, J.G. - \ 1973
    Lisse : [s.n.] (Rapport / Laboratorium voor bloembollenonderzoek, Lisse no. 22) - 46
    groot-brittannië - bloembollen - onderzoek - great britain - ornamental bulbs - research
    Fysiologische afwijkingen bij bloembollen
    Kamerbeek, G.A. - \ 1967
    Lisse : [s.n.] (Publicatie / Laboratorium voor bloembollenonderzoek no. 202) - 7
    bloembollen - plantenziekten - afwijkingen, planten - plantenziektekunde - plantenplagen - gewasbescherming - ornamental bulbs - plant diseases - plant disorders - plant pathology - plant pests - plant protection
    Verslag van een studiereis naar de Verenigde Staten van Noord - Amerika ter gelegenheid van het Internationaal tuinbouwkundig congres, 17e te Maryland, aug. 1966
    Schenk, P.K. ; Kamerbeek, G.A. - \ 1966
    Lisse : [s.n.] (Rapport / Laboratorium voor bloembollenonderzoek no. 5) - 23
    bloembollen - sierplanten - vs - gladiolus - ornamental bulbs - ornamental plants - usa - gladiolus
    Respiration of the iris bulb in relation to the temperature and the growth of the primordia
    Kamerbeek, G.A. - \ 1962
    Amsterdam : North-Holland publ. co. - 70
    sierplanten - iridaceae - ademhaling - katabolisme - groei - meristemen - temperatuur - warmte - ornamental plants - respiration - catabolism - growth - meristems - temperature - heat
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