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Kuipers, prof.dr. Oscar

Oscar Kuipers
Oscar Kuipers

Oscar Kuipers is hoogleraar Moleculaire genetica van prokaryoten aan de RUG en verbonden aan de vakgroep Moleculaire genetica van het Groningen Biomolecular Sciences and Biotechnology Institute. Prokaryoten zijn micro-organismen zonder celkern, zoals bacteriën en blauwwieren. De moleculaire genetica bestudeert de genwerking, genregulatie en interactie tussen genen. Het onderzoek levert onder meer kennis op voor genetische modificatie van bacteriën en is van groot belang voor de biotechnologie. Kuipers studeerde biologie in Utrecht en promoveerde daar bij de vakgroep Biochemie.

Jaarlijks begeleidt Kuipers het RUG-studententeam dat (immer succesvol) meedoet aan de iGEM-competitie in Boston. In 2012 werd dit team zelfs wereldkampioen, met een zelfgebouwde bacterie die rottend vlees kan detecteren. In 2011 werd Kuipers tot 'Simon Stevin Meester 2011' benoemd door de Stichting Technische Wetenschappen (STW). Kuipers kreeg 500.000 euro die hij naar eigen inzicht aan onderzoek kon besteden. In hetzelfde jaar werd hij benoemd tot lid van de afdeling Natuurkunde van de Koninklijke Nederlandse Academie van Wetenschappen (KNAW). In 2012 ontving hij een subsidie van NWO voor de verdere ontwikkeling van microscopische technieken om intracellulaire processen ‘live’ te volgen, hetgeen het begrip van (microbieel) leven enorm zal vergroten. In 2013 kende de EU Kuipers een subsidie van 1 miljoen euro toe om synthetische peptiden te maken, met vooral aandacht voor het ontwikkelen van nieuwe antibiotica.

Kuipers is mede-oprichter en directeur van het Centre for Sustainable Antimicrobials (CeSAM) van RUG en UMCG, een centrum voor onderzoek tegen antibioticaresistentie dat de grenzen tussen vakgebieden en organisaties wil doorbreken en zo de ontwikkeling van nieuwe antibiotica efficiënter wil maken.

Eerder in het nieuws

Persbericht NRC
Persbericht NRC

2018

Boonstra, M., Vesel, N., & Kuipers, O. P. (2018). Fluorescently Labeled DNA Interacts with Competence and Recombination Proteins and Is Integrated and Expressed Following Natural Transformation of Bacillus subtilis. Mbio, 9(5), [e01161-18]. DOI: 10.1128/mBio.01161-18
Cao, H., Villatoro-Hernandez, J., Weme, R. D. O., Frenzel, E., & Kuipers, O. P. (2018). Boosting heterologous protein production yield by adjusting global nitrogen and carbon metabolic regulatory networks in Bacillus subtilis. Metabolic Engineering, 49, 143-152. DOI: 10.1016/j.ymben.2018.08.001
Cao, H., & Kuipers, O. P. (2018). Influence of global gene regulatory networks on single cell heterogeneity of green fluorescent protein production in Bacillus subtilis. Microbial Cell Factories, 17(1), [134]. DOI: 10.1186/s12934-018-0985-9
Solopova, A., Bachmann, H., Teusink, B., Kok, J., & Kuipers, O. P. (2018). Further Elucidation of Galactose Utilization in MG1363. Frontiers in Microbiology, 9, [1803]. DOI: 10.3389/fmicb.2018.01803
Yi, Y., Li, Z., Song, C., & Kuipers, O. P. (2018). Exploring plant-microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR-Cas9 system. Environmental Microbiology. DOI: 10.1111/1462-2920.14305
van Heel, A. J., de Jong, A., Song, C., Viel, J. H., Kok, J., & Kuipers, O. P. (2018). BAGEL4: A user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Research, 46(W1), W278-W281. DOI: 10.1093/nar/gky383
Yi, Y., Li, Z., & Kuipers, O. P. (2018). Plant-Microbe Interaction: Transcriptional Response of Bacillus Mycoides to Potato Root Exudates. Journal of visualized experiments : JoVE, (137). DOI: 10.3791/57606
Mu, D., Lu, J., Qiao, M., Kuipers, O. P., Zhu, J., Li, X., ... Zheng, Z. (2018). Heterologous signal peptides-directing secretion of Streptomyces mobaraensis transglutaminase by Bacillus subtilis. Applied Microbiology and Biotechnology, 102(13), 5533-5543. DOI: 10.1007/s00253-018-9000-y
Afzal, M., Shafeeq, S., & Kuipers, O. P. (2018). NADH-Mediated Gene Expression in Streptococcus pneumoniae and Role of Rex as a Transcriptional Repressor of the Rex-Regulon. Frontiers in Microbiology, 9, 1-9. [fmicb.2018.01300]. DOI: 10.3389/fmicb.2018.01300
Li, Q., Montalban-Lopez, M., & Kuipers, O. P. (2018). Increasing Antimicrobial Activity of Nisin-based Lantibiotics Against Gram-negative Pathogens. Applied and environmental microbiology, 84(12), [UNSP e00052-18]. DOI: 10.1128/AEM.00052-18
Carvalho, S. M., Freitas, C. S., Kuipers, O. P., & Saraiva, L. M. (2018). Staphylococcus aureus metabolic strategies to survive nitrosative stress. Free Radical Biology and Medicine, 120, S149-S150. DOI: 10.1016/j.freeradbiomed.2018.04.493
Nickling, J. H., Baumann, T., Schmitt, F-J., Bartholomae, M., Kuipers, O. P., Friedrich, T., & Budisa, N. (2018). Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids. Journal of visualized experiments : JoVE, (135), [57551]. DOI: 10.3791/57551, 10.3791/57551
Zhi, X., Abdullah, I. T., Gazioglu, O., Manzoor, I., Shafeeq, S., Kuipers, O. P., ... Yesilkaya, H. (2018). Rgg-Shp regulators are important for pneumococcal colonization and invasion through their effect on mannose utilization and capsule synthesis. Scientific Reports, 8(1), [6369]. DOI: 10.1038/s41598-018-24910-1
Bartholomae, M., Baumann, T., Nickling, J. H., Peterhoff, D., Wagner, R., Budisa, N., & Kuipers, O. P. (2018). Expanding the Genetic Code of and to Incorporate Non-canonical Amino Acids for Production of Modified Lantibiotics. Frontiers in Microbiology, 9, 1-11. [657]. DOI: 10.3389/fmicb.2018.00657
Dudnik, A., Almeida, A. F., Andrade, R., Avila, B., Banados, P., Barbay, D., ... Solopova, A. (2018). BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits. Phytochemistry reviews, 17(2), 291-326. DOI: 10.1007/s11101-017-9532-2
Fu, Y., Mu, D., Qiao, W., Zhu, D., Wang, X., Liu, F., ... Qiao, M. (2018). Co-expression of Nisin Z and Leucocin C as a Basis for Effective Protection Againstin Pasteurized Milk. Frontiers in Microbiology, 9, [547]. DOI: 10.3389/fmicb.2018.00547
Carvalho, S. M., Kloosterman, T. G., Manzoor, I., Caldas, J., Vinga, S., Martinussen, J., ... Neves, A. P. (2018). Interplay Between Capsule Expression and Uracil Metabolism in Streptococcus pneumoniae D39. Frontiers in Microbiology, 9, [321]. DOI: 10.3389/fmicb.2018.00321
Omony, J., de Jong, A., Krawczyk, A. O., Eijlander, R. T., & Kuipers, O. P. (2018). Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens: a transcriptomic model. Microbial genomics, 4(2), [mgen.0.000157]. DOI: 10.1099/mgen.0.000157
Montalban-Lopez, M., Deng, J., van Heel, A. J., & Kuipers, O. P. (2018). Specificity and Application of the Lantibiotic Protease NisP. Frontiers in Microbiology, 9. DOI: 10.3389/fmicb.2018.00160
Yi, Y., Frenzel, E., Spoelder, J., Elzenga, J. T. M., van Elsas, J. D., & Kuipers, O. P. (2018). Optimized fluorescent proteins for the rhizosphere-associated bacterium Bacillus mycoides with endophytic and biocontrol agent potential. Environmental microbiology reports, 10(1), 57-74. DOI: 10.1111/1758-2229.12607
Frenzel, E., Legebeke, J., van Stralen, A., van Kranenburg, R., & Kuipers, O. P. (2018). In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria. Biotechnology for Biofuels, 11(8). DOI: 10.1186/s13068-017-1008-5
Bron, P. A., Marcelli, B., Mulder, J., van der Els, S., Morawska, L. P., Kuipers, O. P., ... Kleerebezem, M. (2019). Renaissance of traditional DNA transfer strategies for improvement of industrial lactic acid bacteria. Current Opinion in Biotechnology, 56, 61-68. DOI: 10.1016/j.copbio.2018.09.004

2017

Motib, A., Guerreiro, A., Al-Bayati, F., Piletska, E., Manzoor, I., Shafeeq, S., ... Yesilkaya, H. (2017). Modulation of Quorum Sensing in a Gram Positive Pathogen by Linear Imprinted Copolymers with anti-Infective Properties. Angewandte Chemie - International Edition, 56(52), 16555-16558. [anie.201709313]. DOI: 10.1002/anie.201709313
van den Esker, M. H., Kovács, Á. T., & Kuipers, O. P. (2017). From Cell Death to Metabolism: Holin-Antiholin Homologues with New Functions. Mbio, 8(6), 1-5. [e01963-17]. DOI: 10.1128/mBio.01963-17
Solopova, A., Kok, J., & Kuipers, O. P. (2017). Disruption of a transcriptional repressor by an IS-element integration leads to the activation of a novel silent cellobiose transporter in Lactococcus lactis MG1363. Applied and environmental microbiology, 83(23), [e01279-17]. DOI: 10.1128/AEM.01279-17
Perez, M., Ladero, V., del Rio, B., Redruello, B., de Jong, A., Kuipers, O., ... Alvarez, M. A. (2017). The Relationship among Tyrosine Decarboxylase and Agmatine Deiminase Pathways in Enterococcus faecalis. Frontiers in Microbiology, 8, 1-9. [2107]. DOI: 10.3389/fmicb.2017.02107
van Heel, A. J., Montalban-Lopez, M., Oliveau, Q., & Kuipers, O. P. (2017). Genome-guided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin. Microbial genomics, 3(10), 1-9. [mgen.0.000134]. DOI: 10.1099/mgen.0.000134
Bartholomae, M., Buivydas, A., Viel, J. H., Montalban-Lopez, M., & Kuipers, O. P. (2017). Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis. Molecular Microbiology, 106(2), 186-206. DOI: 10.1111/mmi.13764
Mulder, J., Wels, M., Kuipers, O. P., Kleerebezem, M., & Bron, P. A. (2017). Unleashing Natural Competence in Lactococcus lactis by Induction of the Competence Regulator ComX. Applied and environmental microbiology, 83(20), [e01320-17]. DOI: 10.1128/AEM.01320-17
Díez, L., Solopova, A., Fernández-Pérez, R., González, M., Tenorio, C., Kuipers, O. P., & Ruiz-Larrea, F. (2017). Transcriptome analysis shows activation of the arginine deiminase pathway in Lactococcus lactis as a response to ethanol stress. International Journal of Food Microbiology, 257, 41-48. DOI: 10.1016/j.ijfoodmicro.2017.05.017
Yi, Y., de Jong, A., Frenzel, E., & Kuipers, O. P. (2017). Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates. Frontiers in Microbiology, 8, 1-14. [1487]. DOI: 10.3389/fmicb.2017.01487
Kok, J., van Gijtenbeek, L. A., de Jong, A., van der Meulen, S. B., Solopova, A., & Kuipers, O. P. (2017). The evolution of gene regulation research in Lactococcus lactis. FEMS Microbiology Reviews, 41(Supp_1), S220-S243. DOI: 10.1093/femsre/fux028
Kleerebezem, M., Kuipers, O. P., & Smid, E. J. (2017). Editorial: Lactic acid bacteria-a continuing journey in science and application. FEMS Microbiology Reviews, 41(Supp_1), S1-S2. DOI: 10.1093/femsre/fux036
Carvalho, S. M., de Jong, A., Kloosterman, T. G., Kuipers, O. P., & Saraiva, L. M. (2017). The Staphylococcus aureus α-Acetolactate Synthase ALS Confers Resistance to Nitrosative Stress. Frontiers in Microbiology, 8, [1273]. DOI: 10.3389/fmicb.2017.01273
Hajaj, B., Yesilkaya, H., Shafeeq, S., Zhi, X., Benisty, R., Tchalah, S., ... Porat, N. (2017). CodY Regulates Thiol Peroxidase Expression as Part of the Pneumococcal Defense Mechanism against H2O2 Stress. Frontiers in Cellular and Infection Microbiology, 7, 1-13. [210]. DOI: 10.3389/fcimb.2017.00210
Tracanna, V., de Jong, A., Medema, M. H., & Kuipers, O. P. (2017). Mining prokaryotes for antimicrobial compounds: From diversity to function. FEMS Microbiology Reviews, 41(3), 417-429. [014]. DOI: 10.1093/femsre/fux014
Banin, E., Hughes, D., & Kuipers, O. P. (2017). Editorial: Bacterial pathogens, antibiotics and antibiotic resistance. FEMS Microbiology Reviews, 41(3), 450-452. [016]. DOI: 10.1093/femsre/fux016
Cao, H., van Heel, A. J., Ahmed, H., Mols, M., & Kuipers, O. P. (2017). Cell surface engineering of Bacillus subtilis improves production yields of heterologously expressed α-amylases. Microbial Cell Factories, 16(1), 1-9. [56]. DOI: 10.1186/s12934-017-0674-0
Krawczyk, A. O., de Jong, A., Omony, J., Holsappel, S., Wells-Bennik, M. H. J., Kuipers, O. P., & Eijlander, R. T. (2017). Spore Heat Activation Requirements and Germination Responses Correlate with Sequences of Germinant Receptors and with the Presence of a Specific spoVA(2mob) Operon in Foodborne Strains of Bacillus subtilis. Applied and environmental microbiology, 83(7), [e03122-16]. DOI: 10.1128/AEM.03122-16
Al-Bayati, F. A. Y., Kahya, H. F. H., Damianou, A., Shafeeq, S., Kuipers, O. P., Andrew, P. W., & Yesilkaya, H. (2017). Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase. Scientific Reports, 7, 1-17. [43587 ]. DOI: 10.1038/srep43587
Baumann, T., Nickling, J. H., Bartholomae, M., Buivydas, A., Kuipers, O. P., & Budisa, N. (2017). Prospects of In vivo Incorporation of non-canonical amino acids for the chemical diversification of antimicrobial peptides. Frontiers in Microbiology, 8, [124]. DOI: 10.3389/fmicb.2017.00124
Visweswaran, G. R. R., Kurek, D., Szeliga, M., Pastrana, F. R., Kuipers, O. P., Kok, J., & Buist, G. (2017). Expression of prophage-encoded endolysins contributes to autolysis of Lactococcus lactis. Applied Microbiology and Biotechnology, 101(3), 1099-1110. DOI: 10.1007/s00253-016-7822-z
van den Esker, M. H., Kovacs, A. T., & Kuipers, O. P. (2017). YsbA and LytST are essential for pyruvate utilization in Bacillus subtilis. Environmental Microbiology, 19(1), 83-94. DOI: 10.1111/1462-2920.13454
Afzal, M., Kuipers, O. P., & Shafeeq, S. (2017). Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae. Frontiers in Cellular and Infection Microbiology, 7, 1-11. [70]. DOI: 10.3389/fcimb.2017.00070
Kuipers, O., & Kovacs, A. (2017). Bacterial gangs: United and strong by means of quorum sensing. In J. van Doorn, J. Luirink, J. van der Oost, B. Oudega, L. Robertson, H. Smit, P. Willemsen, ... C. Biemans (Eds.), MIGHTY MICROBES: THE AMAZING WORLD OF MICROORGANISMS (1 ed., Vol. 1, pp. 71-73). The Netherlands: Microcanon Foundation.

2016

Yi, Y., & Kuipers, O. P. (2016). Development of an efficient electroporation method for rhizobacterial Bacillus mycoides strains. Journal of microbiological methods, 133, 82-86. DOI: 10.1016/j.mimet.2016.12.022
Berendsen, E. M., Koning, R. A., Boekhorst, J., de Jong, A., Kuipers, O. P., & Wells-Bennik, M. H. J. (2016). High-Level Heat Resistance of Spores of Bacillus amyloliquefaciens and Bacillus licheniformis Results from the Presence of a spoVA Operon in a Tn1546 Transposon. Frontiers in Microbiology, 7, [1912]. DOI: 10.3389/fmicb.2016.01912
Afzal, M., Manzoor, I., Kuipers, O. P., & Shafeeq, S. (2016). Cysteine-Mediated Gene Expression and Characterization of the CmbR Regulon in Streptococcus pneumoniae. Frontiers in Microbiology, 7, [1929]. DOI: 10.3389/fmicb.2016.01929
Krawczyk, A. O., Berendsen, E. M., de Jong, A., Boekhorst, J., Wells-Bennik, M. H., Kuipers, O. P., & Eijlander, R. T. (2016). A transposon present in specific strains of Bacillus subtilis negatively affects nutrient- and dodecylamine-induced spore germination. Environmental Microbiology, 18(12), 4830-4846. DOI: 10.1111/1462-2920.13386
Afzal, M., Shafeeq, S., Manzoor, I., Henriques-Normark, B., & Kuipers, O. P. (2016). N-acetylglucosamine-Mediated Expression of nagA and nagB in Streptococcus pneumoniae. Frontiers in Cellular and Infection Microbiology, 6, 1-12. [158]. DOI: 10.3389/fcimb.2016.00158
Zhao, X., & Kuipers, O. P. (2016). Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics, 17(1), [882]. DOI: 10.1186/s12864-016-3224-y
Eijlander, R. T., Holsappel, S., de Jong, A., Ghosh, A., Christie, G., & Kuipers, O. (2016). SpoVT: From Fine-Tuning Regulator in Bacillus subtilis to Essential Sporulation Protein in Bacillus . Frontiers in Microbiology, 7, [1607]. DOI: 10.3389/fmicb.2016.01607
Nagler, K., Krawczyk, A. O., De Jong, A., Madela, K., Hoffmann, T., Laue, M., ... Moeller, R. (2016). Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High-Salinity Environments Using RNA Sequencing. Frontiers in Microbiology, 7, 1-15. [1564]. DOI: 10.3389/fmicb.2016.01564
Afzal, M., Shafeeq, S., Ahmed, H., & Kuipers, O. P. (2016). N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae. Frontiers in Cellular and Infection Microbiology, 6, 1-12. [101]. DOI: 10.3389/fcimb.2016.00101
Montalbán-López, M., van Heel, A. J., & Kuipers, O. P. (2016). Employing the promiscuity of lantibiotic biosynthetic machineries to produce novel antimicrobials. FEMS Microbiology Reviews, 41(1), 5-18. [fuw034]. DOI: 10.1093/femsre/fuw034
Perez, M., Ladero, V., Del Rio, B., Redruello, B., Jong, de, A., Kuipers, O. P., ... Alvarez, M. A. (2016). Transcriptome profiling of TDC cluster deletion mutant of Enterococcus faecalis V583. Genomics Data, 9, 67-69. DOI: 10.1016/j.gdata.2016.06.012
Afzal, M., Shafeeq, S., & Kuipers, O. P. (2016). Methionine-mediated gene expression and characterization of the CmhR regulon in Streptococcus pneumoniae. Microbial genomics, 2(10), 1-11. [e000091]. DOI: 10.1099/mgen.0.000091
Mhatre, E., Troszok, A., Gallegos-Monterrosa, R., Lindstädt, S., Hölscher, T., Kuipers, O. P., & Kovács, Á. T. (2016). The impact of manganese on biofilm development of Bacillus subtilis. Microbiology, 162(8), 1468-1478. DOI: 10.1099/mic.0.000320
Back, A., Borges, F., Mangavel, C., Paris, C., Rondags, E., Kapel, R., ... Cailliez-Grimal, C. (2016). Recombinant pediocin in Lactococcus lactis: increased production by propeptide fusion and improved potency by co-production with PedC. Microbial Biotechnology, 9(4), 466-477. DOI: 10.1111/1751-7915.12285
van Heel, A. J., Kloosterman, T. G., Montalban-Lopez, M., Deng, J., Plat, A., Baudu, B., ... Kuipers, O. P. (2016). Discovery, production and modification of 5 novel lantibiotics using the promiscuous nisin modification machinery. ACS Synthetic Biology, 5(10), 1146-1154. [6b00033]. DOI: 10.1021/acssynbio.6b00033
Warda, A. K., Siezen, R. J., Boekhorst, J., Wells-Bennik, M. H. J., Jong, de, A., Kuipers, O. P., ... Abee, T. (2016). Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PLoS ONE, 11(6), [e0156796]. DOI: 10.1371/journal.pone.0156796
Zhou, L., Shao, J., Li, Q., van Heel, A. J., de Vries, M. P., Broos, J., & Kuipers, O. P. (2016). Incorporation of tryptophan analogues into the lantibiotic nisin. Amino Acids, 48(5), 1309-1318. DOI: 10.1007/s00726-016-2186-3
Berendsen, E. M., Boekhorst, J., Kuipers, O. P., & Wells-Bennik, M. H. J. (2016). A mobile genetic element profoundly increases heat resistance of bacterial spores. The ISME journal, 10(11), 2633-2642. [2016.59]. DOI: 10.1038/ismej.2016.59
Alvarez-Sieiro, P., Montalbán-López, M., Mu, D., & Kuipers, O. P. (2016). Bacteriocins of lactic acid bacteria: extending the family. Applied Microbiology and Biotechnology, 100(7), 2939-2951. DOI: 10.1007/s00253-016-7343-9
Zhou, L., van Heel, A. J., Montalban-Lopez, M., & Kuipers, O. P. (2016). Potentiating the Activity of Nisin against Escherichia coli. Frontiers in Cell and Developmental Biology, 4, [7]. DOI: 10.3389/fcell.2016.00007
Wells-Bennik, M. H. J., Eijlander, R. T., den Besten, H. M. W., Berendsen, E. M., Warda, A. K., Krawczyk, A. O., ... Abee, T. (2016). Bacterial Spores in Food: Survival, Emergence, and Outgrowth. Annual Review of Food Science and Technology, 7, 457-482. DOI: 10.1146/annurev-food-041715-033144
Yi, Y., de Jong, A., Spoelder, J., Elzenga, J. T. M., van Elsas, J. D., & Kuipers, O. P. (2016). Draft Genome Sequence of Bacillus mycoides M2E15, a Strain Isolated from the Endosphere of Potato. Genome Announcements, 4(1), 1-2. [e00031-16]. DOI: 10.1128/genomeA.00031-16
Montalbán-López, M., & Kuipers, O. P. (2016). Posttranslational Peptide-Modification Enzymes in Action: Key Roles for Leaders and Glutamate. Cell Chemical Biology, 23(3), 318-319. DOI: 10.1016/j.chembiol.2016.03.001
Berendsen, E. M., Wells-Bennik, M. H. J., Krawczyk, A. O., de Jong, A., van Heel, A., Eijlander, R. T., & Kuipers, O. P. (2016). Draft Genome Sequences of 10 Bacillus subtilis Strains That Form Spores with High or Low Heat Resistance. Genome Announcements, 4(2), 1-2. [e00124-16]. DOI: 10.1128/genomeA.00124-16
Del Rio, B., Redruello, B., Martin, M. C., Fernandez, M., de Jong, A., Kuipers, O. P., ... Alvarez, M. A. (2016). Transcriptome profiling of Lactococcus lactis subsp. cremoris CECT 8666 in response to agmatine. Genomics Data, 7, 112-114. DOI: 10.1016/j.gdata.2015.12.003
Solopova, A., Formosa-Dague, C., Courtin, P., Furlan, S., Veiga, P., Péchoux, C., ... Kulakauskas, S. (2016). Regulation of cell wall plasticity by nucleotide metabolism in Lactococcus lactis. The Journal of Biological Chemistry, 291(21), 11323-11336. DOI: 10.1074/jbc.M116.714303
Krawczyk, A. O., de Jong, A., Holsappel, S., Eijlander, R. T., van Heel, A., Berendsen, E. M., ... Kuipers, O. P. (2016). Genome Sequences of 12 Spore-Forming Bacillus Species, Comprising Bacillus coagulans, Bacillus licheniformis, Bacillus amyloliquefaciens, Bacillus sporothermodurans, and Bacillus vallismortis, Isolated from Foods. Genome Announcements, 4(3), 1-2. [e00103-16]. DOI: 10.1128/genomeA.00103-16
Berendsen, E. M., Wells-Bennik, M. H. J., Krawczyk, A. O., de Jong, A., van Heel, A., Holsappel, S., ... Kuipers, O. P. (2016). Draft Genome Sequences of Seven Thermophilic Spore-Forming Bacteria Isolated from Foods That Produce Highly Heat-Resistant Spores, Comprising Geobacillus spp., Caldibacillus debilis, and Anoxybacillus flavithermus. Genome Announcements, 4(3), 1-2. [00105-16]. DOI: 10.1128/genomeA.00105-16
Hayrapetyan, H., Boekhorst, J., Jong, de, A., Kuipers, O. P., Nierop Groot, M. N., & Abee, T. (2016). Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates. Genome Announcements, 4(3), 1-2. [e00485-16]. DOI: 10.1128/genomeA.00485-16
Fernández Ramírez, M. D., Boekhorst, J., de Jong, A., Kuipers, O. P., Abee, T., & Nierop Groot, M. N. (2016). Draft Whole-Genome Sequences of Three Lactobacillus plantarum Food Isolates. Genome Announcements, 4(3), 1-2. [e00560-16]. DOI: 10.1128/genomeA.00560-16
Kaunietis, A., de Jong, A., Pranckutė, R., Buivydas, A., & Kuipers, O. P. (2016). Draft Genome Sequences of Two Geobacillus Species Strains, Isolated from Oil Wells and Surface Soil above Oil Pools. Genome Announcements, 4(5), 1. [e01129-16]. DOI: 10.1128/genomeA.01129-16

2015

Manzoor, I., Shafeeq, S., & Kuipers, O. (2015). Transcriptome analysis of Streptococcus pneumoniae D39 in the presence of cobalt. Genomics Data, 6, 151-153. DOI: 10.1016/j.gdata.2015.08.033
Del Rio, B., Linares, D. M., Redruello, B., Martin, M. C., Fernandez, M., de Jong, A., ... Alvarez, M. A. (2015). Transcriptomic profile of aguR deletion mutant of Lactococcus lactis subsp. cremoris CECT 8666. Genomics Data, 6, 228-230. DOI: 10.1016/j.gdata.2015.10.002
Manzoor, I., Shafeeq, S., & Kuipers, O. (2015). Ni2+-Dependent and PsaR-Mediated Regulation of the Virulence Genes pcpA, psaBCA, and prtA in Streptococcus pneumoniae. PLoS ONE, 10(11), [e0142839]. DOI: 10.1371/journal.pone.0142839
Afzal, M., Shafeeq, S., Manzoor, I., & Kuipers, O. P. (2015). GalR Acts as a Transcriptional Activator of galKT in the Presence of Galactose in Streptococcus pneumoniae. Journal of Molecular Microbiology and Biotechnology, 25(6), 363-371. DOI: 10.1159/000439429
Berendsen, E. M., Krawczyk, A. O., Klaus, V., de Jong, A., Boekhorst, J., Eijlander, R. T., ... Wells-Bennik, M. H. J. (2015). Bacillus thermoamylovorans Spores with Very-High-Level Heat Resistance Germinate Poorly in Rich Medium despite the Presence of ger Clusters but Efficiently upon Exposure to Calcium-Dipicolinic Acid. Applied and environmental microbiology, 81(22), 7791-7801. [AEM.01993-15]. DOI: 10.1128/AEM.01993-15
Overkamp, W., & Kuipers, O. P. (2015). Transcriptional Profile of Bacillus subtilis sigF-Mutant during Vegetative Growth. PLoS ONE, 10(10), [e0141553]. DOI: 10.1371/journal.pone.0141553
Paixão, L., Caldas, J., Kloosterman, T. G., Kuipers, O. P., Vinga, S., & Neves, A. R. (2015). Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism. Frontiers in Microbiology, 6, [1041]. DOI: 10.3389/fmicb.2015.01041
Detert Oude Weme, R., Seidel, G., & Kuipers, O. P. (2015). Probing the regulatory effects of specific mutations in three major binding domains of the pleiotropic regulator CcpA of Bacillus subtilis. Frontiers in Microbiology, 6, [1051]. DOI: 10.3389/fmicb.2015.01051
de Jong, A., van der Meulen, S., Kuipers, O. P., & Kok, J. (2015). T-REx: Transcriptome analysis webserver for RNA-seq Expression data. BMC Genomics, 16(1), [663]. DOI: 10.1186/s12864-015-1834-4
Ercan, O., Bisschops, M. M. M., Overkamp, W., Jorgensen, T. R., Ram, A. F., Smid, E. J., ... Kleerebezem, M. (2015). Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates. Applied and environmental microbiology, 81(17), 5662-5670. DOI: 10.1128/AEM.00944-15
Berendsen, E. M., Bennik, M. H. J., & Kuipers, O. P. (2015). Heat resistant microorganism (Patent No. WO2015126251.)
Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., ... Glöckner, F. O. (2015). Minimum Information about a Biosynthetic Gene cluster. Nature Chemical Biology, 11(9), 625-631. DOI: 10.1038/nchembio.1890
Manzoor, I., Shafeeq, S., Kloosterman, T., & Kuipers, O. (2015). Co2+-dependent gene expression in Streptococcus pneumoniae: opposite effect of Mn2+ and Co2+ on the expression of the virulence genes psaBCA, pcpA, and prtA. Frontiers in Microbiology, 6, [748]. DOI: 10.3389/fmicb.2015.00748
Michels, K., Heinke, R., Schöne, P., Kuipers, O. P., Arnold, N., & Wessjohann, L. A. (2015). A fluorescence-based bioassay for antibacterials and its application in screening natural product extracts. Journal of Antibiotics, 68(12), 734-740. DOI: 10.1038/ja.2015.71
Grau, R. R., de Oña, P., Kunert, M., Leñini, C., Gallegos-Monterrosa, R., Mhatre, E., ... Kovács, Á. T. (2015). A Duo of Potassium-Responsive Histidine Kinases Govern the Multicellular Destiny of Bacillus subtilis. Mbio, 6(4), [e00581-15]. DOI: 10.1128/mBio.00581-15
Goel, A., Eckhardt, T. H., Puri, P., de Jong, A., Branco dos Santos, F., Giera, M., ... Teusink, B. (2015). Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect? Molecular Microbiology, 97(1), 77-92. DOI: 10.1111/mmi.13012
Linares, D. M., Del Rio, B., Redruello, B., Ladero, V., Martin, M. C., de Jong, A., ... Alvarez, M. A. (2015). AguR is a transmembrane transcription activator of the putrescine biosynthesis operon in Lactococcus lactis, and acts in response to agmatine concentration. Applied and environmental microbiology, 81(18), 6145-6157. DOI: 10.1128/AEM.00959-15
Afzal, M., Shafeeq, S., Manzoor, I., & Kuipers, O. P. (2015). Maltose-Dependent Transcriptional Regulation of the mal Regulon by MalR in Streptococcus pneumoniae. Plos one, 10(6), [e0127579]. DOI: 10.1371/journal.pone.0127579
Mu, D., Montalban-Lopez, M., Deng, J., & Kuipers, O. P. (2015). Lantibiotic Reductase LtnJ Substrate Selectivity Assessed with a Collection of Nisin Derivatives as Substrates. Applied and environmental microbiology, 81(11), 3679-3687. DOI: 10.1128/AEM.00475-15
Grimbergen, A. J., Siebring, J., Solopova, A., & Kuipers, O. P. (2015). Microbial bet-hedging: the power of being different. Current Opinion in Microbiology, 25, 67-72. DOI: 10.1016/j.mib.2015.04.008
Benoit, I., van den Esker, M. H., Patyshakuliyeva, A., Mattern, D. J., Blei, F., Zhou, M., ... Kovács, A. T. (2015). Bacillus subtilis attachment to Aspergillus niger hyphae results in mutually altered metabolism. Environmental Microbiology, 17(6), 2099-2113. DOI: 10.1111/1462-2920.12564
Afzal, M., Shafeeq, S., Ahmed, H., & Kuipers, O. P. (2015). Sialic acid-mediated gene expression in Streptococcus pneumoniae and the role of NanR as a transcriptional activator of the nan gene cluster. Applied and environmental microbiology, 81(9). DOI: 10.1128/AEM.00499-15
Detert Oude Weme, R. G. J., Kovács, Á. T., de Jong, S. J. G., Veening, J-W., Siebring, J., & Kuipers, O. P. (2015). Single Cell FRET Analysis for the Identification of Optimal FRET-Pairs in Bacillus subtilis Using a Prototype MEM-FLIM System. Plos one, 10(4), [e0123239]. DOI: 10.1371/journal.pone.0123239
Schneider, J., Klein, T., Mielich-Süss, B., Koch, G., Franke, C., Kuipers, O. P., ... Lopez, D. (2015). Spatio-temporal Remodeling of Functional Membrane Microdomains Organizes the Signaling Networks of a Bacterium. PLOS Genetics, 11(4), [e1005140]. DOI: 10.1371/journal.pgen.1005140
Sorg, R. A., Kuipers, O. P., & Veening, J-W. (2015). Gene Expression Platform for Synthetic Biology in the Human Pathogen Streptococcus pneumoniae. ACS Synthetic Biology, 4(3), 228-39. DOI: 10.1021/sb500229s
Shafeeq, S., Afzal, M., Henriques-Normark, B., & Kuipers, O. P. (2015). Transcriptional profiling of UlaR-regulated genes in Streptococcus pneumoniae. Genomics Data, 4, 57-59. DOI: 10.1016/j.gdata.2015.02.004
Khusainov, R., van Heel, A. J., Lubelski, J., Moll, G. N., & Kuipers, O. P. (2015). Identification of essential amino acid residues in the nisin dehydratase NisB. Frontiers in Microbiology, 6, [102]. DOI: 10.3389/fmicb.2015.00102
Afzal, M., Shafeeq, S., & Kuipers, O. P. (2015). Ascorbic acid-dependent gene expression in Streptococcus pneumoniae and the activator function of the transcriptional regulator UlaR2. Frontiers in Microbiology, 6, [72]. DOI: 10.3389/fmicb.2015.00072
Berendsen, E. M., Zwietering, M. H., Kuipers, O. P., & Wells-Bennik, M. H. J. (2015). Two distinct groups within the Bacillus subtilis group display significantly different spore heat resistance properties. Food Microbiology, 45 PartA, 18-25. DOI: 10.1016/j.fm.2014.04.009
Zhou, L., van Heel, A. J., & Kuipers, O. P. (2015). The length of a lantibiotic hinge region has profound influence on antimicrobial activity and host specificity. Frontiers in Microbiology, 6, [11]. DOI: 10.3389/fmicb.2015.00011
Kuipers, O. P. (2015). Back to Nature: a revival of natural strain improvement methodologies. Microbial Biotechnology, 8(1), 17-18. DOI: 10.1111/1751-7915.12232
Afzal, M., Shafeeq, S., Henriques-Normark, B., & Kuipers, O. P. (2015). UlaR activates expression of the ula operon in Streptococcus pneumoniae in the presence of ascorbic acid. Microbiology-Reading, 161(Pt 1), 41-9. DOI: 10.1099/mic.0.083899-0
Overkamp, W., Ercan, O., Herber, M., van Maris, A. J. A., Kleerebezem, M., & Kuipers, O. P. (2015). Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis. Environmental Microbiology, 17(2), 346-363. DOI: 10.1111/1462-2920.12676
de Jong, A., van Heel, A. J., Montalban-Lopez, M., Krawczyk, A. O., Berendsen, E. M., Wells-Bennik, M., & Kuipers, O. P. (2015). Draft Genome Sequences of Five Spore-Forming Food Isolates of Bacillus pumilus. Genome Announcements, 3(2), 1-2. [e01539-14]. DOI: 10.1128/genomeA.01539-14
Zhao, X., de Jong, A., Zhou, Z., & Kuipers, O. P. (2015). Complete Genome Sequence of Bacillus amyloliquefaciens Strain BH072, Isolated from Honey. Genome Announcements, 3(2), 1-2. [e00098-15]. DOI: 10.1128/genomeA.00098-15
Krawczyk, A. O., Berendsen, E. M., Eijlander, R. T., de Jong, A., Wells-Bennik, M. H. J., & Kuipers, O. P. (2015). Draft Genome Sequences of Four Bacillus thermoamylovorans Strains Isolated from Milk and Acacia Gum, a Food Ingredient. Genome Announcements, 3(2), 1-2. [e00165-15]. DOI: 10.1128/genomeA.00165-15
Afzal, M., Manzoor, I., & Kuipers, O. P. (2015). A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae. Journal of visualized experiments : JoVE, (98). DOI: 10.3791/52649
Manzoor, I., Shafeeq, S., Afzal, M., & Kuipers, O. P. (2015). Fucose-Mediated Transcriptional Activation of the fcs Operon by FcsR in Streptococcus pneumoniae. Journal of Molecular Microbiology and Biotechnology, 25(2-3), 120-8. DOI: 10.1159/000377724
Manzoor, I., Shafeeq, S., Afzal, M., & Kuipers, O. P. (2015). The Regulation of the AdcR Regulon in Streptococcus pneumoniae Depends Both on Zn(2+)- and Ni(2+)-Availability. Frontiers in Cellular and Infection Microbiology, 5, 1-11. [91]. DOI: 10.3389/fcimb.2015.00091
Krawczyk, A. O., de Jong, A., Eijlander, R. T., Berendsen, E. M., Holsappel, S., Wells-Bennik, M. H. J., & Kuipers, O. P. (2015). Next-Generation Whole-Genome Sequencing of Eight Strains of Bacillus cereus, Isolated from Food. Genome Announcements, 3(6), 1-2. [e01480-15]. DOI: 10.1128/genomeA.01480-15

2014

Daszczuk, A., Dessalegne, Y., Drenth, I., Hendriks, E., Jo, E., van Lente, T., ... Veening, J-W. (2014). Bacillus subtilis Biosensor Engineered To Assess Meat Spoilage. ACS Synthetic Biology, 3(12), 999-1002. DOI: 10.1021/sb5000252
Moll, G., Leenhouts, C. J., Kuipers, O., & Driessen, A. (2014). IPC No. A61K38/14; C07K14/315; C07K9/00; C12N5/06; C12P21/02; C07K14/00. Export and modification of (poly)peptides in the lantibiotic way (Patent No. SI1507798 (T1).)
van Gestel, J., Weissing, F. J., Kuipers, O. P., & Kovacs, A. T. (2014). Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms. ISME Journal, 8(10), 2069-2079. DOI: 10.1038/ismej.2014.52
Bakker, D., Buckley, A. M., de Jong, A., van Winden, V. J. C., Verhoeks, J. P. A., Kuipers, O. P., ... Corver, J. (2014). The HtrA-Like Protease CD3284 Modulates Virulence of Clostridium difficile. Infection and Immunity, 82(10), 4222-4232. DOI: 10.1128/IAI.02336-14
Yuzenkova, Y., Gamba, P., Herber, M., Attaiech, L., Shafeeq, S., Kuipers, O. P., ... Veening, J-W. (2014). Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae. Nucleic Acids Research, 42(17), 10987-10999. DOI: 10.1093/nar/gku790
Afzal, M., Shafeeq, S., & Kuipers, O. P. (2014). LacR Is a Repressor of lacABCD and LacT Is an Activator of lacTFEG, Constituting the lac Gene Cluster in Streptococcus pneumoniae. Applied and environmental microbiology, 80(17), 5349-5358. DOI: 10.1128/AEM.01370-14
Mehne, F. M. P., Schroeder-Tittmann, K., Eijlander, R. T., Herzberg, C., Hewitt, L., Kaever, V., ... Stuelke, J. (2014). Control of the Diadenylate Cyclase CdaS in Bacillus subtilis AN AUTOINHIBITORY DOMAIN LIMITS CYCLIC DI-AMP PRODUCTION. The Journal of Biological Chemistry, 289(30), 21098-21107. DOI: 10.1074/jbc.M114.562066
Smith, C. M., Sandrini, S., Datta, S., Freestone, P., Shafeeq, S., Radhakrishnan, P., ... O'Callaghan, C. (2014). Respiratory Syncytial Virus Increases the Virulence of Streptococcus pneumoniae by Binding to Penicillin Binding Protein 1a A New Paradigm in Respiratory Infection. American Journal of Respiratory and Critical Care Medicine, 190(2), 196-207. DOI: 10.1164/rccm.201311-2110OC
Solopova, A., van Gestel, J., Weissing, F. J., Bachmann, H., Teusink, B., Kok, J., & Kuipers, O. P. (2014). Bet-hedging during bacterial diauxic shift. Proceedings of the National Academy of Science of the United States of America, 111(20), 7427-7432. DOI: 10.1073/pnas.1320063111
Puentes-Téllez, P. E., Kovacs, A., Kuipers, O. P., & van Elsas, J. D. (2014). Comparative genomics and transcriptomics analysis of experimentally evolved Escherichia coli MC1000 in complex environments. Environmental Microbiology, 16(3), 856-870. DOI: 10.1111/1462-2920.12239
Puri, P., Eckhardt, T. H., Franken, L. E., Fusetti, F., Stuart, M. C. A., Boekema, E. J., ... Poolman, B. (2014). Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization. Molecular Microbiology, 91(2), 394-407. DOI: 10.1111/mmi.12468
Siebring, J., Elema, M. J. H., Vega, F. D., Kovacs, A. T., Haccou, P., & Kuipers, O. P. (2014). Repeated triggering of sporulation in Bacillus subtilis selects against a protein that affects the timing of cell division. ISME Journal, 8(1), 77-87. DOI: 10.1038/ismej.2013.128
Diethmaier, C., Newman, J. A., Kovács, Á. T., Kaever, V., Herzberg, C., Rodrigues, C., ... Stülke, J. (2014). The YmdB Phosphodiesterase Is a Global Regulator of Late Adaptive Responses in Bacillus subtilis. Journal of Bacteriology, 196(2), 265-275. DOI: 10.1128/JB.00826-13
Claessen, D., Rozen, D. E., Kuipers, O. P., Søgaard-Andersen, L., & Wezel, G. P. V. (2014). Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies. Nature Reviews Microbiology, 12(2), 115-124. DOI: 10.1038/nrmicro3178
Eijlander, R. T., Jong, A. D., Krawczyk, A. O., Holsappel, S., & Kuipers, O. P. (2014). SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. Nucleic Acids Research, 42(D1), D685-D691. DOI: 10.1093/nar/gkt1007
İrigül-Sönmez, Ö., Köroğlu, T. E., Öztürk, B., Kovács, Á. T., Kuipers, O. P., Yazgan-Karataş, A., & Zuber, P. (Ed.) (2014). In Bacillus subtilis LutR is part of the global complex regulatory network governing the adaptation to the transition from exponential growth to stationary phase. Microbiology, 160(2), 243-260. DOI: 10.1099/mic.0.064675-0
Kovacs, A., & Kuipers, O. (2014). Transcriptional circuits and phenotypic variation. In M. M. Babu (Ed.), Bacterial Gene Regulation and Transcriptional Networks (1 ed., pp. 97-103). [chapter 6] Norfolk: Caister Academic Press.

2002

Leenhouts, C., Ramasamy, R., Steen, A., Kok, J., Buist, G., & Kuipers, O. (2002). IPC No. A61K 38/ 00 A N. Improved methods for binding acma-type protein anchor fusions yo cell-wall material of micro-organisms (Patent No. WO02101026.)
Hamoen, L. W., Smits, W. K., de Jong, A., Holsappel, S., Kuipers, O. P., & Smits, W. K. (2002). Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Research, 30(24), 5517-5528. DOI: 10.1093/nar/gkf698
Darmon, E., Noone, D., Masson, A., Bron, S., Kuipers, O. P., Devine, K. M., & Dijl, J. M. V. (2002). A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. Journal of Bacteriology, 184(20), 5661-5671. DOI: 10.1128/JB.184.20.5661-5671.2002
Kuipers, O. P., Jong, A. D., Baerends, R. J. S., Hijum, S. A. F. T. V., Zomer, A. L., Karsens, H. A., ... Kok, J. (2002). Transcriptome analysis and related databases of Lactococcus lactis. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 82(1-4), 113-122. DOI: 10.1023/A:1020691801251
Klaenhammer, T., Altermann, E., Arigoni, F., Bolotin, A., Breidt, F., Broadbent, J., ... Siezen, R. (2002). Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 82(1-4), 29-58. DOI: 10.1023/A:1020638309912.
Fernández, M., Kleerebezem, M., Kuipers, O. P., Siezen, R. J., & Kranenburg, R. V. (2002). Regulation of the metC-cysK Operon, Involved in Sulfur Metabolism in Lactococcus lactis. Journal of Bacteriology, 184(1), 82-90. DOI: 10.1128/JB.184.1.82-90.2002

2013

Overkamp, W., Beilharz, K., Weme, R. D. O., Solopova, A., Karsens, H., Kovacs, A. T., ... Veening, J-W. (2013). Benchmarking Various Green Fluorescent Protein Variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for Live Cell Imaging. Applied and Environmental Microbiology, 79(20), 6481-6490. DOI: 10.1128/AEM.02033-13
Khusainov, R., & Kuipers, O. P. (2013). The Presence of Modifiable Residues in the Core Peptide Part of Precursor Nisin Is Not Crucial for Precursor Nisin Interactions with NisB- and NisC. PLoS ONE, 8(9), [e74890]. DOI: 10.1371/journal.pone.0074890
Eijlander, R. T., & Kuipers, O. P. (2013). Live-Cell Imaging Tool Optimization To Study Gene Expression Levels and Dynamics in Single Cells of Bacillus cereus. Applied and Environmental Microbiology, 79(18), 5643-5651. DOI: 10.1128/AEM.01347-13
Abts, A., Montalban-Lopez, M., Kuipers, O. P., Smits, S. H., & Schmitt, L. (2013). NisC Binds the FxLx Motif of the Nisin Leader Peptide. Biochemistry, 52(32), 5387-5395. DOI: 10.1021/bi4008116
Visweswaran, G. R. R., Steen, A., Leenhouts, K., Szeliga, M., Ruban, B., Hesseling-Meinders, A., ... Buist, G. (2013). AcmD, a homolog of the major autolysin AcmA of Lactococcus lactis, binds to the cell wall and contributes to cell separation and autolysis. PLoS ONE, 8(8), [e72167]. DOI: 10.1371/journal.pone.0072167
Carvalho, S. M., Farshchi Andisi, V., Gradstedt, H., Neef, J., Kuipers, O. P., Neves, A. R., & Bijlsma, J. J. E. (2013). Pyruvate Oxidase Influences the Sugar Utilization Pattern and Capsule Production in Streptococcus pneumoniae. PLoS ONE, 8(7), [e68277]. DOI: 10.1371/journal.pone.0068277
Carvalho, A. L., Turner, D. L., Fonseca, L. L., Solopova, A., Catarino, T., Kuipers, O. P., ... Santos, H. (2013). Metabolic and Transcriptional Analysis of Acid Stress in Lactococcus lactis, with a Focus on the Kinetics of Lactic Acid Pools. Plos one, 8(7), [e68470]. DOI: 10.1371/journal.pone.0068470
van Heel, A. J., Mu, D., Montalban-Lopez, M., Hendriks, D., & Kuipers, O. P. (2013). Designing and Producing Modified, New-to-Nature Peptides with Antimicrobial Activity by Use of a Combination of Various Lantibiotic Modification Enzymes. ACS Synthetic Biology, 2(7), 397-404. DOI: 10.1021/sb3001084
van Heel, A. J., de Jong, A., Montalban-Lopez, M., Kok, J., & Kuipers, O. P. (2013). BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Research, 41(W1), W448-W453. DOI: 10.1093/nar/gkt391
Mu, D., Montalbán-López, M., Masuda, Y., & Kuipers, O. P. (2013). Zirex: a Novel Zinc-Regulated Expression System for Lactococcus lactis. Applied and Environmental Microbiology, 79(14), 4503-4508. DOI: 10.1128/AEM.00866-13
Shafeeq, S., Kuipers, O. P., & Kloosterman, T. G. (2013). The role of zinc in the interplay between pathogenic streptococci and their hosts. Molecular Microbiology, 88(6), 1047-1057. DOI: 10.1111/mmi.12256
Carvalho, S. M., Kuipers, O. P., & Neves, A. R. (2013). Environmental and Nutritional Factors That Affect Growth and Metabolism of the Pneumococcal Serotype 2 Strain D39 and Its Nonencapsulated Derivative Strain R6. PLoS ONE, 8(3), [e58492]. DOI: 10.1371/journal.pone.0058492
Eckhardt, T. H., Skotnicka, D., Kok, J., & Kuipers, O. P. (2013). Transcriptional Regulation of Fatty Acid Biosynthesis in Lactococcus lactis. Journal of Bacteriology, 195(5), 1081-1089. DOI: 10.1128/JB.02043-12
Shafeeq, S., Kuipers, O. P., Kloosterman, T. G., & Leite, L. C. C. (Ed.) (2013). Cellobiose-Mediated Gene Expression in Streptococcus pneumoniae: A Repressor Function of the Novel GntR-Type Regulator BguR. PLoS ONE, 8(2), [e57586]. DOI: 10.1371/journal.pone.0057586
Boonstra, M., de Jong, I. G., Scholefield, G., Murray, H., Kuipers, O. P., & Veening, J-W. (2013). Spo0A regulates chromosome copy number during sporulation by directly binding to the origin of replication in Bacillus subtilis. Molecular Microbiology, 87(4), 925-938. DOI: 10.1111/mmi.12141
Lehnik-Habrink, M., Rempeters, L., Kovacs, A. T., Wrede, C., Baierlein, C., Krebber, H., ... Stülke, J. (2013). DEAD-Box RNA Helicases in Bacillus subtilis Have Multiple Functions and Act Independently from Each Other. Journal of Bacteriology, 195(3), 534-544. DOI: 10.1128/JB.01475-12
de Jong, A., Hansen, M. E., Kuipers, O. P., Kilstrup, M., & Kok, J. (2013). The Transcriptional and Gene Regulatory Network of Lactococcus lactis MG1363 during Growth in Milk. PLoS ONE, 8(1), [e53085]. DOI: 10.1371/journal.pone.0053085
Kovacs, A., Eckhardt, T., van Kranenburg, R., & Kuipers, O. (2013). Functional Analysis of the ComK Protein of Bacillus coagulans. PLoS ONE, 8(1), [ e53471]. DOI: 10.1371/journal.pone.0053471
Khusainov, R., Moll, G. N., & Kuipers, O. P. (2013). Identification of distinct nisin leader peptide regions that determine interactions with the modification enzymes NisB and NisC. FEBS Open Bio, 3, 237-242. DOI: 10.1016/j.fob.2013.05.001
Arnison, P. G., Bibb, M. J., Bierbaum, G., Bowers, A. A., Bugni, T. S., Bulaj, G., ... Süssmuth, R. D. (2013). Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Natural product reports, 30(1), 108-160. DOI: 10.1039/c2np20085f

2012

de Jong, I. G., Veening, J-W., & Kuipers, O. P. (2012). Single cell analysis of gene expression patterns during carbon starvation in Bacillus subtilis reveals large phenotypic variation. Environmental Microbiology, 14(12), 3110-3121. DOI: 10.1111/j.1462-2920.2012.02892.x
Shafeeq, S., Kloosterman, T. G., Rajendran, V., Kuipers, O. P., & Kilian, M. (Ed.) (2012). Characterization of the ROK-family transcriptional regulator RokA of Streptococcus pneumoniae D39. Microbiology-Sgm, 158(12), 2917-2926. DOI: 10.1099/mic.0.062919-0
Fibriansah, G., Kovacs, A. T., Pool, T. J., Boonstra, M., Kuipers, O. P., & Thunnissen, A-M. W. H. (2012). Crystal Structures of Two Transcriptional Regulators from Bacillus cereus Define the Conserved Structural Features of a PadR Subfamily. PLoS ONE, 7(11), [e48015]. DOI: 10.1371/journal.pone.0048015
Khusainov, R., & Kuipers, O. P. (2012). When the Leader Gets Loose: In Vivo Biosynthesis of a Leaderless Prenisin Is Stimulated by a trans-Acting Leader Peptide. ChemBioChem, 13(16), 2433-2438. DOI: 10.1002/cbic.201200437
Roces, C., Pérez, V., Campelo, A. B., Blanco, D., Kok, J., Kuipers, O. P., ... Martínez, B. (2012). The putative lactococcal extracytoplasmic function anti-sigma factor llmg2447 determines resistance to the cell wall-active bacteriocin lcn972. Antimicrobial Agents and Chemotherapy, 56(11), 5520-5527. DOI: 10.1128/AAC.01206-12
Price, C. E., Zeyniyev, A., Kuipers, O. P., & Kok, J. (2012). From meadows to milk to mucosa - adaptation of Streptococcus and Lactococcus species to their nutritional environments. FEMS Microbiology Reviews, 36(5), 949-971. DOI: 10.1111/j.1574-6976.2011.00323.x
Diez, L., Solopova, A., Kuipers, O. P., & Ruiz-Larrea, F. (2012). Transcriptome analysis shows activation of the arginine deiminase pathway in lactococcus lactis as a short-term adaptation to ethanol stress. Febs Journal, 279, 333-333.
Marciniak, B. C., Pabijaniak, M., de Jong, A., Dűhring, R., Seidel, G., Hillen, W., & Kuipers, O. P. (2012). High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis. BMC Genomics, 13(1), [401]. DOI: 10.1186/1471-2164-13-401
Montalban-Lopez, M., Zhou, L., Buivydas, A., van Heel, A. J., & Kuipers, O. P. (2012). Increasing the success rate of lantibiotic drug discovery by Synthetic Biology. Expert Opinion on Drug Discovery, 7(8), 695-709. DOI: 10.1517/17460441.2012.693476
Lindback, T., Mols, M., Basset, C., Granum, P. E., Kuipers, O. P., Kovacs, A. T., & Lindbäck, T. (2012). CodY, a pleiotropic regulator, influences multicellular behaviour and efficient production of virulence factors in Bacillus cereus. Environmental Microbiology, 14(8), 2233-2246. DOI: 10.1111/j.1462-2920.2012.02766.x
Solopova, A., Bachmann, H., Teusink, B., Kok, J., Neves, A. R., & Kuipers, O. P. (2012). A Specific Mutation in the Promoter Region of the Silent cel Cluster Accounts for the Appearance of Lactose-Utilizing Lactococcus lactis MG1363. Applied and Environmental Microbiology, 78(16), 5612-5621. DOI: 10.1128/AEM.00455-12
de Jong, A., Pietersma, H., Cordes, M., Kuipers, O. P., & Kok, J. (2012). PePPER: a webserver for prediction of prokaryote promoter elements and regulons. BMC Genomics, 13(1), [299]. DOI: 10.1186/1471-2164-13-299
Kovacs, A. T., van Gestel, J., & Kuipers, O. P. (2012). The protective layer of biofilm: A repellent function for a new class of amphiphilic proteins. Molecular Microbiology, 85(1), 8-11. DOI: 10.1111/j.1365-2958.2012.08101.x
Marciniak, B. C., Trip, H., Fusetti, F., Kuipers, O. P., & Marciniak, B. C. (2012). Regulation of ykrL (htpX) by Rok and YkrK, a Novel Type of Regulator in Bacillus subtilis. Journal of Bacteriology, 194(11), 2837-2845. DOI: 10.1128/JB.00324-12
Marciniak, B. C., Trip, H., van-der Veek, P. J., Kuipers, O. P., & Marciniak, B. C. (2012). Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins. Microbial Cell Factories, 11(1), 1-13. [66]. DOI: 10.1186/1475-2859-11-66
Farshchi Andisi, V., Hinojosa, C. A., de Jong, A., Kuipers, O. P., Orihuela, C. J., & Bijlsma, J. J. E. (2012). Pneumococcal Gene Complex Involved in Resistance to Extracellular Oxidative Stress. Infection and Immunity, 80(3), 1037-1049. DOI: 10.1128/IAI.05563-11
Puri, P., Eckhardt, T., Franken, L., Fusetti, F., Stuart, M., Boekema, E., ... Poolman, B. (2012). YfiA is necessary and sufficient for dimerization and inactivation of ribosomes in Lactococcus lactis. Molecular Biology of the Cell, 23, 1695.
Siebring, J., Sorg, R., Herber, M., & Kuipers, O. (2012). Take it of leave it: Mechanisms underlying bacterial bistable regulatory networks. In A. A. M. Filloux (Ed.), Bacterial Regulatory Networks (1 ed., pp. 305-332). [chapter 12] Caister Academic Press.
Villatoro-Hernández, J., Kuipers, O. P., Saucedo-Cárdenas, O., & Montes-de-Oca-Luna, R. (2012). Heterologous Protein Expression by Lactococcus lactis. Methods in Molecular Biology, 824, 155-165.

2011

Kloosterman, T. G., & Kuipers, O. P. (2011). Regulation of Arginine Acquisition and Virulence Gene Expression in the Human Pathogen Streptococcus pneumoniae by Transcription Regulators ArgR1 and AhrC. The Journal of Biological Chemistry, 286(52), 44594-44605. DOI: 10.1074/jbc.M111.295832
Blom, E-J., Ridder, A. N. J. A., Lulko, A. T., Roerdink, J. B. T. M., & Kuipers, O. P. (2011). Time-Resolved Transcriptomics and Bioinformatic Analyses Reveal Intrinsic Stress Responses during Batch Culture of Bacillus subtilis. PLoS ONE, 6(11), [27160]. DOI: 10.1371/journal.pone.0027160
Campelo, A. B., Gaspar, P., Roces, C., Rodriguez, A., Kok, J., Kuipers, O. P., ... Martinez, B. (2011). The Lcn972 Bacteriocin-Encoding Plasmid pBL1 Impairs Cellobiose Metabolism in Lactococcus lactis. Applied and Environmental Microbiology, 77(21), 7576-7585. DOI: 10.1128/AEM.06107-11
Khusainov, R., Heils, R., Lubelski, J., Moll, G. N., & Kuipers, O. P. (2011). Determining sites of interaction between prenisin and its modification enzymes NisB and NisC. Molecular Microbiology, 82(3), 706-718. DOI: 10.1111/j.1365-2958.2011.07846.x
Carvalho, S. M., Kloosterman, T. G., Kuipers, O. P., & Neves, A. R. (2011). CcpA Ensures Optimal Metabolic Fitness of Streptococcus pneumoniae. PLoS ONE, 6(10), [26707]. DOI: 10.1371/journal.pone.0026707
Shafeeq, S., Kloosterman, T. G., Kuipers, O. P., & Mitchell, T. J. (Ed.) (2011). CeIR-mediated activation of the cellobiose-utilization gene cluster in Streptococcus pneumoniae. Microbiology-Sgm, 157(10), 2854-2861. DOI: 10.1099/mic.0.051359-0
Mellegard, H., Kovacs, A. T., Lindback, T., Christensen, B. E., Kuipers, O. P., & Granum, P. E. (2011). Transcriptional Responses of Bacillus cereus towards Challenges with the Polysaccharide Chitosan: Direct Dating, Culture and Behavior. PLoS ONE, 6(9), [24304]. DOI: 10.1371/journal.pone.0024304
Trip, H., van der Veek, P. J., Renniers, T. C., Meima, R., Sagt, C. M., Mohrmann, L., & Kuipers, O. P. (2011). A novel screening system for secretion of heterologous proteins in Bacillus subtilis. Microbial Biotechnology, 4(5), 673-682. DOI: 10.1111/j.1751-7915.2011.00270.x
Shafeeq, S., Yesilkaya, H., Kloosterman, T. G., Narayanan, G., Wandel, M., Andrew, P. W., ... Morrissey, J. A. (2011). The cop operon is required for copper homeostasis and contributes to virulence in Streptococcus pneumoniae. Molecular Microbiology, 81(5), 1255-1270. DOI: 10.1111/j.1365-2958.2011.07758.x
Pinto, J. P. C., Zeyniyev, A., Karsens, H., Trip, H., Lolkema, J. S., Kuipers, O. P., & Kok, J. (2011). pSEUDO, a Genetic Integration Standard for Lactococcus lactis. Applied and Environmental Microbiology, 77(18), 6687-6690. DOI: 10.1128/AEM.05196-11
Marreddy, R. K. R., Coelho Pinto, J., Wolters, J. C., Geertsma, E. R., Fusetti, F., Permentier, H. P., ... Poolman, B. (2011). The response of Lactococcus lactis to membrane protein production. PLoS ONE, 6(8), [24060]. DOI: 10.1371/journal.pone.0024060
Hermans, P. W. M., Bootsma, J. H., Burghout, P. J., Kuipers, O., Bijlsma, J. J. E., Kloosterman, T. G., & Andersen, C. O. (2011). IPC No. A61K39/09; A61P31/04; C07K16/12. NEW VIRULENCE FACTORS OF STREPTOCOCCUS PNEUMONIAE (Patent No. MX2011003754 (A).)
Pinto, J. P. C., Kuipers, O. P., Marreddy, R. K. R., Poolman, B., & Kok, J. (2011). Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR. PLoS ONE, 6(7), [21873]. DOI: 10.1371/journal.pone.0021873
Mironczuk, A., Maňu, A., Kuipers, O. P., & Kovacs, A. (2011). Distinct Roles of ComK1 and ComK2 in Gene Regulation in Bacillus cereus. PLoS ONE, 6(7), [e21859]. DOI: 10.1371/journal.pone.0021859
Bertram, R., Rigali, S., Wood, N., Lulko, A. T., Kuipers, O. P., & Titgemeyer, F. (2011). Regulon of the N-Acetylglucosamine Utilization Regulator NagR in Bacillus subtilis. Journal of Bacteriology, 193(14), 3525-3536. DOI: 10.1128/JB.00264-11
Neef, J., Farshchi Andisi, V., Kim, K. S., Kuipers, O. P., Bijlsma, J. J. E., & Weiser, J. N. (Ed.) (2011). Deletion of a Cation Transporter Promotes Lysis in Streptococcus pneumoniae. Infection and Immunity, 79(6), 2314-2323. DOI: 10.1128/IAI.00677-10
van Heel, A. J., Montalban-Lopez, M., & Kuipers, O. P. (2011). Evaluating the feasibility of lantibiotics as an alternative therapy against bacterial infections in humans. Expert Opinion on Drug Metabolism & Toxicology, 7(6), 675-680. DOI: 10.1517/17425255.2011.573478
Abee, T., & Kuipers, O. P. (2011). Understanding microbial behavior within and outside the host to improve food functionality and safety. Current Opinion in Biotechnology, 22(2), 133-135. DOI: 10.1016/j.copbio.2011.02.001
Abee, T., Kovacs, A. T., Kuipers, O. P., & van der Veen, S. (2011). Biofilm formation and dispersal in Gram-positive bacteria. Current Opinion in Biotechnology, 22(2), 172-179. DOI: 10.1016/j.copbio.2010.10.016
Eijlander, R. T., Abee, T., & Kuipers, O. P. (2011). Bacterial spores in food: how phenotypic variability complicates prediction of spore properties and bacterial behavior. Current Opinion in Biotechnology, 22(2), 180-186. DOI: 10.1016/j.copbio.2010.11.009
Villatoro-Hernandez, J., Montes-de-Oca-Luna, R., & Kuipers, O. P. (2011). Targeting diseases with genetically engineered Lactococcus lactis and its course towards medical translation. Expert Opinion on Biological Therapy, 11(3), 261-267. DOI: 10.1517/14712598.2011.542138
de Jong, I. G., Haccou, P., & Kuipers, O. P. (2011). Bet hedging or not? A guide to proper classification of microbial survival strategies. BioEssays, 33(3), 215-223. DOI: 10.1002/bies.201000127
Kovacs, A. T., & Kuipers, O. P. (2011). Rok Regulates yuaB Expression during Architecturally Complex Colony Development of Bacillus subtilis 168. Journal of Bacteriology, 193(4), 998-1002. DOI: 10.1128/JB.01170-10
Jong, I. G. D., Beilharz, K., Kuipers, O. P., & Veening, J-W. (2011). Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy. Journal of Visualized Experiments, 6(53), 1-6. DOI: 10.3791/3145
Shafeeq, S., Kloosterman, T. G., & Kuipers, O. P. (2011). Transcriptional response of Streptococcus pneumoniae to Zn2+ limitation and the repressor/activator function of AdcR. Metallomics, 3(6), 609-618. DOI: 10.1039/c1mt00030f
de Jong, A., van Heel, A., & Kuipers, O. (2011). Genome exploitation and bioinformatic tools. In D. Drider, & S. Rebuffat (Eds.), Prokaryotic Antimicrobial Peptides: From Genes to Applications (pp. 75-80). Springer. DOI: 10.1007/97814419769251
Coelho Pinto, J., Kuipers, O., & Kok, J. (2011). Responses of lactic acid bacteria to cell envelop stresses. In E. Tsakalidou, & K. Papadimitriou (Eds.), Stress Responses of Lactic Acid Bacteria: Food Microbiology and Food Safety (pp. 141-161). (Food Microbiology and Safety). New York, Dordrecht, Heidelberg, London: Springer. DOI: 10.1007/97803879277188
Kuipers, O. (2011). Bacteriele bendes: samen sterk door Quorum sensing. In H. Smit, & P. Willemsen (Eds.), De Microcanon [Hoofdstuk 19] VBK Media.
de Jong, A., Kok, J., & Kuipers, O. (2011). Data resources and mining tools for reconstructing gene networks in Lactococcus lactis. Japanese Journal of Lactic Acid Bacteria, 22(1), 3-14.

2008

Blom, E-J., Hijum, S. A. F. T. V., Hofstede, K. J., Silvis, R., Roerdink, J. B. T. M., & Kuipers, O. P. (2008). DISCLOSE: DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. Bmc Bioinformatics, 9(1), [535]. DOI: 10.1186/1471-2105-9-535
Zaidi, A. H., Bakkes, P. J., Lubelski, J., Agustiandari, H., Kuipers, O. P., & Driessen, A. J. M. (2008). The ABC-Type Multidrug Resistance Transporter LmrCD Is Responsible for an Extrusion-Based Mechanism of Bile Acid Resistance in Lactococcus lactis. Journal of Bacteriology, 190(22), 7357-7366. DOI: 10.1128/JB.00485-08
Blom, E. J., Breitling, R., Hofstede, K. J., Roerdink, J. B. T. M., van Hijum, S. A. F. T., & Kuipers, O. P. (2008). Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics, 21(9), [495]. DOI: 10.1186/1471-2164-9-495
Brouwer, R. W. W., Kuipers, O. P., & van Hijum, S. A. F. T. (2008). The relative value of operon predictions. Briefings in Bioinformatics, 9(5), 367-375. DOI: 10.1093/bib/bbn019
Steen, A., Buist, G., Kramer, N. E., Jalving, R., Benus, G. F. J. D., Venema, G., ... Kok, J. (2008). Reduced lysis upon growth of Lactococcus lactis on galactose is a consequence of decreased binding of the autolysin AcmA. Applied Environmental Microbiology, 74(15), 4671-4679. DOI: 10.1128/AEM.00103-08
Kloosterman, T. G., Witwicki, R. M., van der Kooi-Pol, M. M., Bijlsma, J. J. E., & Kuipers, O. P. (2008). Opposite effects of Mn2+ and Zn2+ on PsaR-Mediated expression of the virulence genes pcpA, prtA, and psaBCA of Streptococcus pneumoniae. Journal of Bacteriology, 190(15), 5382-5393. DOI: 10.1128/JB.00307-08
Kuipers, O. P., Poolman, B., & Hugenholtz, J. (2008). 9th International Symposium on lactic acid bacteria. Applied and Environmental Microbiology, 74(15), 4589-4589. DOI: 10.1128/AEM.01384-08
Larsen, R., van Hijum, S. A. F. T., Martinussen, J., Kuipers, O. P., & Kok, J. (2008). Transcriptome analysis of the Lactococcus lactis ArgR and AhrC Regulons. Applied and Environmental Microbiology, 74(15), 4768-4771. DOI: 10.1128/AEM.00117-08
Lubelski, J., Overkamp, W., Kluskens, L. D., Moll, G. N., & Kuipers, O. P. (2008). Influence of shifting positions of Ser, Thr, and Cys residues in prenisin on the efficiency of modification reactions and on the antimicrobial activities of the modified prepeptides. Applied and Environmental Microbiology, 74(15), 4680-4685. DOI: 10.1128/AEM.00112-08
Stevens, M. J. A., Wiersma, A., de Vos, W. M., Kuipers, O. P., Smid, E. J., Molenaar, D., ... Vos, W. M. D. (2008). Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis. Applied and Environmental Microbiology, 74(15), 4776-4778. DOI: 10.1128/AEM.00136-08
Kuipers, O. P., Poolman, B., & Hugenholtz, J. (2008). 9th International Symposium on Lactic Acid Bacteria. Applied and Environmental Microbiology, 74(15), 4589.
Kramer, N. E., Hasper, H. E., van den Bogaard, P. T. C., Morath, S., de Kruijff, B., Hartung, T., ... Kuipers, O. P. (2008). Increased D-alanylation of lipoteichoic acid and a thickened septum are main determinants in the nisin resistance mechanism of Lactococcus lactis. Microbiology-Sgm, 154(6), 1755-1762. DOI: 10.1099/mic.0.2007/015412-0
Mironczuk, A. M., Kovács, Á. T., & Kuipers, O. P. (2008). Induction of natural competence in Bacillus cereus ATCC14579. Microbial Biotechnology, 1(3), 226-235. DOI: 10.1111/j.1751-7915.2008.00023.x
Buist, G., Steen, A., Kok, J., & Kuipers, O. P. (2008). LysM, a widely distributed protein motif for binding to (peptido)glycans. Molecular Microbiology, 68(4), 838-847. DOI: 10.1111/j.1365-2958.2008.06211.x
Westenberg, M. A., Hijum, S. A. F. T. V., Kuipers, O. P., & Roerdink, J. B. T. M. (2008). Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context. COMPUTER GRAPHICS FORUM, 27(3), 887-894. DOI: 10.1111/j.1467-8659.2008.01221.x
van der Voort, M., Kuipers, O. P., Buist, G., de Vos, W. M., & Abee, T. (2008). Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereus ATCC 14579. BMC Microbiology, 8(1), [62]. DOI: 10.1186/1471-2180-8-62
Veening, J-W., Igoshin, O. A., Eijlander, R. T., Nijland, R., Hamoen, L. W., & Kuipers, O. P. (2008). Transient heterogeneity in extracellular protease production by Bacillus subtilis. Molecular Systems Biology, 4(6), 184 - 184. [184]. DOI: 10.1038/msb.2008.18
Veening, J-W., Stewart, E. J., Berngruber, T. W., Taddei, F., Kuipers, O. P., & Hamoen, L. W. (2008). Bet-hedging and epigenetic inheritance in bacterial cell development. Proceedings of the National Academy of Sciences of the United States of America, 105(11), 4393-4398. DOI: 10.1073/pnas.0700463105
Hendriksen, W. T., Kloosterman, T. G., Bootsma, H. J., Estevao, S., de Groot, R., Kuipers, O. P., & Hermans, P. W. M. (2008). Site-specific contributions of glutamine-dependent regulator GlnR and GlnR-regulated genes to virulence of Streptococcus pneumoniae. Infection and Immunity, 76(3), 1230-1238. DOI: 10.1128/IAI.01004-07
van Hijum, S. A. F. T., Baerends, R. J. S., Zomer, A. L., Karsens, H. A., Martin-Requena, V., Trelles, O., ... Kuipers, O. P. (2008). Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. Bmc Bioinformatics, 9(93), [93]. DOI: 10.1186/1471-2105-9-93
Barnett, J. P., Eijlander, R. T., Kuipers, O. P., & Robinson, C. (2008). A minimal tat system from a gram-positive organism - A bifunctional TatA subunit participates in discrete TatAC and TatA complexes. The Journal of Biological Chemistry, 283(5), 2534-2542. DOI: 10.1074/jbc.M708134200
Lubelski, J., Rink, R., Khusainov, R., Moll, G. N., & Kuipers, O. P. (2008). Biosynthesis, immunity, regulation, mode of action and engineering of the model lantibiotic nisin. Cellular and Molecular Life Sciences, 65(3), 455-476. DOI: 10.1007/s00018-007-7171-2
Widdick, D. A., Eijlander, R. T., van Dijl, J. M., Kuipers, O. P., & Palmer, T. (2008). A facile reporter system for the experimental identification of twin-arginine translocation (Tat) signal peptides from all kingdoms of life. Journal of Molecular Biology, 375(3), 595-603. DOI: 10.1016/j.jmb.2007.11.002
Mendel, S., McCarthy, A., Barnett, J. P., Eijlander, R. T., Nenninger, A., Kuipers, O. P., & Robinson, C. (2008). The Escherichia coli TatABC system and a Bacillus subtilis TatAC-type system recognise three distinct targeting determinants in twin-arginine signal peptides. Journal of Molecular Biology, 375(3), 661-672. DOI: 10.1016/j.jmb.2007.09.087
Agustiandari, H., Lubelski, J., van Saparoea, H. B. V. D. B., Kuipers, O. P., & Driessen, A. J. M. (2008). LmrR is a transcriptional repressor of expression of the multidrug ABC transporter lmrCD in Lactococcus lactis. Journal of Bacteriology, 190(2), 759-763. DOI: 10.1128/JB.01151-07
Hendriksen, W. T., Bootsma, H. J., Estevao, S., Hoogenboezem, T., de Jong, A., de Groot, R., ... Hermans, P. W. M. (2008). CodY of Streptococcus pneumoniae: Link between nutritional gene regulation and colonization. Journal of Bacteriology, 190(2), 590-601. DOI: 10.1128/JB.00917-07
Nijland, R., & Kuipers, O. P. (2008). Optimization of protein secretion by Bacillus subtilis. Recent patents on biotechnology, 2, 79 - 87. DOI: 10.2174/187220808784619694
Westenberg, M. A., Hijum, S. A. F. T. V., Lulko, A. T., Kuipers, O. P., & Roerdink, J. B. T. M. (2008). Interactive visualization of gene regulatory networks with associated gene expression time series data. In L. Linsen, H. Hagen, & B. Hamann (Eds.), VISUALIZATION IN MEDICINE AND LIFE SCIENCES (pp. 293-+). (MATHEMATICS AND VISUALIZATION). BERLIN: Springer.
Smits, W. K., Veening, J-W., & Kuipers, O. P. (2008). Phenotypic Variation and Bistable Switching in Bacteria. In W. El-Sharoud (Ed.), Bacterial Physiology: a Molecular Approach (pp. 339-365). Berlin: Springer Verlag.
Veening, J-W., Smits, W. K., & Kuipers, O. P. (2008). Bistability, Epigenetics, and Bet-Hedging in Bacteria. Annual Review of Microbiology, 62(1), 193-210. DOI: 10.1146/annurev.micro.62.081307.163002

2010

Neves, A. R., Pool, W., Solopova, A., Kok, J., Santos, H., & Kuipers, O. P. (2010). Towards Enhanced Galactose Utilization by Lactococcus lactis. Applied and Environmental Microbiology, 76(21), 7048 - 7060. DOI: 10.1128/AEM.01195-10
Westenberg, M. A., Roerdink, J. B. T. M., Kuipers, O. P., & van Hijum, S. A. F. T. (2010). SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks. Bioinformatics, 26(22), 2922-2923. DOI: 10.1093/bioinformatics/btq535
Liebal, U. W., Millat, T., de Jong, I. G., Kuipers, O. P., Volker, U., Wolkenhauer, O., & Völker, U. (2010). How mathematical modelling elucidates signalling in Bacillus subtilis. Molecular Microbiology, 77(5), 1083-1095. DOI: 10.1111/j.1365-2958.2010.07283.x
Hyyrylainen, H-L., Marciniak, B. C., Dahncke, K., Pietiainen, M., Courtin, P., Vitikainen, M., ... Pietiäinen, M. (2010). Penicillin-binding protein folding is dependent on the PrsA peptidyl-prolyl cis-trans isomerase in Bacillus subtilis. Molecular Microbiology, 77(1), 108-127. DOI: 10.1111/j.1365-2958.2010.07188.x
de Jong, A., van Heel, A. J., Kok, J., & Kuipers, O. P. (2010). BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Research, 38, W647-W651. DOI: 10.1093/nar/gkq365
Kovacs, A. T., van Hartskamp, M., Kuipers, O. P., & van Kranenburg, R. (2010). Genetic Tool Development for a New Host for Biotechnology, the Thermotolerant Bacterium Bacillus coagulans. Applied and Environmental Microbiology, 76(12), 4085-4088. DOI: 10.1128/AEM.03060-09
Price, C., Santos, F., Molenaar, D., Teusink, B., Poolman, B., & Kuipers, O. (2010). Characterization of cellular composition of evolved strains of Lactococcus lactis. Febs Journal, 277, 114-114.
Chillappagari, S., Seubert, A., Trip, H., Kuipers, O. P., Marahiel, M. A., & Miethke, M. (2010). Copper Stress Affects Iron Homeostasis by Destabilizing Iron-Sulfur Cluster Formation in Bacillus subtilis. Journal of Bacteriology, 192(10), 2512 - 2524. DOI: 10.1128/JB.00058-10
de Jong, I. G., Veening, J-W., & Kuipers, O. P. (2010). Heterochronic Phosphorelay Gene Expression as a Source of Heterogeneity in Bacillus subtilis Spore Formation. Journal of Bacteriology, 192(8), 2053 - 2067. DOI: 10.1128/JB.01484-09
Majchrzykiewicz, J. A., Lubelski, J., Moll, G. N., Kuipers, A., Bijlsma, J. J. E., Kuipers, O. P., & Rink, R. (2010). Production of a Class II Two-Component Lantibiotic of Streptococcus pneumoniae Using the Class I Nisin Synthetic Machinery and Leader Sequence. Antimicrobial Agents and Chemotherapy, 54(4), 1498-1505. DOI: 10.1128/AAC.00883-09
Veening, J-W., & Kuipers, O. P. (2010). Gene position within a long transcript as a determinant for stochastic switching in bacteria. Molecular Microbiology, 76(2), 269-272. DOI: 10.1111/j.1365-2958.2010.07113.x
van Zutphen, T., Baerends, R. J. S., Susanna, K., de Jong, A., Kuipers, O. P., Veenhuis, M., & van der Klei, I. J. (2010). Adaptation of Hansenula polymorpha to methanol: A transcriptome analysis. BMC Genomics, 11(1). DOI: 10.1186/1471-2164-11-1
Majchrzykiewicz, J. A., Kuipers, O. P., & Bijlsma, J. J. E. (2010). Generic and Specific Adaptive Responses of Streptococcus pneumoniae to Challenge with Three Distinct Antimicrobial Peptides, Bacitracin, LL-37, and Nisin. Antimicrobial Agents and Chemotherapy, 54(1), 440-451. DOI: 10.1128/AAC.00769-09

2009

Grande Burgos, M. J., Kovacs, A. T., Mironczuk, A. M., Abriouel, H., Galvez, A., Kuipers, O. P., & Mirończuk, A. M. (2009). Response of Bacillus cereus ATCC 14579 to challenges with sublethal concentrations of enterocin AS-48. BMC Microbiology, 9(1), [227]. DOI: 10.1186/1471-2180-9-227
Leenhouts, C., Ramasamy, R., Steen, A., KOK, J. A. A. M., Buist, G., & Kuipers, O. (2009). IPC No. C07K14/335; C07K19/00; C12N1/00; C12N15/31; C12N15/63; C12P21/00; A61K38/00. Immunization with bacterial ghost-based vaccines (Patent No. US2009239264 (A1).)
Lubelski, J., Khusainov, R., & Kuipers, O. P. (2009). Directionality and coordination of dehydration and ring formation during biosynthesis of the lantibiotic nisin. The Journal of Biological Chemistry, 284(38), 25962-25972. DOI: 10.1074/jbc.M109.026690
van Hijum, S. A. F. T., Medema, M. H., & Kuipers, O. P. (2009). Mechanisms and evolution of control logic in prokaryotic transcriptional regulation. Microbiology and Molecular Biology Reviews, 73(3), 481 - 509. DOI: 10.1128/MMBR.00037-08
Kovacs, A. T., Smits, W. K., Mironczuk, A. M., Kuipers, O. P., & Mirończuk, A. M. (2009). Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries. Environmental Microbiology, 11(8), 1911-1922. DOI: 10.1111/j.1462-2920.2009.01937.x
Ridder, A. N. J. A., de Jong, E. J., Jongbloed, J. D. H., & Kuipers, O. P. (2009). Subcellular Localization of TatAd of Bacillus subtilis Depends on the Presence of TatCd or TatCy. Journal of Bacteriology, 191(13), 4410-4418. DOI: 10.1128/JB.00215-09
Eijlander, R. T., Kolbusz, M. A., Berendsen, E. M., & Kuipers, O. P. (2009). Effects of altered TatC proteins on protein secretion efficiency via the twin-arginine translocation pathway of Bacillus subtilis. Microbiology-Sgm, 155(6), 1776-1785. DOI: 10.1099/mic.0.027987-0
Hendriksen, W. T., Bootsma, H. J., van Diepen, A., Estevao, S., Kuipers, O. P., de Groot, R., & Hermans, P. W. M. (2009). Strain-specific impact of PsaR of Streptococcus pneumoniae on global gene expression and virulence. Microbiology-Sgm, 155, 1569-1579. DOI: 10.1099/mic.0.025072-0
Chillappagari, S., Miethke, M., Trip, H., Kuipers, O. P., & Marahiel, M. A. (2009). Copper acquisition is mediated by YcnJ and regulated by YcnK and CsoR in Bacillus subtilis. Journal of Bacteriology, 191(7), 2362-2370. DOI: 10.1128/JB.01616-08
Blom, E-J., Roerdink, J. B. T. M., Kuipers, O. P., & Hijum, S. A. F. T. V. (2009). MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data. Bioinformatics, 25(4), 550-551. DOI: 10.1093/bioinformatics/btp013
Castro, R., Neves, A. R., Fonseca, L. L., Pool, W. A., Kok, J., Kuipers, O. P., & Santos, H. (2009). Characterization of the individual glucose uptake systems of Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU permease. Molecular Microbiology, 71(3), 795-806. DOI: 10.1111/j.1365-2958.2008.06564.x
Brouwer, R. W. W., van Hijum, S. A. F. T., & Kuipers, O. P. (2009). MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context. Bioinformatics, 25(1), 139-140. DOI: 10.1093/bioinformatics/btn588
Barnett, J. P., van der Ploeg, R., Eijlander, R. T., Nenninger, A., Mendel, S., Rozeboom, R., ... Robinson, C. (2009). The twin-arginine translocation (Tat) systems from Bacillus subtilis display a conserved mode of complex organization and similar substrate recognition requirements. Febs Journal, 276(1), 232-243. DOI: 10.1111/j.1742-4658.2008.06776.x
Eijlander, R. T., Jongbloed, J. D. H., & Kuipers, O. P. (2009). Relaxed specificity of the Bacillus subtilis TatAdCd translocase in Tat-dependent protein secretion. Journal of Bacteriology, 191(1), 196-202. DOI: 10.1128/JB.01264-08

2001

Kleerebezem, M., Kuipers, O. P., de Vos, W. M., Stiles, M. E., Quadri, L. E. N., Vos, W. M. D., ... Quadri, L. E. N. (2001). A two-component signal-transduction cascade in Carnobacterium piscicola LV17B: two signaling peptides and one sensor-transmitter. Peptides, 22(10), 1597-1601. DOI: 10.1016/S0196-9781(01)00494-6
Kuipers, O. P. (2001). Complete DNA sequence of Lactococcus lactis adds flavor to genomics. Genome Research, 11(5), 673-674. DOI: 10.1101/gr.188501
Wiedemann, . N. V., Breukink, E., van Kraaij, C., Kuipers, O. P., Bierbaum, G., de Kruijff, B., & Sahl, H. A. (2001). Specific binding of nisin to the peptidoglycan precursor lipid II combines pore formation and inhibition of cell wall biosynthesis for potent antibiotic activity. The Journal of Biological Chemistry, 276(3), 1772-1779. DOI: 10.1074/jbc.M006770200
Hup, G., Nauta, A., Kemperman, R. A., Kok, J., & Kuipers, O. (2001). IPC No. C07K 14/ 33 A I. Methods and means for producing improved dairy products (Patent No. WO0101786.)
Gunnewijk, M. G. W., van den Bogaard, P. T. C., Veenhoff, L. M., Heuberger, E. H. M. L., de Vos, W. M., Kleerebezem, M., ... Poolman, B. (2001). Hierarchical control versus autoregulation of carbohydrate utilization in bacteria. Journal of Molecular Microbiology and Biotechnology, 3(3), 401 - 413.
Vaughan, E. E., Bogaard, P. T. C. V. D., Catzeddu, P., Kuipers, O. P., & Vos, W. M. D. (2001). Activation of Silent gal Genes in the lac-gal Regulon of Streptococcus thermophilus. Journal of Bacteriology, 183(4). DOI: 10.1128/JB.183.4.1184-1194.2001
Monedero, V., Kuipers, O. P., Jamet, E., & Deutscher, J. (2001). Regulatory Functions of Serine-46-Phosphorylated HPr in Lactococcus lactis. Journal of Bacteriology, 183(11). DOI: 10.1128/JB.183.11.3391-3398.2001
Wouters, J. A., Frenkiel, H., Vos, W. M. D., Kuipers, O. P., & Abee, T. (2001). Cold Shock Proteins of Lactococcus lactis MG1363 Are Involved in Cryoprotection and in the Production of Cold-Induced Proteins. Applied and Environmental Microbiology, 67(11). DOI: 10.1128/AEM.67.11.5171-5178.2001
Kuipers, O. (2001). Leven in een notendop: een genomische benadering van bacteriën. s.n.
Miladinov, N., Kuipers, O. P., & Topisirovic, L. (2001). Casitone-mediated expression of the prtP and prtM genes in Lactococcus lactis subsp. lactis BGIS29. Archives of Microbiology, 177(1). DOI: 10.1007/s00203-001-0361-7

2007

Ventura, M., Zomer, A., Canchaya, C., O'Connell-Motherway, M., Kuipers, O., Turroni, F., ... O’Connell-Motherway, M. (2007). Comparative analyses of prophage-like elements present in two Lactococcus lactis strains. Applied Environmental Microbiology, 73(23), 7771-7780. DOI: 10.1128/AEM.01273-07
Rink, R., Kluskens, L. D., Kuipers, A., Driessen, A. J. M., Kuipers, O. P., & Moll, G. N. (2007). NisC, the cyclase of the lantibiotic nisin, can catalyze Cyclization of designed nonlantibiotic peptides. Biochemistry, 46(45), 13179-13189. DOI: 10.1021/bi700106z
Rink, R., Wierenga, J., Kuipers, A., Kluskens, L. D., Driessen, A. J. M., Kuipers, O. P., & Moll, G. N. (2007). Dissection and modulation of the four distinct activities of nisin by mutagenesis of rings A and B and by C-terminal truncation. Applied Environmental Microbiology, 73(18), 5809-5816. DOI: 10.1128/AEM.01104-07
Burghout, P., Bootsma, H. J., Kloosterman, T. G., Bijlsma, J. J. E., de Jongh, C. E., Kuipers, O. P., & Hermans, P. W. M. (2007). Search for genes essential for pneumococcal transformation: The RadA DNA repair protein plays a role in genomic recombination of donor DNA. Journal of Bacteriology, 189(18), 6540-6550. DOI: 10.1128/jb.00573-07
Lulko, A. T., Veening, J. W., Buist, G., Smits, W. K., Blom, E., Beekman, A. C., ... Kuipers, O. P. (2007). Production and secretion stress caused by overexpression of heterologous alpha-amylase leads to inhibition of sporulation and a prolonged motile phase in Bacillus subtilis. Applied Environmental Microbiology, 73(16), 5354-5362. DOI: 10.1128/AEM.00472-07
Steen, A., van Schalkwijk, S., Buist, G., Twigt, M., Szeliga, M., Meijer, W., ... Hugenholtz, J. (2007). Lytr, a phage-derived amidase is most effective in induced lysis of Lactococcus lactis compared with other lactococcal amidases and glucosaminidases. International Dairy Journal, 17(8), 926-936. DOI: 10.1016/j.idairyj.2006.12.007
Kloosterman, T. G., Van der Kooi-Pol, M. M., Bijlsma, J. J. E., & Kuipers, O. P. (2007). The novel transcriptional regulator SczA mediates protection against Zn2+ stress by activation of the Zn2+-resistance gene czcD in Streptococcus pneumoniae. Molecular Microbiology, 65(4), 1049-1063. DOI: 10.1111/j.1365-2958.2007.05849.x
Veiga, P., Bulbarela-Sampieri, C., Furlan, S., Maisons, A., Chapot-Chartier, M-P., Erkelenz, M., ... Kulakauskas, S. (2007). SpxB regulates O-acetylation-dependent resistance of Lactococcus lactis peptidoglycan to hydrolysis. The Journal of Biological Chemistry, 282(27), 19342-19354. DOI: 10.1074/jbc.M611308200
Susanna, K. A., Mironczuk, A. M., Smits, W. K., Hamoen, L. W., & Kuipers, O. P. (2007). A single, specific thymine mutation in the ComK-Binding site severely decreases binding and transcription activation by the competence transcription factor ComK of Bacillus subtilis. Journal of Bacteriology, 189(13), 4718-4728. DOI: 10.1128/JB.00281-07
Varhimo, E., Savijoki, K., Jalava, J., Kuipers, O. P., & Varmanen, P. (2007). Identification of a novel streptococcal gene cassette mediating SOS mutagenesis in Streptococcus uberis. Journal of Bacteriology, 189(14), 5210-5222. DOI: 10.1128/JB.00473-07
Smits, W. K., Bongiorni, C., Veening, J-W., Hamoen, L. W., Kuipers, O. P., & Perego, M. (2007). Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis. Molecular Microbiology, 65(1), 103-120. DOI: 10.1111/j.1365-2958.2007.05776.x
Duitman, E. H., Wyczawski, D., Boven, L. G., Venema, G., Kuipers, O. P., & Hamoen, L. W. (2007). Novel methods for genetic transformation of natural Bacillus subtilis isolates used to study the regulation of the mycosubtilin and surfactin synthetases. Applied and Environmental Microbiology, 73(11), 3490-3496. DOI: 10.1128/AEM.02751-06
Blom, E. J., Bosman, D. W., van Hijum, S. A. F. T., Breitling, R., Tijsma, L., Silvis, R., ... Kuipers, O. P. (2007). FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinformatics., 23(9), 1161-1163. DOI: 10.1093/bioinformatics/btl658
Reviriego, C., Fernandez, L., Kuipers, O. P., Kok, J., & Rodriguez, J. M. (2007). Enhanced production of pediocin PA-1 in wild nisin- and non-nisin-producing Lactococcus lactis strains of dairy origin. International Dairy Journal, 17(5), 574-577. DOI: 10.1016/j.idairyj.2006.05.013
Nijland, R., Veening, J-W., & Kuipers, O. P. (2007). A derepression system based on the Bacillus subtilis sporulation pathway offers dynamic control of heterologous gene expression. Applied and Environmental Microbiology, 73(7), 2390-2393. DOI: 10.1128/AEM.02266-06
Martinez, B., Zomer, A. L., Rodriguez, A., Kok, J., & Kuipers, O. P. (2007). Cell envelope stress induced by the bacteriocin Lcn972 is sensed by the lactococcal two-component system CesSR. Molecular Microbiology, 64(2), 473-486. DOI: 10.1111/j.1365-2958.2007.05668.x
Romero, D., de Vicente, A., Rakotoaly, R. H., Dufour, S. E., Veening, J-W., Arrebola, E., ... Stacey, G. (Ed.) (2007). The iturin and fengycin families of lipopeptides are key factors in antagonism of Bacillus subtilis toward Podosphaera fusca. Molecular Plant-Microbe Interactions, 20(4), 430-440. DOI: 10.1094/MPMI-20-4-0430
Smits, W. K., Hoa, T. T., Hamoen, L. W., Kuipers, O. P., & Dubnau, D. (2007). Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein. Molecular Microbiology, 64(2), 368-381. DOI: 10.1111/j.1365-2958.2007.05662.x
Wegmann, U., O'Connell-Motherwy, M., Zomer, A., Buist, G., Shearman, C., Canchaya, C., ... Kok, J. (2007). Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp cremoris MG1363. Journal of Bacteriology, 189(8), 3256-3270. DOI: 10.1128/JB.01768-06
Nijland, R., Heerlien, R., Hamoen, L. W., & Kuipers, O. P. (2007). Changing a single amino acid in Clostridium perfringens beta-toxin affects the efficiency of heterologous secretion by Bacillus subtilis. Applied and Environmental Microbiology, 73(5), 1586-1593. DOI: 10.1128/AEM.02356-06
Bijlsma, J. J. E., Burghout, P., Moosterman, T. G., Bootsma, F. J., de Jong, A., Hermans, P. W. M., ... Bootsma, H. J. (2007). Development of genomic array footprinting for identification of conditionally essential genes in Streptococcus pneumoniae. Applied and Environmental Microbiology, 73(5), 1514-1524. DOI: 10.1128/AEM.01900-06
Hendriksen, W. T., Silva, N., Bootsma, H. J., Blue, C. E., Paterson, G. K., Kerr, A. R., ... Mitchell, T. J. (2007). Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is strain dependent. Journal of Bacteriology, 189(4), 1382-1389. DOI: 10.1128/JB.01144-06
Zomer, A. L., Buist, G., Larsen, R., Kok, J., & Kuipers, O. P. (2007). Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp cremoris MG1363. Journal of Bacteriology, 189(4), 1366-1381. DOI: 10.1128/JB.01013-06
Nijland, R., Lindner, C., van Hartskamp, M., Hamoen, L. W., & Kuipers, O. P. (2007). Heterologous production and secretion of Clostridium perfringens beta-toxoid in closely related Gram-positive hosts. Journal of Biotechnology, 127(3), 361-372. DOI: 10.1016/j.jbiotec.2006.07.014
Rink, R., Wierenga, J., Kuipers, A., Kluskens, L. D., Driessen, A. J. M., Kuipers, O. P., & Moll, G. (2007). Production of dehydroamino acid-containing peptides by Lactococcus lactis. Applied Environmental Microbiology, 73(6), 1792 - 1796. DOI: 10.1128/AEM.02350-06
Bosman, D. W., Blom, E. J., Ogao, P. J., Kuipers, O. P., & Roerdink, J. B. T. M. (2007). MOVE: A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks. In Silico Biology, 7(1), 35-59.
Duitman, E. H., Wyczawski, D., Boven, L. G., Venema, G., Kuipers, O. P., & Hamoen, L. W. (2007). Novel methods for genetic transformation of natural Bacillus subtilis isolates used to study regulation of the mycosubtilin and surfactin synthetases. Applied Environmental Microbiology, 73, 3490 - 3496.
Kloosterman, T. G., van der Kooi-Pol, M. M., Bijlsma, J., & Kuipers, O. P. (2007). The novel transcriptional regulator SczA mediates protection against Zn(2+) stress by activation of the Zn(2+)-resistance gene czcD in Streptococcus pneumoniae. Molecular Microbiology, 65, 1049 - 1063.
Lulko, A. T., Buist, G., Kok, J., & Kuipers, O. P. (2007). Transcriptome analysis of temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals additional target genes. Journal of Molecular Microbiology and Biotechnology, 12(1-2), 82-95. DOI: 10.1159/000096463

2006

Neves, A. R., Pool, W. A., Castro, R., Mingote, A., Santos, F., Kok, J., ... Santos, H. (2006). The alpha-phosphoglucomutase of Lactococcus lactis is unrelated to the alpha-D-phosphohexomutase superfamily and is encoded by the essential gene pgmH. The Journal of Biological Chemistry, 281(48), 36864-36873. DOI: 10.1074/jbc.M607044200
Miethke, M., Westers, H., Blom, E-J., Kuipers, O. P., & Marahiel, M. A. (2006). Iron starvation triggers the stringent response and induces amino acid biosynthesis for bacillibactin production in Bacillus subtilis. Journal of Bacteriology, 188(24), 8655-8657. DOI: 10.1128/JB.01049-06
Darmon, E., Dorenbos, R., Meens, J., Freudl, R., Antelmann, H., Hecker, M., ... van Dijl, J. M. (2006). A disulfide bond-containing alkaline phosphatase triggers a BdbC-dependent secretion stress response in Bacillus subtilis. Applied and Environmental Microbiology, 72(11), 6876-6885. DOI: 10.1128/AEM.01176-06
Buist, G., Ridder, A. N. J. A., Kok, J., & Kuipers, O. P. (2006). Different subcellular locations of secretome components of Gram-positive bacteria. Microbiology-Sgm, 152(10), 2867-2874. DOI: 10.1099/mic.0.29113-0
Hasper, H. E., Kramer, N. E., Smith, J. L., Hillman, J. D., Zachariah, C., Kuipers, O. P., ... Breukink, E. (2006). An alternative bactericidal mechanism of action for lantibiotic peptides that target lipid II. Science, 313(5793), 1636-1637. DOI: 10.1126/science.1129818
Kloosterman, T. G., Hendriksen, W. T., Bijlsma, J. J. E., Bootsma, H. J., van Hijum, S. A. F. T., Kok, J., ... Kuipers, O. P. (2006). Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae. The Journal of Biological Chemistry, 281(35), 25097-25109. DOI: 10.1074/jbc.M601661200
Romero, D., Perez-Garcia, A., Veening, J-W., de Vicente, A., Kuipers, O. P., & de, V. A. (2006). Transformation of undomesticated strains of Bacillus subtilis by protoplast electroporation. Journal of microbiological methods, 66(3), 556-559. DOI: 10.1016/j.mimet.2006.01.005
Veening, J. -W., Smits, W. K., Hamoen, L. W., & Kuipers, O. P. (2006). Single cell analysis of gene expression patterns of competence development and initiation of sporulation in Bacillus subtilis grown on chemically defined media. Journal of Applied Microbiology, 101(3), 531-541. DOI: 10.1111/j.1365-2672.2006.02911.x
Pool, W. A., Neves, A. R., Kok, J., Santos, H., & Kuipers, O. P. (2006). Natural sweetening of food products by engineering Lactococcus lactis for glucose production. Metabolic Engineering, 8(5), 456-464. DOI: 10.1016/j.ymben.2006.05.003
Lubelski, J., de Jong, A., van Merkerk, R., Agustiandari, H., Kuipers, O. P., Kok, J., & Driessen, A. J. M. (2006). LmrCD is a major multidrug resistance transporter in Lactococcus lactis. Molecular Microbiology, 61(3), 771-781. DOI: 10.1111/j.1365-2958.2006.05267.x
de Jong, A., van Hijum, S. A. F. T., Bijlsma, J. J. E., Kok, J., & Kuipers, O. P. (2006). BAGEL: a web-based bacteriocin genome mining tool. Nucleic Acids Research, 34, W273-W279. DOI: 10.1093/nar/gkl237
Larsen, R., Kloosterman, T. G., Kok, J., & Kuipers, O. P. (2006). GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis. Journal of Bacteriology, 188(13), 4978-4982. DOI: 10.1128/JB.00025-06
Westenberg, M. A., van Hijum, S. A. F. T., Kuipers, O. P., & Roerdink, J. B. T. M. Gene expression and network visualization
Kramer, N. E., Van Hijum, S. A. F. T., Knol, J., Kok, J., Kuipers, O. P., & Kramer, N. E. (2006). Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance. Antimicrobial Agents and Chemotherapy, 50(5), 1753-1761. DOI: 10.1128/AAC.50.5.1753-1761.2006
den Hengst, C. D., Groeneveld, M., Kuipers, O. P., Kok, J., & Hengst, C. D. D. (2006). Identification and functional characterization of the Lactococcus lactis CodY-regulated branched-chain amino acid permease BcaP (CtrA). Journal of Bacteriology, 188(9), 3280-3289. DOI: 10.1128/JB.188.9.3280-3289.2006
Westenberg, M. A., van Hijum, S. A. F. T., Kuipers, O. P., & Roerdink, J. B. T. M. GENeVis: Gene expression and network visualization
Albers, C. J., Jansen, R. C., Kok, J., Kuipers, O. P., & Hijum, S. A. F. T. V. (2006). SIMAGE: simulation of DNA-microarray gene expression data. Bmc Bioinformatics, 7(205), [205]. DOI: 10.1186/1471-2105-7-205
Smits, W., Kuipers, O. P., & Veening, J. W. (2006). Phenotypic variation in bacteria: The role of feedback regulation. Nature Reviews Microbiology, 4(4), 259-271. DOI: 10.1038/nrmicro1381
Veening, J. W., Kuipers, O. P., Brul, S., Hellingwerf, K. J., & Kort, R. (2006). Effects of Phosphorelay Perturbations on Architecture, Sporulation, and Spore Resistance in Biofilms of Bacillus subtilis. Journal of Bacteriology, 188(8), 3099-3109. DOI: 10.1128/JB.188.8.3099-3109.2006
Susanna, K., Fusetti, F., Thunnissen, A. M. W. H., Hamoen, L. W., & Kuipers, O. P. (2006). Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants. Microbiology-Sgm, 152(2), 473-483. DOI: 10.1099/mic.0.28357-0
van Roosmalen, M. L., Kanninga, R., El Khattabi, M., Neef, J., Audouy, S., Bosma, T., ... Leenhouts, K. (2006). Mucosal vaccine delivery of antigens tightly bound to an adjuvant particle made from food-grade bacteria. Methods., 38(2), 144-149. DOI: 10.1016/j.ymeth.2005.09.015
Kloosterman, T. G., Bijlsma, J. J. E., Kok, J., & Kuipers, O. P. (2006). To have neighbour's fare: extending the molecular toolbox for Streptococcus pneumoniae. Microbiology, 152, 351-359. DOI: 10.1099/mic.0.28521-0
Susanna, K. A., den Hengst, C. D., Hamoen, L. W., & Kuipers, O. P. (2006). Expression of transcription activator ComK of Bacillus subtilis in the heterologous host Lactococcus lactis leads to a genome-wide repression pattern: a case study of horizontal gene transfer. Appl.Environ.Microbiol., 72(1), 404-411. DOI: 10.1128/AEM.72.1.404-411.2006
Bosma, T., Kanninga, R., Neef, J., Audouy, S. A. L., van Roosmalen, M. L., Steen, A., ... Leenhouts, K. (2006). Novel surface display system for proteins on non-genetically modified gram-positive bacteria. Applied and Environmental Microbiology, 72(1), 880-889. DOI: 10.1128/AEM.72.1.880-889.2006
Neves, A. R., Pool, W. A., Castro, R., Mingote, A., Santos, F., Kok, J., ... Santos, H. (2006). The a-phosphoglucomutase of lactococcus lactis is unrelated to the a-D-phosphohexomutase superfamily and encoded by the essential gene pgmH. The Journal of Biological Chemistry, 281, 36864 - 36873.
Kuipers, O. P., & Roerdink, J. B. T. M. (2006). MOVE: A Multilevel Ontology-based Visualization and Exploration framework for genomic networks. In Silico Biology, 7(0004).
Kuipers, A., Wierenga, J., Rink, R., Kluskens, L. D., Driessen, A. J. M., Kuipers, O. P., & Moll, G. N. (2006). Sec-Mediated Transport of Posttranslationally Dehydrated Peptides in Lactococcus lactis. Applied and Environmental Microbiology, 72(12), 7626 - 7633. DOI: 10.1128/AEM.01802-06

2005

Bongers, R. S., Veening, J. W., van Wieringen, M., Kuipers, O. P., & Kleerebezem, M. (2005). Development and characterization of a subtilin-regulated expression system in Bacillus subtilis: Strict control of gene expression by addition of subtilin. Appl.Environ.Microbiol., 71(12), 8818-8824. DOI: 10.1128/AEM.71.12.8818-8824.2005
den Hengst, C. D., van Hijum, S. A. F. T., Geurts, J. M., Nauta, A., Kok, J., & Kuipers, O. P. (2005). The Lactococcus lactis CodY regulon - Identification of a conserved cis-regulatory element. The Journal of Biological Chemistry, 280(40), 34332-34342. DOI: 10.1074/jbc.M502349200
Kluskens, L. D., Kuipers, A., Rink, R., de Boef, E., Fekken, S., Driessen, A. J. M., ... Moll, G. N. (2005). Post-translational modification of therapeutic peptides by NisB, the dehydratase of the lantibiotic nisin. Biochemistry, 44(38), 12827-12834. DOI: 10.1021/bi050805p
Neves, A. R., Pool, W. A., Kok, J., Kuipers, O. P., Santos, H., Neves, A. R., & Pool, W. A. (2005). Overview on sugar metabolism and its control in Lactococcus lactis - The input from in vivo NMR. FEMS Microbiology Reviews, 29(3), 531-554. DOI: 10.1016/j.femsre.2005.04.005
Kok, J., Buist, G., Zomer, A. L., Hijum, S. A. F. T. V., & Kuipers, O. P. (2005). Comparative and functional genomics of lactococci. FEMS Microbiology Reviews, 29(3), 411-433. DOI: 10.1016/j.fmrre.2005.04.004
van Hijum, S. A. F. T., Zomer, A. L., Kuipers, O. P., & Kok, J. (2005). Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res., 33(Web Server issue), W560-W566. DOI: 10.1093/nar/gki356
Rink, R., Kuipers, A., de Boef, E., Leenhouts, K. J., Driessen, A. J. M., Moll, G. N., ... Leenhouts, K. J. (2005). Lantibiotic structures as guidelines for the design of peptides that can be modified by lantibiotic enzymes. Biochemistry, 44(24), 8873-8882. DOI: 10.1021/bi050081h
Smits, W., Dubois, J-Y., Bron, S., van Dijl, J. M., & Kuipers, O. P. (2005). Tricksy business: Transcriptome analysis reveals the involvement of thioredoxin a in redox homeostasis, oxidative stress, sulfur metabolism, and cellular differentiation in Bacillus subtilis. Journal of Bacteriology, 187(12), 3921-3930. DOI: 10.1128/JB.187.12.3921-3930.2005
Barrière, C., Veiga-da-Cunha, M., Pons, N., Guédon, E., Hijum, S. A. F. T. V., Kok, J., ... Renault, P. (2005). Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: Its regulator, signal, and DNA-binding. Journal of Bacteriology, 187(11), 3752-3761. DOI: 10.1128/JB.187.11.3752?3761.2005
Veening, J. W., Hamoen, L. W., & Kuipers, O. P. (2005). Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis. Molecular Microbiology, 56(6), 1481-1494. DOI: 10.1111/j.1365-2958.2005.04659.x
Steen, A., Buist, G., Horsburgh, G. J., Venema, G., Kuipers, O. P., Foster, S. J., ... Foster, S. J. (2005). AcmA of Lactococcus lactis is an N-acetylglucosaminidase with an optimal number of LysM domains for proper functioning. Febs Journal, 272(11), 2854-2868. DOI: 10.1111/j.1742-4658.2005.04706.x
van Hijum, S. A. F. T., de Jong, A., Baerends, R. J. S., Karsens, H. A., Kramer, N. E., Larsen, R., ... Hengst, C. D. D. (2005). A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics, 6(1), [77]. DOI: 10.1186/1471-2164-6-77
Larsen, R., Kok, J., & Kuipers, O. P. (2005). Interaction between ArgR and AhrC controls regulation of arginine metabolism in Lactococcus lactis. The Journal of Biological Chemistry, 280(19), 19319-19330. DOI: 10.1074/jbc.M413983200
Smits, W. K., Eschevins, C. C., Susanna, K. A., Bron, S., Kuipers, O. P., & Hamoen, L. W. (2005). Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development. Mol.Microbiol., 56(3), 604-614. DOI: 10.1111/j.1365-2958.2005.04488.x
Hijum, S. A. F. T. V., Jong, A. D., Baerends, R. J. S., Karsens, H. A., Kramer, N. E., Larsen, R., ... Kuipers, O. P. (2005). A novel scheme to assess factors involved in the reproducibility of DNA-microarray data. BMC Genomics, 6(1). DOI: 10.1186/gb-2005-6-4-p4
Albano, M., Smits, W. K., Ho, L. T. Y., Kraigher, B., Mandic-Mulec, . N. V., Kuipers, O. P., ... Mandic-Mulec, I. (2005). The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions. Journal of Bacteriology, 187(6), 2010-2019. DOI: 10.1128/JB.187.6.2010-2019.2005
den Hengst, C., Gajic, O., Kuipers, O., Kok, J., Sikkema, J., Geurts, J. M. W., & Nauta, A. (2005). IPC No. C12N 15/ 74 A I. Methods and means for regulating gene expression (Patent No. WO2005003354.)
Steen, A., Palumbo, E., Deghorain, M., Cocconcelli, P. S., Delcour, J., Kuipers, O. P., ... Hols, P. (2005). Autolysis of Lactococcus lactis is increased upon D-alanine depletion of peptidoglycan and lipoteichoic acids. Journal of Bacteriology, 187(1), 114-124. DOI: 10.1128/JB.187.1.114-124.2005
den Hengst, C. D., Curley, P., Larsen, R., Buist, G., Nauta, A., van Sinderen, D., ... Hengst, C. D. D. (2005). Probing direct interactions between CodY and the oppD promoter of Lactococcus lactis. Journal of Bacteriology, 187(2), 512-521. DOI: 10.1128/JB.187.2.512-521.2005
Barriere, C., Veiga-da-Cunha, M., Pons, N., Guedon, E., van Hijum, S. A. F. T., Kok, J., ... Renault, P. (2005). Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. J.Bacteriol., 187(11), 3752 - 3761.
de Vos, W. M., Kleerebezem, M., & Kuipers, O. P. (2005). Lactic acid bacteria - Genetics, metabolism and application. FEMS Microbiol.Rev., 29(3), 391.
Vos, W. M. D., Kleerebezem, M., & Kuipers, O. P., (2005). Lactic acid bacteria – Genetics, metabolism and application, 1 p.

2003

Westers, H., Dorenbos, R., Dijl, J. M. V., Kabel, J., Flanagan, T., Devine, K. M., ... Quax, W. J. (2003). Genome engineering reveals large dispensable regions in Bacillus subtilis. Molecular Biology and Evolution, 20(12), 2076-2090. DOI: 10.1093/molbev/msg.219
van Hijum, S. A. F. T., Zomer, A. L., Kuipers, O. P., & Kok, J. (2003). Projector: automatic contig mapping for gap closure purposes. Nucleic Acids Research, 31(22), [144]. DOI: 10.1093/nar/gng144
Leenhouts Cornelis, J., Ramasamy, R., Steen, A., Kok, J., Buist, G., & Kuipers, O. (2003). IPC No. A61K 38/ 00 A N. Bacterial ghosts provided with antigens (Patent No. US2003186851.)
Kemperman, R., Jonker, M., Nauta, A., Kuipers, O. P., & Kok, J. (2003). Functional analysis of the gene cluster involved in production of the bacteriocin circularin A by Clostridium beijerinckii ATCC 25752. Applied and Environmental Microbiology, 69(10), 5839-5848. DOI: 10.1128/AEM.69.10.5839-5848.2003
Leenhouts, C., Ramasamy, R., Steen, A., Kok, J., Buist, G., & Kuipers, O. (2003). IPC No. A61K 38/ 00 A N. Method to provide bacterial ghosts provided with antigens (Patent No. US2003180816.)
Gajic, O., Buist, G., Kojic, M., Topisirovic, L., Kuipers, O. P., & Kok, J. (2003). Novel mechanism of bacteriocin secretion and immunity carried out by lactococcal multidrug resistance proteins. The Journal of Biological Chemistry, 278(36), 34291-34298. DOI: 10.1074/jbc.M211100200
van Hijum, S. A. F. T., de Jong, A., Buist, G., Kok, J., & Kuipers, O. P. (2003). UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. Bioinformatics, 19(12), 1580-1582. DOI: 10.1093/bioinformatics/btg203
Steen, A., Buist, G., Leenhouts, K. J., El Khattabi, M., Grijpstra, F., Zomer, A. L., ... Leenhouts, K. J. (2003). Cell wall attachment of a widely distributed peptidoglycan binding domain is hindered by cell wall constituents. The Journal of Biological Chemistry, 278(26), 23874-23881. DOI: 10.1074/jbc.M211055200
Kemperman, R., Kuipers, A., Karsens, H., Nauta, A., Kuipers, O., & Kok, J. (2003). Identification and characterization of two novel clostridial bacteriocins, circularin A and closticin 574. Applied and Environmental Microbiology, 69(3), 1589-1597. DOI: 10.1128/AEM.69.3.1589-1597.2003
Hamoen, L. W., Venema, G., & Kuipers, O. P. (2003). Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology-Sgm, 149(1), 9-17. DOI: 10.1099/mic.0.26003-0
Antelmann, H., Darmon, E., Noone, D., Veening, J. W., Westers, H., Bron, S., ... van Dijl, J. M. (2003). The extracellular proteome of Bacillus subtilis under secretion stress conditions. Molecular Microbiology, 49(1), 143 - 156. DOI: 10.1046/j.1365-2958.2003.03565.x
Kleerebezem, M., Boekhorst, J., Kranenburg, R. V., Molenaar, D., Kuipers, O. P., Leer, R., ... Siezen, R. J. (2003). Complete genome sequence of Lactobacillus plantarum WCFS1. Proceedings of the National Academy of Sciences, 100(4). DOI: 10.1073/pnas.0337704100

2004

Veening, J. W., Smits, W. K., Hamoen, L. W., Jongbloed, J. D. H., Kuipers, O. P., & Smits, W. K. (2004). Visualization of differential gene expression by improved cyan fluorescent protein and yellow fluorescent protein production in Bacillus subtilis. Applied Environmental Microbiology, 70(11), 6809-6815. DOI: 10.1128/AEM.70.11.6809-6815.2004
Kramer, N. E., Smid, E. J., Kok, J., de Kruijff, B., Kuipers, O. P., Breukink, E., ... Smid, E. J. (2004). Resistance of Gram-positive bacteria to nisin is not determined by Lipid II levels. FEMS Microbiology Letters, 239(1), 157-161. DOI: 10.1016/j.femsle.2004.08.033
Moll, G. N., Kuipers, A., de Boef, E., Rink, R., Fekken, S., Kluskens, L. D., ... Kuipers, O. P. (2004). NisT, the transporter of the lantibiotic nisin, can transport fully modified, dehydrated and unmodified prenisin and Fusions of the leader peptide with non-lantibiotic peptides. Protein Science, 13, 151-151.
Westers, H., Darmon, E., Zanen, G., Veening, J-W., Kuipers, O. P., Bron, S., ... Dijl, J. M. V. (2004). The Bacillus secretion stress response is an indicator for α-amylase production levels. Letters in Applied Microbiology, 39(1), 65-73. DOI: 10.1111/j.1472-765X.2004.01539.x
Tjalsma, H., Antelmann, H., Jongbloed, J. D. H., Braun, P. G., Darmon, E., Dorenbos, R., ... van Dijl, J. M. (2004). Proteomics of protein secretion by Bacillus subtilis: Separating the "secrets" of the secretome. Microbiology and Molecular Biology Reviews, 68(2), 207-233. DOI: 10.1128/mmbr.68.2.207-233.2004
Kuipers, O. P. (2004). Genomics and bioinformatics enhance research on food and gut bacteria - Editorial overview. Current Opinion in Biotechnology, 15(2), 83-85. DOI: 10.1016/j.copbio.2004.03.003
Susanna, K. A., van der Werff, A. F., den Hengst, C. D., Calles, B., Salas, M., Venema, G., ... Kuipers, O. P. (2004). Mechanism of transcription activation at the comG promoter by the competence transcription factor ComK of Bacillus subtilis. Journal of Bacteriology, 186(4), 1120-1128. DOI: 10.1128/JB.186.4.1120-1128.2004
Lindner, C., Nijland, R., Hartskamp, M. V., Bron, S., Hamoen, L. W., & Kuipers, O. P. (2004). Differential Expression of Two Paralogous Genes of Bacillus subtilis Encoding Single-Stranded DNA Binding Protein. Journal of Bacteriology, 186(4), 1097 - 1105. DOI: 10.1128/JB.186.4.1097-1105.2004
Larsen, R., Buist, G., Kuipers, O. P., & Kok, J. (2004). ArgR and AhrC are both required for regulation of arginine metabolism in Lactococcus lactis. Journal of Bacteriology, 186(4), 1147-1157. DOI: 10.1128/JB.186.4.1147-1157.2004
Baerends, R. J. S., Smits, W. K., Jong, A. D., Hamoen, L. W., Kok, J., & Kuipers, O. P. (2004). Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biology, 5(5), [37]. DOI: 10.1186/gb-2004-5-5-r37
Kleerebezem, M., Bongers, R., Rutten, G., de Vos, W. M., & Kuipers, O. P. (2004). Autoregulation of subtilin biosynthesis in Bacillus subtilis: the role of the spa-box in subtilin-responsive promoters. Peptides, 25(9), 1415-1424. DOI: 10.1016/j.peptides.2003.11.025
Tjalsma, H., Koetje, E. J., Kiewiet, R., Kuipers, O. P., Kolkman, M., van der Laan, J., ... Bron, S. (2004). Engineering of quorum-sensing systems for improved production of alkaline protease by Bacillus subtilis. Journal of Applied Microbiology, 96(3), 569 - 578. DOI: 10.1111/j.1365-2672.2004.02179.x
van den Boogaard, P. T., Hols, P., Kuipers, O. P., Kleerebezem, M., & de Vos, W. M. (2004). Sugar Utilisation and Conservation of the gal-lac Gene Cluster in Streptococcus thermophilus. Applied Microbiology, 27(1), 10 - 17. DOI: 10.1078/0723-2020-00258
Swertz, M. A., Brock, E. O. . B. D., Hijum, S. A. F. T. V., Jong, A. D., Buist, G., Baerends, R. J. S., ... Jansen, R. C. (2004). Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases. Bioinformatics, 20(13), 2075 - 2083. DOI: 10.1093/bioinformatics/bth206
Campo, N., Tjalsma, H., Buist, G., Stepniak, D., Meijer, M., Veenhuis, M., ... Jongbloed, J. D. H. (2004). Subcellular sites for bacterial protein export. Molecular Microbiology, 53(6), 1583 - 1599. DOI: 10.1111/j.1365-2958.2004.04278.x
Kuipers, A., Boef, E. D., Rink, R., Fekken, S., Kluskens, L. D., Driessen, A. J. M., ... Moll, G. N. (2004). NisT, the Transporter of the Lantibiotic Nisin, Can Transport Fully Modified, Dehydrated, and Unmodified Prenisin and Fusions of the Leader Peptide with Non-lantibiotic Peptides. The Journal of Biological Chemistry, 279(21), 22176 - 22182. DOI: 10.1074/jbc.M312789200
Kluskens, L. D., Kuipers, A., Rink, R., de Boef, E., Fekken, S., Driessen, A. J. M., ... Moll, G. N. (2004). USE OF LANTIBIOTIC ENZYMES FOR SYNTHESIS OF THIOETHER BRIDGES IN A BROAD RANGE OF PEPTIDES. Journal of Peptide Science, 10, 165-165.

1999

Breukink, E., Wiedemann, . N. V., van Kraaij, C., Kuipers, O. P., Sahl, H. G., de Kruijff, B., & Wiedemann, I. (1999). Use of the cell wall precursor lipid II by a pore-forming peptide antibiotic. Science, 286(5448), 2361-2364. DOI: 10.1126/science.286.5448.2361
Wegmann, U., Klein, J. R., Drumm, I., Kuipers, O. P., & Henrich, B. (1999). Introduction of peptidase genes from Lactobacillus delbrueckii subsp. lactis into Lactococcus lactis and controlled expression. Applied and Environmental Microbiology, 65(11), 4729-4733.
Kuipers, O. P., Jong, A. D., Holsappel, S., Bron, S., Kok, J., & Hamoen, L. W. (1999). DNA-microarrays and food-biotechnology. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 76(1-4), 353-355. DOI: 10.1023/A:1002021812783
Konings, W. N., in't Veld, J. H. J. H., & Kuipers, O. P. (1999). The sixth symposium on Lactic Acid Bacteria. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 76(1-4), 1-1.
van Kraaij, C., de Vos, W. M., Siezen, R. J., Kuipers, O. P., Vos, W. M. D., & Siezen, R. J. (1999). Lantibiotics: biosynthesis, mode of action and applications. Natural product reports, 16(5), 575-587. DOI: 10.1039/a804531c
Kuipers, O. P. (1999). Genomics for food biotechnology: prospects of the use of high-throughput technologies for the improvement of food microorganisms. Current Opinion in Biotechnology, 10(5), 511-516. DOI: 10.1016/S0958-1669(99)00019-1
Ra, R., Beerthuyzen, M. M., Vos, W. M. D., Saris, P. E. J., & Kuipers, O. P. (1999). Effects of gene disruptions in the nisin gene cluster of Lactococcus lactis on nisin production and producer immunity. Microbiology, 145(5). DOI: 10.1099/13500872-145-5-1227
Wouters, J. A., Jeynov, B., Rombouts, F. M., Vos, W. M. D., Kuipers, O. P., & Abee, T. (1999). Analysis of the role of 7 kDa cold-shock proteins of Lactococcus lactis MG1363 in cryoprotection. Default journal.
Wouters, J. A., Rombouts, F. M., Vos, W. M. D., Kuipers, O. P., & Abee, T. (1999). Cold Shock Proteins and Low-Temperature Response of Streptococcus thermophilus CNRZ302. Default journal.
Luesink, E. J., Beumer, C. M. A., Kuipers, O. P., & Vos, W. M. D. (1999). Molecular Characterization of the Lactococcus lactis ptsHI Operon and Analysis of the Regulatory Role of HPr. Default journal.
Luesink, E. J., Marugg, J. D., Kuipers, O. P., & Vos, W. M. D. (1999). Characterization of the Divergent sacBK and sacAR Operons, Involved in Sucrose Utilization by Lactococcus lactis. Default journal.

2000

Kuipers, O. P., Buist, G., & Kok, J. (2000). Current strategies for improving food bacteria. Research in Microbiology, 151(10), 815-822. DOI: 10.1016/S0923-2508(00)01147-5
van Kraaij, C., Breukink, E., Rollema, H. S., Bongers, R. S., Kosters, H. A., de Kruijff, B., ... Bongers, R. S. (2000). Engineering a disulfide bond and free thiols in the lantibiotic nisin Z. European Journal of Biochemistry, 267(3), 901-909. DOI: 10.1046/j.1432-1327.2000.01075.x
Konings, W. N., Kok, J., Kuipers, O. P., & Poolman, B. (2000). Lactic acid bacteria: the bugs of the new millennium. Current Opinion in Microbiology, 3(3), 276-282. DOI: 10.1016/S1369-5274(00)00089-8
Fernández, M., Doesburg, W. V., Rutten, G. A. M., Marugg, J. D., Alting, A. C., Kranenburg, R. V., & Kuipers, O. P. (2000). Molecular and Functional Analyses of the metC Gene of Lactococcus lactis, Encoding Cystathionine β-Lyase. Default journal.
Fernández, L., Beerthuyzen, M. M., Brown, J., Siezen, R. J., Coolbear, T., Holland, R., & Kuipers, O. P. (2000). Cloning, Characterization, Controlled Overexpression, and Inactivation of the Major Tributyrin Esterase Gene of Lactococcus lactis. Default journal.
Koebmann, B. J., Nilsson, D., Kuipers, O. P., & Jensen, P. R. (2000). The Membrane-Bound H+-ATPase Complex Is Essential for Growth of Lactococcus lactis. Journal of Bacteriology, 182(17). DOI: 10.1128/JB.182.17.4738-4743.2000
Wouters, J. A., Kamphuis, H. H., Hugenholtz, J., Kuipers, O. P., Vos, W. M. D., & Abee, T. (2000). Changes in Glycolytic Activity of Lactococcus lactis Induced by Low Temperature. Applied and Environmental Microbiology, 66(9). DOI: 10.1128/AEM.66.9.3686-3691.2000
Bogaard, P. T. C. V. D., Kleerebezem, M., Kuipers, O. P., & Vos, W. M. D. (2000). Control of Lactose Transport, β-Galactosidase Activity, and Glycolysis by CcpA in Streptococcus thermophilus: Evidence for Carbon Catabolite Repression by a Non-Phosphoenolpyruvate-Dependent Phosphotransferase System Sugar. Journal of Bacteriology, 182(21). DOI: 10.1128/JB.182.21.5982-5989.2000
Wouters, J. A., Mailhes, M., Rombouts, F. M., Vos, W. M. D., Kuipers, O. P., & Abee, T. (2000). Physiological and Regulatory Effects of Controlled Overproduction of Five Cold Shock Proteins of Lactococcus lactis MG1363. Applied and Environmental Microbiology, 66(9). DOI: 10.1128/AEM.66.9.3756-3763.2000
Wouters, J. A., Rombouts, F. M., Kuipers, O. P., Vos, W. M. D., & Abee, T. (2000). The Role of Cold-Shock Proteins in Low-Temperature Adaptation of Food-Related Bacteria. Systematic and applied microbiology, 23(2), 165-173. DOI: 10.1016/S0723-2020(00)80001-6

1998

Wouters, J. A., Sanders, J-W., Kok, J., Vos, W. M. D., Kuipers, O. P., Abee, T., & Wouters, J. W. (1998). Clustered organization and transcriptional analysis of a family of five csp genes of Lactococcus lactis MG1363. Microbiology, 144(10), 2885 - 2893. DOI: 10.1099/00221287-144-10-2885
Eichenbaum, Z., Federle, M. J., Marra, D., Vos, W. M. D., Kuipers, O. P., Kleerebezem, M., & Scott, J. R. (1998). Use of the Lactococcal nisA Promoter To Regulate Gene Expression in Gram-Positive Bacteria: Comparison of Induction Level and Promoter Strength. Default journal.
Luesink, E. J., Herpen, R. E. M. A. V., Grossiord, B. P., Kuipers, O. P., & Vos, W. M. D. (1998). Transcriptional activation of the glycolytic las operon and catabolite repression of the gal operon in Lactococcus lactis are mediated by the catabolite control protein CcpA. Molecular Microbiology, 30(4). DOI: 10.1046/j.1365-2958.1998.01111.x
Vos, W. M. D., Hols, P., Kranenburg, R. V., Luesink, E., Kuipers, O. P., Oost, J. V. D., ... Hugenholtz, J. (1998). Making More of Milk Sugar by Engineering Lactic Acid Bacteria. International Dairy Journal, 8(3). DOI: 10.1016/S0958-6946(98)00049-1
Kuipers, O. P., Ruyter, P. G. G. A. D., Kleerebezem, M., & Vos, W. M. D. (1998). Quorum sensing-controlled gene expression in lactic acid bacteria. Journal of Biotechnology, 64(1). DOI: 10.1016/S0168-1656(98)00100-X
Kraaij, C. V., Breukink, E., Noordermeer, M. A., Demel, R. A., Siezen, R. J., Kuipers, O. P., & Kruijff, B. D. (1998). Pore Formation by Nisin Involves Translocation of Its C-Terminal Part across the Membrane. Biochemistry, 37(46). DOI: 10.1021/bi980931b
Breukink, E., Kraaij, C. V., Dalen, A. V., Demel, R. A., Siezen, R. J., Kruijff, B. D., & Kuipers, O. P. (1998). The Orientation of Nisin in Membranes. Biochemistry, 37(22). DOI: 10.1021/bi972797l

1997

Quadri, L. E. N., Kleerebezem, M., Kuipers, O. P., Vos, W. M. D., Roy, K. L., Vederas, J. C., & Stiles, M. E. (1997). Characterization of a Locus from Carnobacterium piscicola LV17B Involved in Bacteriocin Production and Immunity: Evidence for Global Inducer-Mediated Transcriptional Regulation. Default journal.
Kleerebezem, M., Beerthuyzen, M. M., Vaughan, E. E., Vos, W. M. D., & Kuipers, O. P. (1997). Controlled Gene Expression Systems for Lactic Acid Bacteria: Transferable Nisin-Inducible Expression Cassettes for Lactococcus, Leuconostoc, and Lactobacillus spp. Default journal.
Ruyter, P. G. G. A. D., Kuipers, O. P., Meijer, W. C., & Vos, W. M. D. (1997). Food-grade controlled lysis of Lactococcus lactis for accelerated cheese ripening. Nature Biotechnology, 15(10). DOI: 10.1038/nbt1097-976
Kleerebezem, M., Quadri, L. E. N., Kuipers, O. P., & Vos, W. M. D. (1997). Quorum sensing by peptide pheromones and two-component signal-transduction systems in Gram-positive bacteria. Molecular Microbiology, 24(5). DOI: 10.1046/j.1365-2958.1997.4251782.x
Kraaij, C. V., Breukink, E., Rollema, H. S., Siezen, R. J., Demel, R. A., Kruijff, B. D., & Kuipers, O. P. (1997). Influence of charge differences in the C-terminal part of nisin on antimicrobial activity and signaling capacity. European Journal of Biochemistry, 247(1). DOI: 10.1111/j.1432-1033.1997.00114.x
Kuipers, O. P., Ruyter, P. G. G. A. D., Kleerebezem, M., & Vos, W. M. D. (1997). Controlled overproduction of proteins by lactic acid bacteria. Trends in Biotechnology, 15(4). DOI: 10.1016/S0167-7799(97)01029-9
Vos, W. M. D., Kleerebezem, M., & Kuipers, O. P. (1997). Expression systems for industrial Gram-positive bacteria with low guanine and cytosine content. Current Opinion in Biotechnology, 8(5). DOI: 10.1016/S0958-1669(97)80027-4
Breukink, E., Kraaij, C. V., Demel, R. A., Siezen, R. J., Kuipers, O. P., & Kruijff, B. D. (1997). The C-Terminal Region of Nisin Is Responsible for the Initial Interaction of Nisin with the Target Membrane. Biochemistry, 36(23). DOI: 10.1021/bi970008u
Hooven, H. W. V. D., Rollema, H. S., Siezen, R. J., Hilbers, C. W., & Kuipers, O. P. (1997). Structural Features of the Final Intermediate in the Biosynthesis of the Lantibiotic Nisin. Influence of the Leader Peptide. Biochemistry, 36(46). DOI: 10.1021/bi9713106

1996

Kuipers, O. P., Bierbaum, G., Ottenwälder, B., Dodd, H. M., Horn, N., Metzger, J., ... Gasson, M. J. (1996). Protein engineering of lantibiotics. Antonie van Leeuwenhoek: Journal of Microbiology, 69(2), 161-170. DOI: 10.1007/BF00399421
Ruyter, P. G. G. A. D., Kuipers, O. P., & Vos, W. M. D. (1996). Controlled Gene Expression Systems for Lactococcus lactis with the Food-Grade Inducer Nisin. Default journal.
Ruyter, P. G. G. A. D., Kuipers, O. P., Beerthuyzen, M. M., Alen-Boerrigter, I. V., & Vos, W. M. D. (1996). Functional Analysis of Promoters in the Nisin Gene Cluster of Lactococcus lactis. Default journal.
Siezen, R. J., Kuipers, O. P., & Vos, W. M. D. (1996). Comparison of lantibiotic gene clusters and encoded proteins. Antonie van Leeuwenhoek, 69(2). DOI: 10.1007/BF00399422
Demel, R. A., Peelen, T., Siezen, R. J., Kruijff, B. D., & Kuipers, O. P. (1996). Nisin Z, mutant nisin Z and lacticin 481 interactions with anionic lipids correlate with antimicrobial activity. A monolayer study. European Journal of Biochemistry, 235(1). DOI: 10.1111/j.1432-1033.1996.00267.x
Rollema, H. S., Metzger, J. W., Both, P., Kuipers, O. P., & Siezen, R. J. (1996). Structure and biological activity of chemically modified nisin A species. European Journal of Biochemistry, 241(3). DOI: 10.1111/j.1432-1033.1996.00716.x
Hooven, H. W. V. D., Lagerwerf, F. M., Heerma, W., Haverkamp, J., Piard, J-C., Hilbers, C. W., ... Rollema, H. S. (1996). The structure of the lantibiotic lacticin 481 produced by Lactococcus lactis: location of the thioether bridges. FEBS Letters, 391(3). DOI: 10.1016/0014-5793(96)00771-5

1995

Siezen, R. J., Rollema, H. S., Kuipers, O. P., & Vos, W. M. D. (1995). Homology modelling of the Lactococcus lactis leader peptidase NisP and its interaction with the precursor of the lantibiotic nisin. %22Protein Engineering%2C Design and Selection%22, 8(2). DOI: 10.1093/protein/8.2.117
Vos, W. M. D., Kuipers, O. P., & Siezen, R. J. (1995). Maturation pathway of nisin and other lantibiotics: post-translationally modified antimicrobial peptides exported by Gram-positive bacteria. Molecular Microbiology, 17(3). DOI: 10.1111/j.1365-2958.1995.mmi_17030427.x
Kuipers, O. P., Beerthuyzen, M. M., Ruyter, P. G. G. A. D., Luesink, E. J., & Vos, W. M. D. (1995). Autoregulation of Nisin Biosynthesis in Lactococcus lactis by Signal Transduction. The Journal of Biological Chemistry, 270(45). DOI: 10.1074/jbc.270.45.27299
Rollema, H. S., Kuipers, O. P., Both, P., Vos, W. M. D., & Siezen, R. J. (1995). Improvement of Solubility and Stability of the Antimicrobial Peptide Nisin by Protein Engineering. International Dairy Journal, 5(8).
Kamp, M. V. D., Hooven, H. W. V. D., Konings, R. N. H., Bierbaum, G., Sahl, H-G., Kuipers, O. P., ... Ven, F. J. M. V. D. (1995). Elucidation of the primary structure of the lantibiotic epilancin K7 from Staphylococcus epidermidis K7. Cloning and characterisation of the epilancin-K7-encoding gene and NMR analysis of mature epilancin K7. European Journal of Biochemistry, 230(2). DOI: 10.1111/j.1432-1033.1995.tb20600.x
Kuipers, O. P., Rollema, H. S., Beerthuyzen, M. M., Siezen, R. J., & Vos, W. M. D. (1995). Protein Engineering and Biosynthesis of Nisin and Regulation of Transcription of the Structural nisA Gene. International Dairy Journal, 5(8). DOI: 10.1016/0958-6946(95)00032-1

1994

Rollema, H. S., Siezen, R. J., Beerthuyzen, M. M., Kuipers, O. P., & Vos, W. M. D. (1994). Influence of Amino Acid Substitutions in the Nisin Leader Peptide on Biosynthesis and Secretion of Nisin by Lactococcus lactis. Default journal.

1993

Polman, J., Beerthuyzen, M. M., Siezen, R. J., Kuipers, O. P., & Vos, W. M. D. (1993). Characterization of the Lactococcus lactis Nisin A Operon Genes nisP, Encoding a Subtilisin-Like Serine Protease Involved in Precursor Processing, and nisR, Encoding a Regulatory Protein Involved in Nisin Biosynthesis. Default journal.
Vos, W. M. D., Mulders, J. W. M., Siezen, R. J., Hugenholtz, J., & Kuipers, O. P. (1993). Properties of Nisin Z and Distribution of Its Gene, nisZ, in Lactococcus lactis. European Journal of Biochemistry, 216(1).
Piard, J-C., Kuipers, O. P., Rollema, H. S., Desmazeaud, M. J., & Vos, W. M. D. (1993). Structure, Organization, and Expression of the lct Gene for Lacticin 481, a Novel Lantibiotic Produced by Lactococcus lactis. Default journal.
Spee, J. H., Vos, W. M. D., & Kuipers, O. P. (1993). Efficient random mutagenesis method with adjustable mutation frequency use PCR dITP. Nucleic Acids Research, 21(3). DOI: 10.1093/nar/21.3.777
Kuipers, O. P., Beerthuyzen, M. M., Siezen, R. J., & Vos, W. M. D. (1993). Characterization of the nisin gene cluster nisABTCIPR of Lactococcus lactis. Requirement of expression of the nisA and nisI genes for development of immunity. European Journal of Biochemistry, 216(1). DOI: 10.1111/j.1432-1033.1993.tb18143.x
Kuipers, O. P., Rollema, H. S., Vos, W. M. D., & Siezen, R. J. (1993). Biosynthesis and secretion of a precursor of nisin Z by Lactococcus lactis, directed by the leader peptide of the homologous lantibiotic subtilin from Bacillus subtilis. FEBS Letters, 330(1). DOI: 10.1016/0014-5793(93)80911-D

1992

Kuipers, O. P., Rollema, H. S., Yap, W. M. G. J., Boot, H. J., Siezen, R. J., & Vos, W. M. D. (1992). Engineering Dehydrated Amino Acid Residues in the Antimicrobial Peptide Nisin. Default journal.

1991

Kuipers, O. P., Vincent, M., Brochon, J-C., Verheij, H. M., Haas, G. H. D., & Gallay, J. (1991). Insight into the Conformational Dynamics of Specific Regions of Porcine Pancreatic Phospholipase A2 from a Time-Resolved Fluorescence Study of a Genetically Inserted Single Tryptophan Residue. Biochemistry, 30(36). DOI: 10.1021/bi00100a008
Kuipers, O. P., Boot, H. J., & Vos, W. M. D. (1991). Improved site-directed mutagenesis method using PCR. Nucleic Acids Research, 19(16). DOI: 10.1093/nar/19.16.4558

1990

Thunnissen, M. M. G. M., AB, E., Kalk, K. H., Drenth, J., Dijkstra, B. W., Kuipers, O. P., ... Verheij, H. M. (1990). X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor. Nature, 347(6294), 689-691. DOI: 10.1038/347689a0
Kuipers, O. P., Franken, P. A., Hendriks, R., Verheij, H. M., & Haas, G. H. D. (1990). Function of the fully conserved residues Asp99, Tyr52 and Tyr73 in phospholipase A2. %22Protein Engineering%2C Design and Selection%22, 4(2). DOI: 10.1093/protein/4.2.199
Kuipers, O. P., Kerver, J., Meersbergen, J. V., Vis, R., Dijkman, R., Verheij, H. M., & Haas, G. H. D. (1990). Influence of size and polarity of residue 31 in porcine pancreatic phospholipase A2 on catalytic properties. %22Protein Engineering%2C Design and Selection%22, 3(7). DOI: 10.1093/protein/3.7.599
Kuipers, O. P., Bergh, C. J. V. D., Verheij, H. M., & Haas, G. H. D. (1990). Probing the Mechanism of Pancreatic Phospholipase A2 with the Aid of Recombinant DNA Techniques. In A. B. Mukherjee (Ed.), Biochemistry, Molecular Biology, and Physiology of Phospholipase A2 and Its Regulatory Factors (279 ed., pp. 65-84). (Advances in Experimental Medicine and Biology; No. 279).
Kuipers, O. P., Dekker, N., Verheij, H. M., & Haas, G. H. D. (1990). Activities of Native and Tyrosine-69 Mutant Phospholipases A2 on Phospholipid Analogues. A Reevaluation of the Minimal Substrate Requirements. Biochemistry, 29(25). DOI: 10.1021/bi00477a029

1989

Kuipers, O. P., Thunnissen, M. M. G. M., Geus, P. D., Dijkstra, B. W., Drenth, J., Verheij, H. M., & Haas, G. H. D. (1989). Enhanced Activity and Altered Specificity of Phospholipase A2 by Deletion of a Surface Loop. Science, 244(4900), 82-85. DOI: 10.1126/science.2704992
Kuipers, O. P., Dijkman, R., Pals, C. E. G. M., Verheij, H. M., & Haas, G. H. D. (1989). Evidence for the involvement of tyrosine-69 in the control of stereospecificity of porcine pancreatic phospholipase A2. %22Protein Engineering%2C Design and Selection%22, 2(6). DOI: 10.1093/protein/2.6.467

1987

Geus, P. D., Bergh, C. J. V. D., Kuipers, O., Verheij, H. M., Hoekstra, W. P. M., & Haas, G. H. D. (1987). Expression of porcine pancreatic phospholipase A2. Generation of active enzyme by sequence-specific cleavage of a hybrid protein from Escherichia coli. Nucleic Acids Research, 15(9). DOI: 10.1093/nar/15.9.3743

1986

Ley, P. V. D., Kuipers, O., Tommassen, J., & Lugtenberg, B. (1986). O-antigenic chains of lipopolysaccharide prevent binding of antibody molecules to an outer membrane pore protein in Enterobacteriaceae. Microbial Pathogenesis, 1(1). DOI: 10.1016/0882-4010(86)90030-6
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