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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    Reduction Kinetics of 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1
    Sucharitakul, J. ; Wongnate, T. ; Montersino, S. ; Berkel, W.J.H. van; Chaiyen, P. - \ 2012
    Biochemistry 51 (2012)21. - ISSN 0006-2960 - p. 4309 - 4321.
    para-hydroxybenzoate hydroxylase - biochemical-characterization - pseudomonas-fluorescens - acinetobacter-baumannii - p-hydroxyphenylacetate - genus rhodococcus - mechanism - flavoprotein - purification - degradation
    3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is a nicotinamide adenine dinucleotide (NADH)-specific flavoprotein monooxygenase involved in microbial aromatic degradation. The enzyme catalyzes the para hydroxylation of 3-hydroxybenzoate (3-HB) to 2,5-dihydroxybenzoate (2,5-DHB), the ring-fission fuel of the gentisate pathway. In this study, the kinetics of reduction of the enzyme-bound flavin by NADH was investigated at pH 8.0 using a stopped-flow spectrophotometer, and the data were analyzed comprehensively according to kinetic derivations and simulations. Observed rate constants for reduction of the free enzyme by NADH under anaerobic conditions were linearly dependent on NADH concentrations, consistent with a one-step irreversible reduction model with a bimolecular rate constant of 43 ± 2 M–1 s–1. In the presence of 3-HB, observed rate constants for flavin reduction were hyperbolically dependent on NADH concentrations and approached a limiting value of 48 ± 2 s–1. At saturating concentrations of NADH (10 mM) and 3-HB (10 mM), the reduction rate constant is 51 s–1, whereas without 3-HB, the rate constant is 0.43 s–1 at a similar NADH concentration. A similar stimulation of flavin reduction was found for the enzyme–product (2,5-DHB) complex, with a rate constant of 45 ± 2 s–1. The rate enhancement induced by aromatic ligands is not due to a thermodynamic driving force because Em0 for the enzyme–substrate complex is -179 ± 1 mV compared to an Em0 of -175 ± 2 mV for the free enzyme. It is proposed that the reduction mechanism of 3HB6H involves an isomerization of the initial enzyme–ligand complex to a fully activated form before flavin reduction takes place
    Functional annotation and characterization of 3-hydroxybenzoate 6-hydroxylase from Rhodococcus jostii RHA1
    Montersino, S. ; Berkel, W.J.H. van - \ 2012
    Biochimica et Biophysica Acta. Proteins & Proteomics 1824 (2012)3. - ISSN 1570-9639 - p. 433 - 442.
    para-hydroxybenzoate hydroxylase - dinculeotide-dependent monooxygenase - polaromonas-naphthalenivorans cj2 - baeyer-villiger monooxygenases - biochemical-characterization - pseudomonas-fluorescens - ornithine hydroxylase - 4-hydroxybenzoate 1-hydroxylase - coryn
    The genome of Rhodococcus jostii RHA1 contains an unusually large number of oxygenase encoding genes. Many of these genes have yet an unknown function, implying that a notable part of the biochemical and catabolic biodiversity of this Gram-positive soil actinomycete is still elusive. Here we present a multiple sequence alignment and phylogenetic analysis of putative R. jostii RHA1 flavoprotein hydroxylases. Out of 18 candidate sequences, three hydroxylases are absent in other available Rhodococcus genomes. In addition, we report the biochemical characterization of 3-hydroxybenzoate 6-hydroxylase (3HB6H), a gentisate-producing enzyme originally mis-annotated as salicylate hydroxylase. R. jostii RHA1 3HB6H expressed in Escherichia coli is a homodimer with each 47 kDa subunit containing a non-covalently bound FAD cofactor. The enzyme has a pH optimum around pH 8.3 and prefers NADH as external electron donor. 3HB6H is active with a series of 3-hydroxybenzoate analogues, bearing substituents in ortho- or meta-position of the aromatic ring. Gentisate, the physiological product, is a non-substrate effector of 3HB6H. This compound is not hydroxylated but strongly stimulates the NADH oxidase activity of the enzyme --------------------------------------------------------------------------------
    Fidelity in Archaeal Information Processing
    Koning, B. de; Blombach, F. ; Brouns, S.J.J. ; Oost, J. van der - \ 2010
    Archaea : an international microbiological journal 2010 (2010). - ISSN 1472-3646
    transfer-rna synthetases - termination factor erf1 - translation initiation - pyrococcus-furiosus - protein-synthesis - sulfolobus-solfataricus - escherichia-coli - dna-polymerases - biochemical-characterization - pyrobaculum-aerophilum
    A key element during the flow of genetic information in living systems is fidelity. The accuracy of DNA replication influences the genome size as well as the rate of genome evolution. The large amount of energy invested in gene expression implies that fidelity plays a major role in fitness. On the other hand, an increase in fidelity generally coincides with a decrease in velocity. Hence, an important determinant of the evolution of life has been the establishment of a delicate balance between fidelity and variability. This paper reviews the current knowledge on quality control in archaeal information processing. While the majority of these processes are homologous in Archaea, Bacteria, and Eukaryotes, examples are provided of nonorthologous factors and processes operating in the archaeal domain. In some instances, evidence for the existence of certain fidelity mechanisms has been provided, but the factors involved still remain to be identified
    Molecular characterization of the glucose isomerase from the thermophilic bacterium Fervidobacterium gondwanense
    Kluskens, L.D. ; Zeilstra, J.B. ; Geerling, A.C.M. ; Vos, W.M. de; Oost, J. van der - \ 2010
    Environmental Technology 31 (2010)10. - ISSN 0959-3330 - p. 1083 - 1090.
    d-xylose isomerase - biochemical-characterization - thermotoga-neapolitana - thermus-thermophilus - escherichia-coli - thermostability - cloning - purification - expression - fructose
    The gene coding for xylose isomerase from the thermophilic bacterium Fervidobacterium gondwanense was cloned and overexpressed in Escherichia coli. The produced xylose isomerase (XylA), which closely resembles counterparts from Thermotoga maritima and T. neapolitana, was purified and characterized. It is optimally active at 70 degrees C, pH 7.3, with a specific activity of 15.0 U/mg for the interconversion of glucose to fructose. When compared with T. maritima XylA at 85 degrees C, a higher catalytic efficiency was observed. Divalent metal ions Co2+ and Mg2+ were found to enhance the thermostability
    Hyperthermophilic enzymes - stability, activity and implementation strategies for high temperature applications
    Unsworth, L.D. ; Oost, J. van der; Koutsopoulos, S. - \ 2007
    FEBS Journal 274 (2007)16. - ISSN 1742-464X - p. 4044 - 4056.
    archaeon pyrococcus-furiosus - extremely thermophilic archaebacteria - thermostable dna-polymerase - alpha-glucosidase gene - sulfolobus-solfataricus - escherichia-coli - biochemical-characterization - thermococcus-litoralis - thermotoga-maritima - protein stabili
    Current theories agree that there appears to be no unique feature responsible for the remarkable heat stability properties of hyperthermostable proteins. A concerted action of structural, dynamic and other physicochemical attributes are utilized to ensure the delicate balance between stability and functionality of proteins at high temperatures. We have thoroughly screened the literature for hyperthermostable enzymes with optimal temperatures exceeding 100 °C that can potentially be employed in multiple biotechnological and industrial applications and to substitute traditionally used, high-cost engineered mesophilic/thermophilic enzymes that operate at lower temperatures. Furthermore, we discuss general methods of enzyme immobilization and suggest specific strategies to improve thermal stability, activity and durability of hyperthermophilic enzymes.
    Influence of temperature on the production of archaeal thermoactive alcohol dehydrogenases from Pyrococcus furiosus with recombinant E. coli
    Kube, J. ; Brokamp, C. ; Machielsen, M.P. ; Oost, J. van der; Markl, H. - \ 2006
    Extremophiles 10 (2006)3. - ISSN 1431-0651 - p. 221 - 227.
    high-cell-density - hyperthermophilic archaea - biochemical-characterization - sulfolobus-solfataricus - expression - cloning - growth - gene - fermentation - overexpression
    The heterologous production of a thermoactive alcohol dehydrogenase (AdhC) from Pyrococcus furiosus in Escherichia coli was investigated. E. coli was grown in a fed-batch bioreactor in minimal medium to high cell densities (cell dry weight 76 g/l, OD600 of 150). Different cultivation strategies were applied to optimize the production of active AdhC, such as lowering the cultivation temperature from 37 to 28°C, heat shock of the culture from 37 to 42°C and from 37 to 45°C, and variation of time of induction (induction at an OD600 of 40, 80 and 120). In addition to the production of active intracellular protein, inclusion bodies were always observed. The maximal activity of 30 U/l (corresponding to 6 mg/l active protein) was obtained after a heat shock from 37 to 42°C, and IPTG induction of the adhC expression at an OD600 of 120. Although no general rules can be provided, some of the here presented variations may be applicable for the optimization of the heterologous production of proteins in general, and of thermozymes in particular
    The remarkable conservation of corticotropin-releasing hormone (CRH)-binding protein in the honeybee (Apis mellifera) dates the CRH system to a common ancestor of insects and vertebrates
    Huising, M.O. ; Flik, G. - \ 2005
    Endocrinology 146 (2005)5. - ISSN 0013-7227 - p. 2165 - 2170.
    factor-binding-protein - diuretic hormone - biochemical-characterization - divergence time - manduca-sexta - urotensin-i - ligand - stress - neuropeptides - pharmacology
    CRH-binding protein (CRH-BP) is a key factor in the regulation of CRH signaling; it modulates the bioactivity and bioavailability of CRH and its related peptides. The conservation of CRH-BP throughout vertebrates was only recently demonstrated. Here we report the presence of CRH-BP in the honeybee (Apis mellifera) and other insects. Honeybee CRH-BP resembles previously characterized vertebrate CRH-BP sequences with respect to conserved cysteine residues, gene organization, and overall sequence identity. Phylogenetic analyses confirm the unambiguous orthology of insect and vertebrate CRH-BP sequences. Soon after their discovery, it was noted that insect diuretic hormone-I (DH-I) and its receptor share similarities with the vertebrate CRH family and their receptors. Despite these similarities, demonstration of common ancestry of DH-I and the vertebrate CRH family is still speculative: the mature neuropeptides are short, and their genes differ substantially with regard to the number of coding exons. Moreover, DH and CRH receptors belong to the much larger family of G protein-coupled receptors. In contrast, the unique and conspicuous features of CRH-BP greatly facilitate the establishment of orthology over much larger evolutionary distances. The identification of CRH-BP in insects clearly indicates that this gene predates vertebrates by at least several hundred million years. Moreover, our findings imply that a CRH system is shared by insects and vertebrates alike and, consequently, that it has been present at least since the common ancestor to both phylogenetic lines of proto- and deuterostomians.
    The role of interfacial rheological properties on Ostwald ripening in emusions
    Meinders, M.B.J. ; Vliet, T. van - \ 2004
    Advances in Colloid and Interface Science 108-109 (2004). - ISSN 0001-8686 - p. 119 - 126.
    filled albumin microspheres - biochemical-characterization - contrast agent - stability - stabilization - simulation - proteins - kinetics
    The coarsening of emulsion droplets by Ostwald ripening is studied by means of numerical simulations in which time-dependent (elastic) interfacial behaviour is taken into account. Theoretical calculations on the dissolution of a single emulsion droplet in an infinite medium at saturated conditions show that the dissolution process can be stopped only when the interfacial tension goes to zero. When interfacial stress relaxation is included, which prevents a continuous zero interfacial tension, no stabilisation of the dissolution process is observed and the droplet dissolves completely. In the case of an ensemble of droplets, numerical calculations on the coarsening of emulsion droplets with finite interfacial elasticity show that a stable situation occurs at finite interfacial tensions of the droplets. This applies for a closed system with the same assumptions as those made in the Lifshitz–Slyozov–Wagner (LSW) theory. The coarsening behaviour strongly depends on the saturation of the dispersed phase in the continuous phase. If the system is in contact with atmosphere, saturation will finally go to unity and stabilisation will only occur for zero interfacial tension of the droplets. For an ensemble of droplets in a closed system, the calculations show that stress–relaxation of the interface causes the Ostwald-ripening process to continue, so no stable situation is reached. Stabilisation can only be accomplished by adding insoluble species to the dispersed phase, by using particles as stabilisers or by micro-encapsulation of the emulsion droplets by thick insoluble interfacial layers, which have a thickness that is in the order of the radius of the droplet.
    Identification and molecular characterization of a novel type of alpha-galactosidase from Pyrococcus furiosus
    Lieshout, J.F.T. van; Verhees, C.H. ; Ettema, T.J.G. ; Sar, S. van der; Imamura, H. ; Matsuzawa, H. ; Oost, J. van der; Vos, W.M. de - \ 2003
    Biocatalysis and Biotransformation 21 (2003)4-5. - ISSN 1024-2422 - p. 243 - 252.
    geobacillus-stearothermophilus t-6 - catalytically essential residues - site-directed mutagenesis - adolescentis dsm 20083 - biochemical-characterization - escherichia-coli - hyperthermophilic archaebacterium - thermococcus-litoralis - sulfolobus-solfataricus - l-
    An -galactosidase gene from Pyrococcus furiosus was identified, cloned and functionally expressed in Escherichia coli. It is the first -galactosidase from a hyperthermophilic archaeon described to date. The gene encodes a unique amino acid sequence compared to other -galactosidases. Highest homology was found with -amylases classified in family 57 of glycoside hydrolases. The 364 amino acid protein had a calculated mass of 41.6 kDa. The recombinant -galactosidase specifically catalyzed the hydrolysis of para-nitrophenyl--galactopyranoside, and to some extent that of melibiose and raffinose. The enzyme proved to be an extremely thermo-active and thermostable -galactosidase with a temperature optimum of 115°C and a half-life time of 15 hours at 100°C. The pH optimum is between 5.0 and 5.5. Sequence analysis showed four conserved carboxylic residues. Site-directed mutagenesis was applied to identify the potential catalytic residues. Glu117Ala showed decreased enzyme activity, which could be rescued by the addition of azide or formate. It is concluded that glutamate 117 is the catalytic nucleophile, whereas the acid/base catalyst remains to be identified.
    An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi
    Cohen, G. ; Barbe, V. ; Flament, D. ; Galperin, M. ; Heilig, R. ; Lecompte, O. ; Prieur, D. ; Poch, O. ; Querellou, J. ; Thierry, J.C. ; Oost, J. van der; Weissenbach, J. ; Zivanovic, Y. ; Forterre, P. - \ 2003
    Molecular Microbiology 47 (2003). - ISSN 0950-382X - p. 1495 - 1512.
    horizontal gene exchange - transfer-rna synthetase - replication factor-c - bacterial hyperthermophiles - hydrothermal vent - dna-polymerases - phylogenetic characterization - biochemical-characterization - thermus-thermophilus - transcription factor
    The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii , whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.
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