Works by van der Oost, John

Results: 100

The evolutionary journey of Argonaute proteins.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 9, p. 743, doi. 10.1038/nsmb.2879

By:

Swarts, Daan C;
Makarova, Kira;
Wang, Yanli;
Nakanishi, Kotaro;
Ketting, René F;
Koonin, Eugene V;
Patel, Dinshaw J;
van der Oost, John

Publication type:

Article

Structural basis for CRISPR RNA-guided DNA recognition by Cascade.

Published in:

Nature Structural & Molecular Biology, 2011, v. 18, n. 5, p. 529, doi. 10.1038/nsmb.2019

By:

Jore, Matthijs M.;
Lundgren, Magnus;
van Duijn, Esther;
Bultema, Jelle B.;
Westra, Edze R.;
Waghmare, Sakharam .P;
Wiedenheft, Blake;
Pul, Ümit;
Wurm, Reinhild;
Wagner, Rolf;
Beijer, Marieke R.;
Barendregt, Arjan;
Kaihong Zhou;
Snijders, Ambrosius P. L.;
Dickman, Mark J.;
Doudna, Jennifer A.;
Boekema, Egbert J.;
Heck, Albert J. R.;
van der Oost, John;
Brouns, Stan J. J.

Publication type:

Article

Evolution and classification of the CRISPR-Cas systems.

Published in:

2011

By:

Makarova, Kira S.;
Haft, Daniel H.;
Barrangou, Rodolphe;
Brouns, Stan J. J.;
Charpentier, Emmanuelle;
Horvath, Philippe;
Moineau, Sylvain;
Mojica, Francisco J. M.;
Wolf, Yuri I.;
Yakunin, Alexander F.;
van der Oost, John;
Koonin, Eugene V.

Publication type:

Opinion

Discovering novel biology by in silico archaeology.

Published in:

Nature Reviews Microbiology, 2005, v. 3, n. 11, p. 859, doi. 10.1038/nrmicro1268

By:

Ettema, Thijs J. G.;
de Vos, Willem M.;
van der Oost, John

Publication type:

Article

Establishment of markerless gene deletion tools in thermophilic Bacillus smithii and construction of multiple mutant strains.

Published in:

Microbial Cell Factories, 2015, v. 14, n. 1, p. 1, doi. 10.1186/s12934-015-0286-5

By:

Bosma, Elleke F.;
van de Weijer, Antonius H. P.;
van der Vlist, Laurens;
de Vos, Willem M.;
van der Oost, John;
van Kranenburg, Richard

Publication type:

Article

Carboxylic ester hydrolases from hyperthermophiles.

Published in:

Extremophiles, 2009, v. 13, n. 4, p. 567, doi. 10.1007/s00792-009-0260-4

By:

Levisson, Mark;
van der Oost, John;
Kengen, Servé W. M.

Publication type:

Article

Laboratory evolution of Pyrococcus furiosus alcohol dehydrogenase to improve the production of (2S,5S)-hexanediol at moderate temperatures.

Published in:

Extremophiles, 2008, v. 12, n. 4, p. 587, doi. 10.1007/s00792-008-0164-8

By:

Machielsen, Ronnie;
Leferink, Nicole G. H.;
Hendriks, Annemarie;
Brouns, Stan J. J.;
Hennemann, Hans-Georg;
Dauβmann, Thomas;
Van Der Oost, John

Publication type:

Article

The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner–Doudoroff pathway.

Published in:

Extremophiles, 2008, v. 12, n. 1, p. 75, doi. 10.1007/s00792-007-0082-1

By:

Ettema, Thijs J. G.;
Ahmed, Hatim;
Geerling, Ans C. M.;
van der Oost, John;
Siebers, Bettina

Publication type:

Article

Influence of temperature on the production of an archaeal thermoactive alcohol dehydrogenase from Pyrococcus furiosus with recombinant Escherichia coli.

Published in:

Extremophiles, 2006, v. 10, n. 3, p. 221, doi. 10.1007/s00792-005-0490-z

By:

Kube, Jürgen;
Brokamp, Christian;
Machielsen, Ronnie;
Oost, John Van der;
Märkl, Herbert

Publication type:

Article

Molecular characterization of fervidolysin, a subtilisin-like serine protease from the thermophilic bacterium Fervidobacterium pennivorans.

Published in:

Extremophiles, 2002, v. 6, n. 3, p. 185, doi. 10.1007/s007920100239

By:

Kluskens, Leon D.;
Voorhorst, Wilfried G.;
Siezen, Roland J.;
Schwerdtfeger, Ruth M.;
Antranikian, Garabed;
van der Oost, John;
de Vos, Willem M.

Publication type:

Article

Activity and stability of hyperthermophilic enzymes: a comparative study on two archaeal β-glycosidases.

Published in:

Extremophiles, 2000, v. 4, n. 3, p. 157, doi. 10.1007/s007920070030

By:

Pouwels, Jeroen;
Moracci, Marco;
Cobucci-Ponzano, Beatrice;
Perugino, Giuseppe;
van der Oost, John;
Kaper, Thijs;
Lebbink, J.H.G.;
de Vos, W.M.;
Ciaramella, Maria;
Rossi, M.

Publication type:

Article

SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25337-5

By:

Steens, Jurre A.;
Zhu, Yifan;
Taylor, David W.;
Bravo, Jack P. K.;
Prinsen, Stijn H. P.;
Schoen, Cor D.;
Keijser, Bart J. F.;
Ossendrijver, Michel;
Hofstra, L. Marije;
Brouns, Stan J. J.;
Shinkai, Akeo;
van der Oost, John;
Staals, Raymond H. J.

Publication type:

Article

Towards a synthetic cell cycle.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24772-8

By:

Olivi, Lorenzo;
Berger, Mareike;
Creyghton, Ramon N. P.;
De Franceschi, Nicola;
Dekker, Cees;
Mulder, Bela M.;
Claassens, Nico J.;
ten Wolde, Pieter Rein;
van der Oost, John

Publication type:

Article

Effects of Argonaute on Gene Expression in Thermus thermophilus.

Published in:

PLoS ONE, 2015, v. 10, n. 4, p. 1, doi. 10.1371/journal.pone.0124880

By:

Swarts, Daan C.;
Koehorst, Jasper J.;
Westra, Edze R.;
Schaap, Peter J.;
van der Oost, John

Publication type:

Article

Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering.

Published in:

Microbial Cell Factories, 2019, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12934-019-1255-1

By:

Mougiakos, Ioannis;
Orsi, Enrico;
Ghiffary, Mohammad Rifqi;
Post, Wilbert;
de Maria, Alberto;
Adiego-Perez, Belén;
Kengen, Servé W. M.;
Weusthuis, Ruud A.;
van der Oost, John

Publication type:

Article

Improved oligosaccharide synthesis by protein engineering of β-glucosidase CelB from hyperthermophilic Pyrococcus furiosus.

Published in:

Biotechnology & Bioengineering, 2001, v. 73, n. 3, p. 203, doi. 10.1002/bit.1052

By:

Hansson, Therese;
Kaper, Thijs;
van der Oost, John;
de Vos, Willem M.;
Adlercreutz, Patrick

Publication type:

Article

Multiplex genome engineering in Clostridium beijerinckii NCIMB 8052 using CRISPR-Cas12a.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-37220-y

By:

Patinios, Constantinos;
de Vries, Stijn T.;
Diallo, Mamou;
Lanza, Lucrezia;
Verbrugge, Pepijn L. J. V. Q.;
López-Contreras, Ana M.;
van der Oost, John;
Weusthuis, Ruud A.;
Kengen, Servé W. M.

Publication type:

Article

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T.

Published in:

Standards in Genomic Sciences, 2016, v. 11, p. 1, doi. 10.1186/s40793-016-0172-8

By:

Bosma, Elleke F.;
Koehorst, Jasper J.;
van Hijum, Sacha A. F. T.;
Renckens, Bernadet;
Vriesendorp, Bastienne;
van de Weijer, Antonius H. P.;
Schaap, Peter J.;
de Vos, Willem M.;
van der Oost, John;
van Kranenburg, Richard

Publication type:

Article

Eat1-Like Alcohol Acyl Transferases From Yeasts Have High Alcoholysis and Thiolysis Activity.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.579844

By:

Patinios, Constantinos;
Lanza, Lucrezia;
Corino, Inge;
Franssen, Maurice C. R.;
Van der Oost, John;
Weusthuis, Ruud A.;
Kengen, Servé W. M.

Publication type:

Article

Transcriptomic and Phenotypic Analysis of a spoIIE Mutant in Clostridium beijerinckii.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.556064

By:

Diallo, Mamou;
Kint, Nicolas;
Monot, Marc;
Collas, Florent;
Martin-Verstraete, Isabelle;
van der Oost, John;
Kengen, Servé W. M.;
López-Contreras, Ana M.

Publication type:

Article

H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO.

Published in:

Molecular Microbiology, 2010, v. 77, n. 6, p. 1380, doi. 10.1111/j.1365-2958.2010.07315.x

By:

Westra, Edze R.;
Pul, Ümit;
Heidrich, Nadja;
Jore, Matthijs M.;
Lundgren, Magnus;
Stratmann, Thomas;
Wurm, Reinhild;
Raine, Amanda;
Mescher, Melina;
Heereveld, Luc van;
Mastop, Marieke;
Wagner, E. Gerhart H.;
Schnetz, Karin;
Van der Oost, John;
Wagner, Rolf;
Brouns, Stan J. J.

Publication type:

Article

Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator.

Published in:

Molecular Microbiology, 2008, v. 70, n. 1, p. 151, doi. 10.1111/j.1365-2958.2008.06399.x

By:

Levy, Colin;
Pike, Katharine;
Heyes, Derren J.;
Joyce, M. Gordon;
Gabor, Krisztina;
Smidt, Hauke;
Van der Oost, John;
Leys, David

Publication type:

Article

The Lrp family of transcriptional regulators.

Published in:

Molecular Microbiology, 2003, v. 48, n. 2, p. 287, doi. 10.1046/j.1365-2958.2003.03442.x

By:

Brinkman, Arie B.;
Ettema, Thijs J. G.;
de Vos, Willem M.;
van der Oost, John

Publication type:

Article

An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi.

Published in:

Molecular Microbiology, 2003, v. 47, n. 6, p. 1495, doi. 10.1046/j.1365-2958.2003.03381.x

By:

Cohen, Georges N.;
Barbe, Valérie;
Flament, Didier;
Galperin, Michael;
Heilig, Roland;
Lecompte, Odile;
Poch, Olivier;
Prieur, Daniel;
Quérellou, Joël;
Ripp, Raymond;
Thierry, Jean-Claude;
Van der Oost, John;
Weissenbach, Jean;
Zivanovic, Yvan;
Forterre, Patrick

Publication type:

Article

Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome.

Published in:

Gut Microbes, 2021, v. 13, n. 1, p. 1, doi. 10.1080/19490976.2021.1897217

By:

Manrique, Pilar;
Zhu, Yifan;
van der Oost, John;
Herrema, Hilde;
Nieuwdorp, Max;
de Vos, Willem M.;
Young, Mark

Publication type:

Article

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples.

Published in:

Current Microbiology, 2019, v. 76, n. 4, p. 425, doi. 10.1007/s00284-019-01630-x

By:

van der Oost, Hans;
van der Oost, John;
van Vliet, Daan M.;
Plugge, Caroline M.;
Palakawong Na Ayudthaya, Susakul

Publication type:

Article

Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications.

Published in:

Current Microbiology, 2018, v. 75, n. 1, p. 49, doi. 10.1007/s00284-017-1349-0

By:

Daas, Martinus J. A.;
Vriesendorp, Bastienne;
van de Weijer, Antonius H. P.;
van der Oost, John;
van Kranenburg, Richard

Publication type:

Article

Structural and biochemical characterisation of Archaeoglobus fulgidus esterase reveals a bound CoA molecule in the vicinity of the active site.

Published in:

Scientific Reports, 2016, p. 25542, doi. 10.1038/srep25542

By:

Sayer, Christopher;
Finnigan, William;
Isupov, Michail N.;
Levisson, Mark;
Kengen, Servé W. M.;
van der Oost, John;
Harmer, Nicholas J.;
Littlechild, Jennifer A.

Publication type:

Article

Substrate Specificity and Stereoselectivity of Two Sulfolobus 2-Keto-3-deoxygluconate Aldolases towards Azido-Substituted Aldehydes.

Published in:

ChemCatChem, 2014, v. 6, n. 4, p. 1073, doi. 10.1002/cctc.201300785

By:

Schurink, Marloes;
Wolterink‐van Loo, Suzanne;
van der Oost, John;
Sonke, Theo;
Franssen, Maurice C. R.

Publication type:

Article

Isolation of a genetically accessible thermophilic xylan degrading bacterium from compost.

Published in:

Biotechnology for Biofuels, 2016, v. 9, p. 1, doi. 10.1186/s13068-016-0618-7

By:

Daas, Martinus J. A.;
van de Weijer, Antonius H. P.;
de Vos, Willem M.;
van der Oost, John;
van Kranenburg, Richard

Publication type:

Article

Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms.

Published in:

PLoS ONE, 2017, v. 12, n. 9, p. 1, doi. 10.1371/journal.pone.0184355

By:

Claassens, Nico J.;
Siliakus, Melvin F.;
Spaans, Sebastiaan K.;
Creutzburg, Sjoerd C. A.;
Nijsse, Bart;
Schaap, Peter J.;
Quax, Tessa E. F.;
van der Oost, John

Publication type:

Article

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

Published in:

Proteins, 2009, v. 76, n. 3, p. 608, doi. 10.1002/prot.22374

By:

Kuipers, Remko K. P.;
Joosten, Henk-Jan;
Verwiel, Eugene;
Paans, Sjoerd;
Akerboom, Jasper;
van der Oost, John;
Leferink, Nicole G. H.;
van Berkel, Willem J. H.;
Vriend, Gert;
Schaap, Peter J.

Publication type:

Article

Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering.

Published in:

Proteins, 2005, v. 61, n. 2, p. 377, doi. 10.1002/prot.20606

By:

Koutsopoulos, Sotirios;
van der Oost, John;
Norde, Willem

Publication type:

Article

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase.

Published in:

Biomolecules (2218-273X), 2019, v. 9, n. 6, p. 212, doi. 10.3390/biom9060212

By:

Subramanian, Kalyanasundaram;
Mitusińska, Karolina;
Raedts, John;
Almourfi, Feras;
Joosten, Henk-Jan;
Hendriks, Sjon;
Sedelnikova, Svetlana E.;
Kengen, Servé W. M.;
Hagen, Wilfred R.;
Góra, Artur;
Martins dos Santos, Vitor A. P.;
Baker, Patrick J.;
van der Oost, John;
Schaap, Peter J.

Publication type:

Article

NADPH-generating systems in bacteria and archaea.

Published in:

Frontiers in Microbiology, 2015, p. 1, doi. 10.3389/fmicb.2015.00742

By:

Spaans, Sebastiaan K.;
Weusthuis, Ruud A.;
van der Oost, John;
Kengen, Servé W. M.;
Whitman, Barny;
Guiral, Marianne;
Trchounian, Armen;
Leigh, John

Publication type:

Article

Functional study on GTP hydrolysis by the GTP-binding protein from Sulfolobus solfataricus, a member of the HflX family.

Published in:

Journal of Biochemistry, 2010, v. 148, n. 1, p. 103, doi. 10.1093/jb/mvq039

By:

Bo Huang;
Hao Wu;
Ning Hao;
Blombach, Fabian;
Van der Oost, John;
Xuemei Li;
Zhang, Xuejun C.;
Zihe Rao

Publication type:

Article

Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus.

Published in:

EMBO Journal, 2001, v. 20, n. 5, p. 990, doi. 10.1093/emboj/20.5.990

By:

Leonard, Philip M.;
Smits, Sander H. J.;
Sedelnikova, Svetlana E.;
Brinkman, Arie B.;
de Vos, Willem M.;
van der Oost, John;
Rice, David W.;
Rafferty, John B.

Publication type:

Article

Metabolic engineering of Clostridium autoethanogenum for ethyl acetate production from CO.

Published in:

Microbial Cell Factories, 2022, v. 21, n. 1, p. 1, doi. 10.1186/s12934-022-01964-5

By:

Dykstra, James C.;
van Oort, Jelle;
Yazdi, Ali Tafazoli;
Vossen, Eric;
Patinios, Constantinos;
van der Oost, John;
Sousa, Diana Z.;
Kengen, Servé W. M.

Publication type:

Article

Cofactor engineering of Lactobacillus brevis alcohol dehydrogenase by computational design.

Published in:

Engineering in Life Sciences, 2009, v. 9, n. 1, p. 38, doi. 10.1002/elsc.200800046

By:

Machielsen, Ronnie;
Looger, Loren L.;
Raedts, John;
Dijkhuizen, Sjoerd;
Hummel, Werner;
Hennemann, Hans-Georg;
Daussmann, Thomas;
van der Oost, John

Publication type:

Article

Characterization of the AcrIIC1 anti‒CRISPR protein for Cas9‒based genome engineering in E. coli.

Published in:

Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-05418-5

By:

Trasanidou, Despoina;
Potocnik, Ana;
Barendse, Patrick;
Mohanraju, Prarthana;
Bouzetos, Evgenios;
Karpouzis, Efthymios;
Desmet, Amber;
van Kranenburg, Richard;
van der Oost, John;
Staals, Raymond H. J.;
Mougiakos, Ioannis

Publication type:

Article

FnrP and NNR of Paracoccus denitrificans are both members of the FNR family of transcriptional activators but have distinct roles in respiratory adaptation in response to oxygen limitation.

Published in:

Molecular Microbiology, 1997, v. 23, n. 5, p. 893, doi. 10.1046/j.1365-2958.1997.2801638.x

By:

Van Spanning, Rob J. M.;
De Boer, Anthonius P. N.;
Reijnders, Willem N. M.;
Westertoff, Hans V.;
Stouthamer, Adriaan H.;
Van Der Oost, John

Publication type:

Article

An alternative model for haem ligation in nitrate reductase and analogous respiratory cytochrome β complexes.

Published in:

1996

By:

Van der Oost, John;
Nederkoorn, Paul H. J.;
Stouthamer, Adriaan H.;
Westerhoff, Hans V.;
Van Spanning, Rob J. M.

Publication type:

Letter

Structural and functional analysis of aa3-type and cbb3-type cytochrome c oxidases of Paracoccus denitrificans reveals significant differences in proton-pump design.

Published in:

Molecular Microbiology, 1996, v. 20, n. 6, p. 1247, doi. 10.1111/j.1365-2958.1996.tb02644.x

By:

De Gier, Jan-Wiliem L.;
Schepper, Mike;
Reijnders, Willem N. M.;
Van Dyck, Stef J.;
Slotboom, Dirk Jan;
Warne, Antony;
Saraste, Matti;
Krab, Klaas;
Finel, Moshe;
Stouthamer, Adriaan H.;
van Spanning, Rob J. M.;
Van der Oost, John

Publication type:

Article

The terminal oxidases of Paracoccus denitrificans.

Published in:

Molecular Microbiology, 1994, v. 13, n. 2, p. 183, doi. 10.1111/j.1365-2958.1994.tb00414.x

By:

De Gier, Jan-Willem L.;
Lübben, Mathias;
Reijnders, Willem N. M.;
Tipker, Corinne A.;
Slotboom, Dirk-Jan;
Van Spanning, Rob J. M.;
Stouthamer, Adriaan H.;
Van der Oost, John

Publication type:

Article

The crystal structure of a hyperthermoactive exopolygalacturonase from Thermotoga maritima reveals a unique tetramer

Published in:

FEBS Letters, 2009, v. 583, n. 22, p. 3665, doi. 10.1016/j.febslet.2009.10.047

By:

Pijning, Tjaard;
van Pouderoyen, Gertie;
Kluskens, Leon;
van der Oost, John;
Dijkstra, Bauke W.

Publication type:

Article

Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors.

Published in:

Nature, 2001, v. 411, n. 6835, p. 269, doi. 10.1038/35077011

By:

Brejc, Katjusa;
van Dijk, Willem J.;
Klaassen, Remco V.;
Schuurmans, Mascha;
van der Oost, John;
Smit, August B.;
Sixma, Titia K.

Publication type:

Article

Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives.

Published in:

Life (2075-1729), 2013, v. 3, n. 1, p. 52, doi. 10.3390/life3010052

By:

Bielen, Abraham A. M.;
Verhaart, Marcel R. A.;
van der Oost, John;
Kengen, Servé W. M.

Publication type:

Article

Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 5, p. 2363, doi. 10.1093/nar/gkad035

By:

Nieuwkoop, Thijs;
Terlouw, Barbara R;
Stevens, Katherine G;
Scheltema, Richard A;
de Ridder, Dick;
van der Oost, John;
Claassens, Nico J

Publication type:

Article

Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters.

Published in:

Nucleic Acids Research, 2022, v. 50, n. 14, p. 8377, doi. 10.1093/nar/gkac578

By:

Rossetti, Marianna;
Merlo, Rosa;
Bagheri, Neda;
Moscone, Danila;
Valenti, Anna;
Saha, Aakash;
Arantes, Pablo R;
Ippodrino, Rudy;
Ricci, Francesco;
Treglia, Ida;
Delibato, Elisabetta;
van der Oost, John;
Palermo, Giulia;
Perugino, Giuseppe;
Porchetta, Alessandro

Publication type:

Article

Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 19, p. 11392, doi. 10.1093/nar/gkab893

By:

Patinios, Constantinos;
Creutzburg, Sjoerd C A;
Arifah, Adini Q;
Adiego-Pérez, Belén;
Gyimah, Evans A;
Ingham, Colin J;
Kengen, Servé W M;
van der Oost, John;
Staals, Raymond H J

Publication type:

Article