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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    Crystal structure of the CRISPR RNA–guided surveillance complex from Escherichia coli
    Jackson, R.N. ; Golden, S.M. ; Erp, P.B. ; Carter, J. ; Westra, E.R. ; Brouns, S.J.J. ; Oost, J. van der; Terwilliger, T.C. ; Read, R.J. ; Wiedenheft, B. - \ 2014
    Science 345 (2014)6203. - ISSN 0036-8075 - p. 1473 - 1479.
    bacterial immune-system - processes pre-crrna - thermus-thermophilus - cas systems - interference complex - target recognition - antiviral defense - seed sequence - dna - cascade
    Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade. Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence. Conserved sequences on the 3' and 5' ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo–A-form configuration. The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.
    Unravelling the structural and mechanistic basis of CRISPR-Cas systems
    Oost, J. van der; Westra, E.R. ; Jackson, R.N. ; Wiedenheft, B. - \ 2014
    Nature Reviews Microbiology 12 (2014)7. - ISSN 1740-1526 - p. 479 - 492.
    short palindromic repeats - bacterial immune-system - rna silencing complex - processes pre-crrna - human gut virome - crystal-structure - escherichia-coli - streptococcus-thermophilus - thermus-thermophilus - interference complex
    Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments of foreign DNA into CRISPR loci, and following transcription and processing of these loci, the CRISPR RNAs (crRNAs) guide the Cas proteins to complementary invading nucleic acid, which results in target interference. In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR–Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.
    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
    Structure of the ribosome associating GTPase HflX
    Wu, H. ; Sun, L. ; Blombach, F. ; Brouns, S.J.J. ; Snijders, A.P.L. ; Lorenzen, K. ; Heuvel, R.H.H. van den; Heck, A.J.R. ; Fu, S. ; Li, X. ; Zhang, X.C. ; Rao, Z. ; Oost, J. van der - \ 2010
    Proteins : Structure, Function, and Bioinformatics 78 (2010)3. - ISSN 0887-3585 - p. 705 - 713.
    elongation-factor-g - bacillus-subtilis - binding protein - escherichia-coli - crystal-structure - thermus-thermophilus - nucleotide-binding - subunit - refinement - domain
    The HflX-family is a widely distributed but poorly characterized family of translation factor-related guanosine triphosphatases (GTPases) that interact with the large ribosomal subunit. This study describes the crystal structure of HflX from Sulfolobus solfataricus solved to 2.0-Å resolution in apo- and GDP-bound forms. The enzyme displays a two-domain architecture with a novel HflX domain at the N-terminus, and a classical G-domain at the C-terminus. The HflX domain is composed of a four-stranded parallel -sheet flanked by two -helices on either side, and an anti-parallel coiled coil of two long -helices that lead to the G-domain. The cleft between the two domains accommodates the nucleotide binding site as well as the switch II region, which mediates interactions between the two domains. Conformational changes of the switch regions are therefore anticipated to reposition the HflX-domain upon GTP-binding. Slow GTPase activity has been confirmed, with an HflX domain deletion mutant exhibiting a 24-fold enhanced turnover rate, suggesting a regulatory role for the HflX domain. The conserved positively charged surface patches of the HflX-domain may mediate interaction with the large ribosomal subunit. The present study provides a structural basis to uncover the functional role of this GTPases family whose function is largely unknown. Proteins 2009. © 2009 Wiley-Liss, Inc
    Effect of O2 concentrations on Sulfolobus solfataricus P2
    Simon, G. ; Walther, J. ; Zabeti, N. ; Combet-Blanc, Y. ; Auria, R. ; Oost, J. van der; Casalot, L. - \ 2009
    FEMS Microbiology Letters 299 (2009)2. - ISSN 0378-1097 - p. 255 - 260.
    superoxide-dismutase - thermus-thermophilus - cytochrome ba(3) - oxidase - oxygen - archaeon - stress - identification - metabolism - enzyme
    Sulfolobus solfataricus P2 was grown aerobically at various O(2) concentrations. Based on growth parameters in microcosms, four types of behavior could be distinguished. At 35% O(2) (v/v; gas phase), the cultures did not grow, indicating a lethal dose of oxygen. For 26-32% O(2), the growth was significantly affected compared with the reference (21%), suggesting a moderate toxicity by O(2). For 16-24% O(2), standard growth was observed. For 1.5-15% O(2), growth was comparable with the reference, but the yield on O(2) indicated a more efficient use of oxygen. These results indicate that S. solfataricus P2 grows optimally in the range of 1.5-24% O(2), most likely by adjusting its energy-transducing machinery. To gain some insight into control of the respiratory system, transcriptomes of the strain cultivated at different O(2) concentrations, corresponding to each behavior (1.5%, 21% and 26%), were compared using a DNA microarray approach. It showed differential expression of several genes encoding terminal oxidases, indicating an adaptation of the strain's respiratory system in response to fluctuating oxygen concentrations
    Engineering a selectable marker for hyperthermophiles
    Brouns, S.J.J. ; Wu, H. ; Akerboom, A.P. ; Turnbull, A.P. ; Vos, W.M. de; Oost, J. van der - \ 2005
    Journal of Biological Chemistry 280 (2005)12. - ISSN 0021-9258 - p. 11422 - 11431.
    bleomycin-resistance determinant - thermus-thermophilus - streptoalloteichus-hindustanus - streptomyces-verticillus - extreme thermophile - directed evolution - crystal-structure - binding protein - alpha-helix - ion-pairs
    Limited thermostability of antibiotic resistance markers has restricted genetic research in the field of extremely thermophilic Archaea and bacteria. In this study, we used directed evolution and selection in the thermophilic bacterium Thermus thermophilus HB27 to find thermostable variants of a bleomycin-binding protein from the mesophilic bacterium Streptoalloteichus hindustanus. In a single selection round, we identified eight clones bearing five types of double mutated genes that provided T. thermophilus transformants with bleomycin resistance at 77 °C, while the wild-type gene could only do so up to 65 °C. Only six different amino acid positions were altered, three of which were glycine residues. All variant proteins were produced in Escherichia coli and analyzed biochemically for thermal stability and functionality at high temperature. A synthetic mutant resistance gene with low GC content was designed that combined four substitutions. The encoded protein showed up to 17 °C increased thermostability and unfolded at 85 °C in the absence of bleomycin, whereas in its presence the protein unfolded at 100 °C. Despite these highly thermophilic properties, this mutant was still able to function normally at mesophilic temperatures in vivo. The mutant protein was co-crystallized with bleomycin, and the structure of the binary complex was determined to a resolution of 1.5 Å. Detailed structural analysis revealed possible molecular mechanisms of thermostabilization and enhanced antibiotic binding, which included the introduction of an intersubunit hydrogen bond network, improved hydrophobic packing of surface indentations, reduction of loop flexibility, and -helix stabilization. The potential applicability of the thermostable selection marker is discussed
    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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