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Research Output 1996 2020

2020

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier, E., Cheng, D., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Scott, D., Shah, S. A., Siksnys, V., Terns, M. P., Venclovas, Č., White, M. F., Yakunin, A. F., Yan, W. & 6 others, Zhang, F., Garrett, R. A., Backofen, R., van der Oost, J., Barrangou, R. & Koonin, E. V., Feb 2020, In : Nature Reviews Microbiology. 18, p. 67-83 16 p.

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Interspersed Repetitive Sequences
Adaptive Immunity
Genes
Publications
2019
1 Citation (Scopus)

Adaptation and application of a two-plasmid inducible CRISPR-Cas9 system in Clostridium beijerinckii

Diallo, M., Hocq, R., Collas, F., Chartier, G., Wasels, F., Wijaya, H. S., Werten, M. W. T., Wolbert, E. J. H., Kengen, S. W. M., van der Oost, J., Ferreira, N. L. & López-Contreras, A. M., 27 Jul 2019, In : Methods. 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Clostridium
Butanols
Plasmids

Addiction systems antagonize bacterial adaptive immunity

van Sluijs, L., van Houte, S., van der Oost, J., Brouns, S. J. J., Buckling, A. & Westra, E. R., 1 Mar 2019, In : FEMS Microbiology Letters. 366, 5, fnz047.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Adaptive Immunity
Plasmids
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Microbial Drug Resistance

Argonaute bypasses cellular obstacles without hindrance during target search

Cui, T. J., Klein, M., Hegge, J. W., Chandradoss, S. D., van der Oost, J., Depken, M. & Joo, C., 26 Sep 2019, In : Nature Communications. 10, 4390.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
bypasses
nucleic acids
Nucleic Acids
proteins
Kinetics

Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli

Claassens, N. J., Finger-Bou, M., Scholten, B., Muis, F., De Groot, J. J., De Gier, J. W., De Vos, W. M. & Van Der Oost, J., 17 Jun 2019, In : ACS synthetic biology. 8, 7, p. 1685-1690 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Escherichia coli
Membrane Proteins
Proteins
Membranes
Cell Engineering
9 Citations (Scopus)

Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?

Tytgat, H. L. P., Nobrega, F. L., van der Oost, J. & de Vos, W. M., Jan 2019, In : Trends in Microbiology. 27, 1, p. 17-25

Research output: Contribution to journalArticleAcademicpeer-review

Biofilms
Mucous Membrane
Intestinal Diseases
Health
Colonic Neoplasms
1 Citation (Scopus)
Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Microalgae
Ribonucleoproteins
Homologous Recombination
homology

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

Subramanian, K., Mitusińska, K., Raedts, J., Almourfi, F., Joosten, H. J., Hendriks, S., Sedelnikova, S. E., Kengen, S. W. M., Hagen, W. R., Góra, A., Martins Dos Santos, V. A. P., Baker, P. J., van der Oost, J. & Schaap, P. J., 31 May 2019, In : Biomolecules. 9, 6, 212.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Glucose-6-Phosphate Isomerase
Protein Engineering
Metals
Glucose-6-Phosphate
Mutation
2 Citations (Scopus)

DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute

Hegge, J. W., Swarts, D. C., Chandradoss, S. D., Cui, T. J., Kneppers, J., Jinek, M., Joo, C. & van der Oost, J., 20 Jun 2019, In : Nucleic acids research. 47, 11, p. 5809-5821 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clostridium butyricum
DNA Cleavage
Argonaute Proteins
Temperature
DNA
1 Citation (Scopus)

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

Mougiakos, I., Orsi, E., Ghiffary, M. R., Post, W., de Maria, A., Adiego-Perez, B., Kengen, S. W. M., Weusthuis, R. A. & van der Oost, J., 25 Nov 2019, In : Microbial Cell Factories. 18, 1, 1 p., 204.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Metabolic engineering
Metabolic Engineering
Rhodobacter sphaeroides
Genes
Hydroxybutyrates

Enrichment of nucleic acids

Bau, H., Song, J., Liu, C., Mauk, M., van der Oost, J. & Hegge, J. W., 19 Sep 2019, Patent No. WO2019178346, Priority date 14 Mar 2018

Research output: PatentOther research output

Open Access
Nucleic Acids
Antigens
Molecules

Haarfijn gewassen verbeteren

van der Oost, J., 31 May 2019

Research output: Non-textual formWeb publication/siteProfessional

Open Access

Harnessing type I CRISPR–Cas systems for genome engineering in human cells

Cameron, P., Coons, M. M., Klompe, S. E., Lied, A. M., Smith, S. C., Vidal, B., Donohoue, P. D., Rotstein, T., Kohrs, B. W., Nyer, D. B., Kennedy, R., Banh, L. M., Williams, C., Toh, M. S., Irby, M. J., Edwards, L. S., Lin, C. H., Owen, A. L. G., Künne, T., van der Oost, J. & 7 others, Brouns, S. J. J., Slorach, E. M., Fuller, C. K., Gradia, S., Kanner, S. B., May, A. P. & Sternberg, S. H., 18 Dec 2019, In : Nature Biotechnology. 37, p. 1471-1477

Research output: Contribution to journalLetterAcademicpeer-review

Human Engineering
RNA
CRISPR-Associated Proteins
Guide RNA
Genes
5 Citations (Scopus)

Improved protein production and codon optimization analyses in Escherichia coli by bicistronic design

Nieuwkoop, T., Claassens, N. J. & van der Oost, J., 2019, In : Microbial Biotechnology. 12, 1, p. 173-179

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Codon
Escherichia coli
Proteins
Genes
5' Untranslated Regions
2 Citations (Scopus)

Incorporation of a Synthetic Amino Acid into dCas9 Improves Control of Gene Silencing

Koopal, B., Kruis, A. J., Claassens, N. J., Nobrega, F. L. & Van Der Oost, J., 1 Jan 2019, In : ACS synthetic biology. 8, 2, p. 216-222

Research output: Contribution to journalArticleAcademicpeer-review

Terminator Codon
Gene Silencing
Amino acids
Genes
Amino Acids
1 Citation (Scopus)

Inducible Fibril Formation of Silk-Elastin Diblocks

Willems, L., Roberts, S., Weitzhandler, I., Chilkoti, A., Mastrobattista, E., Van Der Oost, J. & De Vries, R., 23 May 2019, In : ACS Omega. 4, 5, p. 9135-9143 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Elastin
Silk
Block copolymers
Polymers
Tuning

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples

Palakawong Na Ayudthaya, S., van der Oost, H., van der Oost, J., van Vliet, D. M. & Plugge, C. M., Apr 2019, In : Current Microbiology. 76, 4, p. 425-434

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Poaceae
Guinea Pigs
Acids
formic acid
Starch
3 Citations (Scopus)

Multiplex genome editing of microorganisms using CRISPR-Cas

Adiego-Pérez, B., Randazzo, P., Daran, J. M., Verwaal, R., Roubos, J. A., Daran-Lapujade, P. & van der Oost, J., 14 May 2019, In : FEMS Microbiology Letters. 366, 8

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Gene Expression Regulation
Bacteria
Gene Editing

Nature of Amorphous Hydrophilic Block Affects Self-Assembly of an Artificial Viral Coat Polypeptide

Willems, L., Van Westerveld, L., Roberts, S., Weitzhandler, I., Calcines Cruz, C., Hernandez-Garcia, A., Chilkoti, A., Mastrobattista, E., Van Der Oost, J. & De Vries, R., Oct 2019, In : Biomacromolecules. 20, 10, p. 3641-3647

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Polypeptides
Self assembly
Peptides
DNA
Elastin
2 Citations (Scopus)

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Carrión, V. J., Perez-Jaramillo, J., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz-Buck, D., Mendes, L. W., van Ijcken, W. F. J., Gomez-Exposito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., van der Oost, J., Paulson, J. N., Mendes, R., van Wezel, G. P., Medema, M. H. & Raaijmakers, J. M., 1 Nov 2019, In : Science. 366, 6465, p. 606-612 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

Microbiota
Peptide Synthases
Polyketide Synthases
Flavobacterium
Mycoses

Thermostable Cas9 nucleases with reduced off-target activity

van der Oost, J., van Kranenburg, R., Bosma, E. F., Mougiakos, I. & Mohanraju, P., 18 Apr 2019, Patent No. WO2019072596, Priority date 10 Oct 2017

Research output: PatentOther research output

Open Access
Micrococcal Nuclease
Gene Deletion
Geobacillus
Pseudomonas putida
Temperature
7 Citations (Scopus)

The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut

Elzinga, J., van der Oost, J., de Vos, W. M. & Smidt, H., 13 Mar 2019, In : Microbiology and Molecular Biology Reviews. 83, 2, p. 1-40

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Synbiotics
Organoids
Germ-Free Life
Microbiota
Probiotics
2018

Alcohol acetyl transferases for alkyl alkanoate production

Kruis, A. J., Levisson, M., Mars, A. E., Kengen, S. W. M., van der Oost, J., Sanders, J. P. M. & Weusthuis, R. A., 8 Jun 2018, Patent No. WO2018099719, Priority date 1 Dec 2016

Research output: PatentOther research output

Open Access
Transferases
Kluyveromyces
Acetyl Coenzyme A
Alcohols
Peptides
11 Citations (Scopus)

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

Vlot, M., Houkes, J., Lochs, S. J. A., Swarts, D. C., Zheng, P., Kunne, T., Mohanraju, P., Anders, C., Jinek, M., Van Der Oost, J., Dickman, M. J. & Brouns, S. J. J., 25 Jan 2018, In : Nucleic acids research. 46, 2, p. 873-885

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacteriophages
DNA
T-Phages
Interspersed Repetitive Sequences
Bacteriophage T4
8 Citations (Scopus)

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

Daas, T., Vriesendorp, B., van de Weijer, T., van der Oost, J. & van Kranenburg, R., Jan 2018, In : Current Microbiology. 75, 1, p. 49-56

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Genome
Denitrification
Lactic Acid
Genes

Contribution of Eat1 and other alcohol acyltransferases to ester production in Saccharomyces cerevisiae

Kruis, A. J., Gallone, B., Jonker, T., Mars, A. E., van Rijswijck, I. M. H., Wolkers-Rooijackers, J. C. M., Smid, E. J., Steensels, J., Verstrepen, K. J., Kengen, S. W. M., van der Oost, J. & Weusthuis, R. A., 21 Dec 2018, In : Frontiers in Microbiology. 9, 11 p., 3202.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Acyltransferases
Saccharomyces cerevisiae
Esters
Transferases
Alcohols
13 Citations (Scopus)

Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane

Caforio, A., Siliakus, M. F., Exterkate, M., Jain, S., Jumde, V. R., Andringa, R. L. H., Kengen, S. W. M., Minnaard, A. J., Driessen, A. J. M. & van der Oost, J., 3 Apr 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 14, p. 3704-3709

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Archaea
Escherichia coli
Lipids
Membranes
Membrane Lipids
2 Citations (Scopus)

Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

Daas, M. J. A., Nijsse, B., van de Weijer, A. H. P., Groenendaal, B. W. A. J., Janssen, F., van der Oost, J. & van Kranenburg, R., 27 Jun 2018, In : BMC Biotechnology. 18, 1, 42.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Cellulase
Genes
Glucosides
Hydrolases
10 Citations (Scopus)

Exploration and exploitation of the environment for novel specialized metabolites

Loureiro, C., Medema, M. H., van der Oost, J. & Sipkema, D., 1 Apr 2018, In : Current Opinion in Biotechnology. 50, p. 206-213

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Multigene Family
Metabolites
Genes
Peptide Synthases
Polyketide Synthases
21 Citations (Scopus)

Genome editing by natural and engineered CRISPR-associated nucleases

Wu, W. Y., Lebbink, J. H. G., Kanaar, R., Geijsen, N. & van der Oost, J., 1 Jul 2018, In : Nature Chemical Biology. 14, 7, p. 642-651

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Peptides
Research
Gene Editing
20 Citations (Scopus)

Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects

Mougiakos, I., Bosma, E. F., Ganguly, J., van der Oost, J. & van Kranenburg, R., 1 Apr 2018, In : Current Opinion in Biotechnology. 50, p. 146-157

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Metabolic engineering
Metabolic Engineering
Throughput
Clostridium

Microbial genome editing

van der Oost, J., van Kranenburg, R., Bosma, E. F. & Mougiakos, I., 11 May 2018, Patent No. WO2018083128, Priority date 11 Feb 2016

Research output: PatentOther research output

Open Access
Microbial Genome
Homologous Recombination
Temperature
Plasmids
Microbial Genes
1 Citation (Scopus)

Mining for novel bacterial defence systems

Barrangou, R. & van der Oost, J., 30 Apr 2018, In : Nature Microbiology. 3, p. 535-536

Research output: Contribution to journalArticleAcademicpeer-review

Metagenomics
Plasmids
Viruses
Bacteria
Infection
14 Citations (Scopus)

Progress of CRISPR-Cas based genome editing in Photosynthetic microbes

Naduthodi, M. I. S., Barbosa, M. J. & van der Oost, J., Sep 2018, In : Biotechnology Journal. 13, 9

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Carbon Footprint
CRISPR-Cas Systems
Fossil Fuels
Metabolic Engineering
17 Citations (Scopus)

Prokaryotic Argonaute proteins: novel genome-editing tools?

Hegge, J. W., Swarts, D. C. & van der Oost, J., 1 Jan 2018, In : Nature Reviews Microbiology. 16, 1, p. 5-11

Research output: Contribution to journalArticleAcademicpeer-review

Argonaute Proteins
Nucleic Acids
Archaea
RNA Interference
Eukaryota

Prokaryotic argonaute proteins and uses thereof

van der Oost, J. & Hegge, J. W., 18 Jan 2018, Patent No. WO2018011236, Priority date 7 Dec 2016

Research output: PatentOther research output

Open Access
Argonaute Proteins
Nucleic Acids
Biotechnology
Peptides
Synthetic Biology
3 Citations (Scopus)

Shooting the messenger: RNA-targetting CRISPR-Cas systems

Zhu, Y., Klompe, S. E., Vlot, M., van der Oost, J. & Staals, R. H. J., 21 Jun 2018, In : Bioscience Reports. 38, 3, BSR20170788.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Genes
Messenger RNA
RNA
Deoxyribonucleases
4 Citations (Scopus)

The alcohol acetyltransferase Eat1 is located in yeast mitochondria

Kruis, A. J., Mars, A. E., Kengen, S. W. M., Borst, J. W., van der Oost, J. & Weusthuis, R. A., Oct 2018, In : Applied and Environmental Microbiology. 84, 19, p. 1-11 e01640-18.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
acetyltransferases
Acetyltransferases
mitochondrion
yeast
alcohol

Thermostable Cas9 nucleases

van der Oost, J., van Kranenburg, R., Bosma, E. F., Mougiakos, I. & Mohanraju, P., 21 Jun 2018, Patent No. WO2018108339, Priority date 14 Dec 2016

Research output: PatentOther research output

Open Access
Micrococcal Nuclease
Genetic Engineering
Nucleic Acids
Peptides
Polynucleotides

Thermostable Cas9 nucleases

van der Oost, J., van Kranenburg, R., Bosma, E. F., Mougiakos, I. & Mohanraju, P., 21 Jun 2018, Patent No. WO2018109101, Priority date 14 Dec 2016

Research output: PatentOther research output

Open Access
Micrococcal Nuclease
Guide RNA
Polynucleotides
Endonucleases
Plasmids
2017
45 Citations (Scopus)

Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure

Siliakus, M. F., van der Oost, J. & Kengen, S. W. M., 2017, In : Extremophiles. 21, 4, p. 651-670

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lipids
Pressure
Temperature
Membranes
Archaea
1 Citation (Scopus)

A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts

van Rossum, T., Muras, A., Baur, M. J. J., Creutzburg, S. C. A., van der Oost, J. & Kengen, S. W. M., 2017, In : Microbial Biotechnology. 10, 3, p. 625-641

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bioluminescence
Biocatalysts
Isomerases
Screening
Arabinose
21 Citations (Scopus)

Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute

Swarts, D. C., Szczepaniak, M., Sheng, G., Chandradoss, S. D., Zhu, Y., Timmers, E. M., Zhang, Y., Zhao, H., Lou, J., Wang, Y., Joo, C. & van der Oost, J., 2017, In : Molecular Cell. 65, 6, p. 985-998

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Argonaute Proteins
Thermus thermophilus
Deoxycytidine
Deoxyguanosine
DNA
3 Citations (Scopus)

Biochemical characterization of the xylan hydrolysis profile of the extracellular endo-xylanase from Geobacillus thermodenitrificans T12

Daas, T., Martínez, P. M., van de Weijer, T., van der Oost, J., de Vos, W. M., Kabel, M. A. & van Kranenburg, R., 2017, In : BMC Biotechnology. 17, 1, 44.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Xylans
Hydrolysis
Triticum
Enzymes
28 Citations (Scopus)

Characterizing a thermostable Cas9 for bacterial genome editing and silencing

Mougiakos, I., Mohanraju, P., Bosma, E. F., Vrouwe, V., Finger Bou, M., Naduthodi, M. I. S., Gussak, A., Brinkman, R. B. L., Van Kranenburg, R. & Van Der Oost, J., 1 Dec 2017, In : Nature Communications. 8, 1, 1647.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacterial Genomes
editing
genome
deletion
Clustered Regularly Interspaced Short Palindromic Repeats
16 Citations (Scopus)

Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9

Mougiakos, I., Bosma, E. F., Weenink, K., Vossen, E., Goijvaerts, K., van der Oost, J. & van Kranenburg, R., 2017, In : ACS synthetic biology. 6, 5, p. 849-861

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Streptococcus pyogenes
Genes
Gene Knockout Techniques
Insertional Mutagenesis
Gene Deletion
27 Citations (Scopus)

Ethyl acetate production by the elusive alcohol acetyltransferase from yeast

Kruis, A., Levisson, M., Mars, A. E., van der Ploeg, M., Garcés Daza, F., Ellena, V., Kengen, S. W. M., van der Oost, J. & Weusthuis, R. A., 2017, In : Metabolic Engineering. 41, p. 92-101

Research output: Contribution to journalArticleAcademicpeer-review

Acetyltransferases
Yeast
Alcohols
Yeasts
Saccharomyces cerevisiae
25 Citations (Scopus)

FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae

Swiat, M. A., Dashko, S., den Ridder, M., Wijsman, M., van der Oost, J., Daran, J. M. & Daran-Lapujade, P., 1 Dec 2017, In : Nucleic acids research. 45, 21, p. 12585-12598

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Saccharomyces cerevisiae
Acidaminococcus
Francisella
Yeasts

Improved CRISPR-Cas9 genome editing tool

Louwen, R. & van der Oost, J., 14 Sep 2017, Patent No. WO2017155408, Priority date 11 Mar 2016

Research output: PatentOther research output

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Proteins
Gene Editing

Improved CRISPR-Cpf1 genome editing tool 

van der Oost, J., van Baarlen, P. & Louwen, R., 14 Sep 2017, Patent No. WO2017155407, Priority date 11 Mar 2016

Research output: PatentOther research output

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Proteins
Gene Editing