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Kuipers, Prof. Oscar

Oscar Kuipers
Oscar Kuipers

Oscar Kuipers is professor of Molecular Genetics of Prokaryotes at the University of Groningen, and  a member of the department of Molecular Genetics of the Groningen Biomolecular Sciences and Biotechnology Institute.  Prokaryotes are micro-organisms without a nucleus, such as bacteria and Cyanobacteria. The field of molecular genetics studies gene functions and regulation and the interaction between genes. This research results, for example, in increasing knowledge about the gene modification of bacteria and is very important to biotechnology. Kuipers  studied Biology at Utrecht University and in 1990 gained his PhD in the department of Biochemistry of the same university. After that, he  worked at NIZO Food Research in Ede and the Wageningen Centre for Food Sciences.

Each year Kuipers supervises the (always successful) University of Groningen student team that competes in the iGEM competition in Boston. In 2012 this team became world champion, with a biological detection system to check how fresh meat is. In 2011 Kuipers received the ‘Simon Stevin Master' Award by the Technical Sciences Foundation (STW) and a grant of EUR 500,000 to spend on research. In the same year he became member of the prestigious Royal Netherlands Academy of Arts and Sciences (KNAW).  

At the end of May 2013, the EU awarded Kuipers a grant of € 1 million to make synthetic peptides, with particular attention to the development of new antibiotics.

Previously in the news

2020

Hernandez-Valdes, J. A., van Gestel, J., & Kuipers, O. P. (2020). A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium. Nature Communications, 11(1), [1203]. https://doi.org/10.1038/s41467-020-15017-1
Zhao, X., Yin, Z., Breukink, E., Moll, G. N., & Kuipers, O. P. (2020). An Engineered Double Lipid II Binding Motifs-Containing Lantibiotic Displays Potent and Selective Antimicrobial Activity against Enterococcus faecium. Antimicrobial Agents and Chemotherapy, 64(6), [ e02050-19]. https://doi.org/10.1128/AAC.02050-19
Boonstra, M., Schaffer, M., Sousa, J., Morawska, L., Holsappel, S., Hildebrandt, P., ... Kuipers, O. P. (2020). Analyses of competent and non-competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence. Environmental Microbiology, 22(6), 2312-2328. https://doi.org/10.1111/1462-2920.15005
Hernandez-Valdes, J. A., Huang, C., Kok, J., & Kuipers, O. P. (2020). Another Breaker of the Wall: the Biological Function of the Usp45 Protein of Lactococcus lactis. Applied and environmental microbiology, 86(16), [e00903-20]. https://doi.org/10.1128/AEM.00903-20
Caro-Astorga, J., Frenzel, E., Perkins, J. R., Álvarez-Mena, A., de Vicente, A., Ranea, J. A. G., ... Romero, D. (2020). Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus. NPJ biofilms and microbiomes, 6(1), [3]. https://doi.org/10.1038/s41522-019-0112-7
Li, Z., Song, C., Yi, Y., & Kuipers, O. P. (2020). Characterization of plant growth-promoting rhizobacteria from perennial ryegrass and genome mining of novel antimicrobial gene clusters. BMC Genomics, 21(1), [157]. https://doi.org/10.1186/s12864-020-6563-7
Li, Z., Chakraborty, P., de Vries, R. H., Song, C., Zhao, X., Roelfes, G., ... Kuipers, O. P. (2020). Characterization of two relacidines belonging to a novel class of circular lipopeptides that act against Gram-negative bacterial pathogens. Environmental Microbiology. https://doi.org/10.1111/1462-2920.15145
Marcelli, B., de Jong, A., Janzen, T., Serrano, M., Kok, J., & Kuipers, O. P. (2020). Complete Genome Sequences of 28 Lactococcal Bacteriophages Isolated from Failed Dairy Fermentation Processes. Microbiology resource announcements, 9(12), [e01535-19]. https://doi.org/10.1128/MRA.01535-19
Hernandez-Valdes, J. A., Solopova, A., & Kuipers, O. P. (2020). Development of Lactococcus lactis Biosensors for Detection of Diacetyl. Frontiers in Microbiology, 11, [1032]. https://doi.org/10.3389/fmicb.2020.01032
Hernandez-Valdes, J. A., Dalglish, M. M., Hermans, J., & Kuipers, O. P. (2020). Development ofLactococcus lactisBiosensors for Detection of Sulfur-Containing Amino Acids. Frontiers in Microbiology, 11, [1654]. https://doi.org/10.3389/fmicb.2020.01654
Hernandez-Valdes, J. A., de Jong, A., Kok, J., & Kuipers, O. P. (2020). Draft Genome Sequences of Three Amino Acid-Secreting Lactococcus lactis Strains. Microbiology resource announcements, 9(16), [e00158-20]. https://doi.org/10.1128/MRA.00158-20
Marcelli, B., Karsens, H., Nijland, M., Oudshoorn, R., Kuipers, O. P., & Kok, J. (2020). Employing lytic phage-mediated horizontal gene transfer in Lactococcus lactis. PLoS ONE, 15(9), [e0238988]. https://doi.org/10.1371/journal.pone.0238988
Xia, Y., Weng, Y., Xu, C., Wang, D., Pan, X., Tian, Z., ... Wu, W. (2020). Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa. Mbio, 11(3), [e00659-20]. https://doi.org/10.1128/mBio.00659-20
Hernandez-Valdes, J. A., Aan de Stegge, M., Hermans, J., Teunis, J., van Tatenhove-Pel, R. J., Teusink, B., ... Kuipers, O. P. (2020). Enhancement of amino acid production and secretion by Lactococcus lactis using a droplet-based biosensing and selection system. Metabolic Engineering Communications, 11, [e00133]. https://doi.org/10.1016/j.mec.2020.e00133
Zhao, X., Cebrian, R., Fu, Y., Rink, R., Bosma, T., Moll, G. N., & Kuipers, O. P. (2020). High-throughput screening for substrate specificity-adapted mutants of the nisin dehydratase NisB. ACS Synthetic Biology, 9(6), 1468-1478. https://doi.org/10.1021/acssynbio.0c00130
Hernandez-Valdes, J. A., Zhou, L., de Vries, M. P., & Kuipers, O. P. (2020). Impact of spatial proximity on territoriality among human skin bacteria. NPJ biofilms and microbiomes, 6(1), [30]. https://doi.org/10.1038/s41522-020-00140-0
Huang, C., Hernandez-Valdes, J. A., Kuipers, O. P., & Kok, J. (2020). Lysis of an Lactococcus lactis Dipeptidase Mutant and Rescue by Mutation in the Pleiotropic Regulator CodY. Applied and environmental microbiology, 86(8), [e02937-19]. https://doi.org/10.1128/AEM.02937-19
Zhao, X., Li, Z., & Kuipers, O. P. (2020). Mimicry of a Non-ribosomally Produced Antimicrobial, Brevicidine, by Ribosomal Synthesis and Post-translational Modification. Cell Chemical Biology, [j.chembiol.2020.07.005]. https://doi.org/10.1016/j.chembiol.2020.07.005
van Tilburg, A. Y., van Heel, A. J., Stülke, J., de Kok, N. A. W., Rueff, A-S., & Kuipers, O. P. (2020). MiniBacillus PG10 as a Convenient and Effective Production Host for Lantibiotics. ACS Synthetic Biology, 9(7), 1833-1842. [acssynbio.0c00194]. https://doi.org/10.1021/acssynbio.0c00194
Montalbán-López, M., Scott, T. A., Ramesh, S., Rahman, I. R., van Heel, A. J., Viel, J. H., ... van der Donk, W. A. (2020). New developments in RiPP discovery, enzymology and engineering. Natural product reports, [D0NP00027B]. https://doi.org/10.1039/d0np00027b
Li, Z., de Vries, R. H., Chakraborty, P., Song, C., Zhao, X., Scheffers, D-J., ... Kuipers, O. P. (2020). Novel modifications of nonribosomal peptides from Brevibacillus laterosporus MG64 and investigation of their mode of action. Applied and environmental microbiology, [AEM.01981-20]. https://doi.org/10.1128/AEM.01981-20
Deng, J., Viel, J. H., Chen, J., & Kuipers, O. P. (2020). Synthesis and Characterization of Heterodimers and Fluorescent Nisin Species by Incorporation of Methionine Analogs and Subsequent Click Chemistry. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.0c00308

2019

van Tatenhove-Pel, R. J., Hernandez-Valdes, J. A., Teusink, B., Kuipers, O. P., Fischlechner, M., & Bachmann, H. (2020). Microdroplet screening and selection for improved microbial production of extracellular compounds. Current Opinion in Biotechnology, 61, 72-81. https://doi.org/10.1016/j.copbio.2019.10.007
Marcelli, B., de Jong, A., Karsens, H., Janzen, T., Kok, J., & Kuipers, O. P. (2019). A specific sugar moiety in the Lactococcus lactis cell wall pellicle is required for infection by CHPC971, a member of the rare 1706 phage species. Applied and environmental microbiology, 85(19), [e01224-19]. https://doi.org/10.1128/AEM.01224-19
Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., ... Kuipers, O. P. (2019). Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evolutionary Biology, 19(1), [15]. https://doi.org/10.1186/s12862-018-1331-x
van Tatenhove-Pel, R. J., Zwering, E., Solopova, A., Kuipers, O. P., & Bachmann, H. (2019). Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells. Scientific Reports, 9(1), [9867]. https://doi.org/10.1038/s41598-019-46344-z
Schmitt, S., Montalbán-López, M., Peterhoff, D., Deng, J., Wagner, R., Held, M., ... Panke, S. (2019). Analysis of modular bioengineered antimicrobial lanthipeptides at nanoliter scale. Nature Chemical Biology, 15(5), 437-443. https://doi.org/10.1038/s41589-019-0250-5
Perez, M., Calles-Enríquez, M., Del Rio, B., Redruello, B., de Jong, A., Kuipers, O. P., ... Alvarez, M. A. (2019). Construction and characterization of a double mutant of Enterococcus faecalis that does not produce biogenic amines. Scientific Reports, 9(1), [16881]. https://doi.org/10.1038/s41598-019-53175-5
Cebrian, R., Macia-Valero, A., Jati, A. P., & Kuipers, O. P. (2019). Design and Expression of Specific Hybrid Lantibiotics Active Against Pathogenic Clostridium spp. Frontiers in Microbiology, 10, [2154]. https://doi.org/10.3389/fmicb.2019.02154
Li, Z., Song, C., de Jong, A., & Kuipers, O. P. (2019). Draft Genome Sequences of Six Bacillus Strains and One Brevibacillus Strain Isolated from the Rhizosphere of Perennial Ryegrass (Lolium perenne). Microbiology resource announcements, 8(4), [ARTN e01586-18]. https://doi.org/10.1128/MRA.01586-18
Zhou, L., Song, C., de Jong, A., & Kuipers, O. P. (2019). Draft Genome Sequences of 10 Paenibacillus and Bacillus sp. Strains Isolated from Healthy Tomato Plants and Rhizosphere Soil. Microbiology resource announcements, 8(12), [e00055-19]. https://doi.org/10.1128/MRA.00055-19
Solopova, A., van Tilburg, A. Y., Foito, A., Allwood, J. W., Stewart, D., Kulakauskas, S., & Kuipers, O. P. (2019). Engineering Lactococcus lactis for the production of unusual anthocyanins using tea as substrate. Metabolic Engineering, 54, 160-169. https://doi.org/10.1016/j.ymben.2019.04.002
Li, Q., Montalban-Lopez, M., & Kuipers, O. P. (2019). Feasability of Introducing a Thioether Ring in Vasopressin by nisBTC Co-expression in Lactococcus lactis. Frontiers in Microbiology, 10, [1508]. https://doi.org/10.3389/fmicb.2019.01508
Kaunietis, A., Buivydas, A., Čitavičius, D. J., & Kuipers, O. P. (2019). Heterologous biosynthesis and characterization of a glycocin from a thermophilic bacterium. Nature Communications, 10(1), [1115]. https://doi.org/10.1038/s41467-019-09065-5
van Tilburg, A. Y., Cao, H., van der Meulen, S. B., Solopova, A., & Kuipers, O. P. (2019). Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories. Current Opinion in Biotechnology, 59, 1-7. https://doi.org/10.1016/j.copbio.2019.01.007
Morabbi Heravi, K., Manzoor, I., Watzlawick, H., de Jong, A., Kuipers, O. P., & Altenbuchner, J. (2019). Phosphosugar stress in Bacillus subtilis: Intracellular accumulation of mannose 6-phosphate derepresed the glcR-phoC operon from repression by GlcR. Journal of Bacteriology, 201(9), [e00732-18]. https://doi.org/10.1128/JB.00732-18
de Vries, R., Viel, J., Oudshoorn, R., Kuipers, O., & Roelfes, G. (2019). Selective Modification of RiPPs via Diels-Alder Cycloadditions on Dehydroalanine Residues. Chemistry, 25(55), 12698–12702. https://doi.org/10.1002/chem.201902907
Motib, A. S., Al-Bayati, F. A. Y., Manzoor, I., Shafeeq, S., Kadam, A., Kuipers, O. P., ... Yesilkaya, H. (2019). TprA/PhrA Quorum Sensing System Has a Major Effect on Pneumococcal Survival in Respiratory Tract and Blood, and Its Activity Is Controlled by CcpA and GInR. Frontiers in Cellular and Infection Microbiology, 9, [326]. https://doi.org/10.3389/fcimb.2019.00326

2018

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. https://doi.org/10.1016/j.copbio.2018.09.004
Kuipers, O. P., & Li, Q. (2018). Antimicrobial peptides and admixtures thereof showing antimicrobial activity against gram-negative pathogens. (Patent No. WO2018231058).
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]. https://doi.org/10.3791/57551, https://doi.org/10.3791/57551
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. https://doi.org/10.1007/s11101-017-9532-2
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. https://doi.org/10.1093/nar/gky383
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. https://doi.org/10.1016/j.ymben.2018.08.001
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]. https://doi.org/10.3389/fmicb.2018.00547
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]. https://doi.org/10.1099/mgen.0.000157
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]. https://doi.org/10.3389/fmicb.2018.00657
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, 20(12), 4245-4260. https://doi.org/10.1111/1462-2920.14305
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]. https://doi.org/10.1128/mBio.01161-18
Solopova, A., Bachmann, H., Teusink, B., Kok, J., & Kuipers, O. P. (2018). Further Elucidation of Galactose Utilization in MG1363. Frontiers in Microbiology, 9, [1803]. https://doi.org/10.3389/fmicb.2018.01803
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. https://doi.org/10.1007/s00253-018-9000-y
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]. https://doi.org/10.1186/s13068-017-1008-5
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]. https://doi.org/10.1128/AEM.00052-18
Mulder, J., Wels, M., Kuipers, O. P., Kleerebezem, M., & Bron, P. A. (2018). Induction of Natural Competence in Genetically-modified Lactococcus lactis. Bio-Protocol, 8(13), [2922]. https://doi.org/10.21769/BioProtoc.2922
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]. https://doi.org/10.1186/s12934-018-0985-9
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]. https://doi.org/10.3389/fmicb.2018.00321
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]. https://doi.org/10.3389/fmicb.2018.01300
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), [57606]. https://doi.org/10.3791/57606
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]. https://doi.org/10.1038/s41598-018-24910-1
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. https://doi.org/10.3389/fmicb.2018.00160
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. https://doi.org/10.1016/j.freeradbiomed.2018.04.493

2017

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. https://doi.org/10.1111/1758-2229.12607
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.
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]. https://doi.org/10.1186/s12934-017-0674-0
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]. https://doi.org/10.3389/fcimb.2017.00210
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]. https://doi.org/10.3389/fmicb.2017.01487
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]. https://doi.org/10.1128/AEM.01279-17
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. https://doi.org/10.1093/femsre/fux036
Banin, E., Hughes, D., & Kuipers, O. P. (2017). Editorial: Bacterial pathogens, antibiotics and antibiotic resistance. FEMS Microbiology Reviews, 41(3), 450-452. [016]. https://doi.org/10.1093/femsre/fux016
Montalbán-López, M., van Heel, A. J., & Kuipers, O. P. (2017). Employing the promiscuity of lantibiotic biosynthetic machineries to produce novel antimicrobials. FEMS Microbiology Reviews, 41(1), 5-18. [fuw034]. https://doi.org/10.1093/femsre/fuw034
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. https://doi.org/10.1007/s00253-016-7822-z
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]. https://doi.org/10.1128/mBio.01963-17
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]. https://doi.org/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. https://doi.org/10.1111/mmi.13764
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]. https://doi.org/10.1093/femsre/fux014
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]. https://doi.org/10.1002/anie.201709313
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]. https://doi.org/10.3389/fcimb.2017.00070
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 ]. https://doi.org/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]. https://doi.org/10.3389/fmicb.2017.00124
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]. https://doi.org/10.1128/AEM.03122-16
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. https://doi.org/10.1093/femsre/fux028
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]. https://doi.org/10.3389/fmicb.2017.02107
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]. https://doi.org/10.3389/fmicb.2017.01273
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. https://doi.org/10.1016/j.ijfoodmicro.2017.05.017
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]. https://doi.org/10.1128/AEM.01320-17
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. https://doi.org/10.1111/1462-2920.13454

2016

Yi, Y., & Kuipers, O. P. (2017). Development of an efficient electroporation method for rhizobacterial Bacillus mycoides strains. Journal of microbiological methods, 133, 82-86. https://doi.org/10.1016/j.mimet.2016.12.022
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]. https://doi.org/10.1038/ismej.2016.59
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. https://doi.org/10.1111/1462-2920.13386
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. https://doi.org/10.1146/annurev-food-041715-033144
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. https://doi.org/10.1007/s00253-016-7343-9
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]. https://doi.org/10.3389/fmicb.2016.01929
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]. https://doi.org/10.1021/acssynbio.6b00033
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]. https://doi.org/10.1128/genomeA.00031-16
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]. https://doi.org/10.1128/genomeA.00105-16
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]. https://doi.org/10.1128/genomeA.01129-16
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]. https://doi.org/10.1128/genomeA.00124-16
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]. https://doi.org/10.1128/genomeA.00560-16
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]. https://doi.org/10.1128/genomeA.00485-16
Afzal, M., Shafeeq, S., Manzoor, I., & Kuipers, O. P. (2016). 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. https://doi.org/10.1159/000439429
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]. https://doi.org/10.1128/genomeA.00103-16
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]. https://doi.org/10.3389/fmicb.2016.01912
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]. https://doi.org/10.1186/s12864-016-3224-y
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]. https://doi.org/10.3389/fmicb.2016.01564
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. https://doi.org/10.1007/s00726-016-2186-3
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]. https://doi.org/10.1371/journal.pone.0156796
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]. https://doi.org/10.1099/mgen.0.000091
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]. https://doi.org/10.3389/fcimb.2016.00101
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]. https://doi.org/10.3389/fcimb.2016.00158
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. https://doi.org/10.1016/j.chembiol.2016.03.001
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]. https://doi.org/10.3389/fcell.2016.00007
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. https://doi.org/10.1111/1751-7915.12285
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. https://doi.org/10.1074/jbc.M116.714303
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]. https://doi.org/10.3389/fmicb.2016.01607
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. https://doi.org/10.1099/mic.0.000320
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. https://doi.org/10.1016/j.gdata.2015.12.003
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. https://doi.org/10.1016/j.gdata.2016.06.012

2015

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]. https://doi.org/10.1128/mBio.00581-15
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, [e52649]. https://doi.org/10.3791/52649
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. https://doi.org/10.1038/ja.2015.71
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. https://doi.org/10.1128/AEM.00959-15
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]. https://doi.org/10.3389/fmicb.2015.00072
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]. https://doi.org/10.1128/AEM.01993-15
Kuipers, O. P. (2015). Back to Nature: a revival of natural strain improvement methodologies. Microbial Biotechnology, 8(1), 17-18. https://doi.org/10.1111/1751-7915.12232
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]. https://doi.org/10.1128/genomeA.00098-15
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]. https://doi.org/10.3389/fmicb.2015.00748
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]. https://doi.org/10.1128/genomeA.01539-14
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]. https://doi.org/10.1128/genomeA.00165-15
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), 120-128. https://doi.org/10.1159/000377724
Berendsen, E. M., Bennik, M. H. J., & Kuipers, O. P. (2015). Heat resistant microorganism. (Patent No. WO2015126251).
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]. https://doi.org/10.3389/fmicb.2015.00102
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. https://doi.org/10.1128/AEM.00475-15
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]. https://doi.org/10.1371/journal.pone.0127579
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. https://doi.org/10.1016/j.mib.2015.04.008
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. https://doi.org/10.1038/nchembio.1890
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]. https://doi.org/10.1128/genomeA.01480-15
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]. https://doi.org/10.1371/journal.pone.0142839
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. https://doi.org/10.1128/AEM.00944-15
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]. https://doi.org/10.3389/fmicb.2015.01051
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. https://doi.org/10.1111/mmi.13012
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), 3121-3131. https://doi.org/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]. https://doi.org/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]. https://doi.org/10.1371/journal.pgen.1005140
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]. https://doi.org/10.3389/fmicb.2015.00011
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]. https://doi.org/10.3389/fcimb.2015.00091
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]. https://doi.org/10.3389/fmicb.2015.01041
Overkamp, W., & Kuipers, O. P. (2015). Transcriptional Profile of Bacillus subtilis sigF-Mutant during Vegetative Growth. PLoS ONE, 10(10), [e0141553]. https://doi.org/10.1371/journal.pone.0141553
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. https://doi.org/10.1016/j.gdata.2015.02.004
Manzoor, I., Shafeeq, S., & Kuipers, O. (2015). Transcriptome analysis of Streptococcus pneumoniae D39 in the presence of cobalt. Genomics Data, 6, 151-153. https://doi.org/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. https://doi.org/10.1016/j.gdata.2015.10.002
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]. https://doi.org/10.1186/s12864-015-1834-4
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(Part A), 18-25. https://doi.org/10.1016/j.fm.2014.04.009
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(1), 41-49. https://doi.org/10.1099/mic.0.083899-0

2014

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. https://doi.org/10.1111/1462-2920.12564
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. https://doi.org/10.1021/sb500229s
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. https://doi.org/10.1111/1462-2920.12676
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. https://doi.org/10.1021/sb5000252
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. https://doi.org/10.1038/nrmicro3178
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. https://doi.org/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. https://doi.org/10.1111/1462-2920.12239
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. https://doi.org/10.1074/jbc.M114.562066
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. https://doi.org/10.1093/nar/gku790
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. https://doi.org/10.1038/ismej.2014.52
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)).
İrigül-Sönmez, Ö., Köroğlu, T. E., Öztürk, B., Kovács, Á. T., Kuipers, O. P., & Yazgan-Karataş, A. (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. https://doi.org/10.1099/mic.0.064675-0
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. https://doi.org/10.1128/AEM.01370-14
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. https://doi.org/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. https://doi.org/10.1038/ismej.2013.128
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. https://doi.org/10.1164/rccm.201311-2110OC
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. https://doi.org/10.1093/nar/gkt1007
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. https://doi.org/10.1128/IAI.02336-14
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. https://doi.org/10.1128/JB.00826-13
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.

2013

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]. https://doi.org/10.1371/journal.pone.0072167
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. https://doi.org/10.1093/nar/gkt391
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. https://doi.org/10.1128/AEM.02033-13
Shafeeq, S., Kuipers, O. P., & Kloosterman, T. G. (2013). Cellobiose-Mediated Gene Expression in Streptococcus pneumoniae: A Repressor Function of the Novel GntR-Type Regulator BguR. PLoS ONE, 8(2), [e57586]. https://doi.org/10.1371/journal.pone.0057586
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. https://doi.org/10.1128/JB.01475-12
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. https://doi.org/10.1021/sb3001084
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]. https://doi.org/10.1371/journal.pone.0058492
Kovacs, A., Eckhardt, T., van Kranenburg, R., & Kuipers, O. (2013). Functional Analysis of the ComK Protein of Bacillus coagulans. PLoS ONE, 8(1), [ e53471]. https://doi.org/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. https://doi.org/10.1016/j.fob.2013.05.001
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. https://doi.org/10.1128/AEM.01347-13
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]. https://doi.org/10.1371/journal.pone.0068470
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. https://doi.org/10.1021/bi4008116
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]. https://doi.org/10.1371/journal.pone.0068277
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. https://doi.org/10.1039/c2np20085f
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. https://doi.org/10.1111/mmi.12141
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]. https://doi.org/10.1371/journal.pone.0074890
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. https://doi.org/10.1111/mmi.12256
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]. https://doi.org/10.1371/journal.pone.0053085
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. https://doi.org/10.1128/JB.02043-12
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. https://doi.org/10.1128/AEM.00866-13

2012

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. https://doi.org/10.1128/AEM.00455-12
Shafeeq, S., Kloosterman, T. G., Rajendran, V., & Kuipers, O. P. (2012). Characterization of the ROK-family transcriptional regulator RokA of Streptococcus pneumoniae D39. Microbiology-Sgm, 158(12), 2917-2926. https://doi.org/10.1099/mic.0.062919-0
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. https://doi.org/10.1111/j.1462-2920.2012.02766.x
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]. https://doi.org/10.1186/1475-2859-11-66
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]. https://doi.org/10.1371/journal.pone.0048015
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. https://doi.org/10.1111/j.1574-6976.2011.00323.x
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]. https://doi.org/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. https://doi.org/10.1517/17460441.2012.693476
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]. https://doi.org/10.1186/1471-2164-13-299
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. https://doi.org/10.1128/IAI.05563-11
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. https://doi.org/10.1128/JB.00324-12
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. https://doi.org/10.1111/j.1462-2920.2012.02892.x
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.
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. https://doi.org/10.1111/j.1365-2958.2012.08101.x
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. https://doi.org/10.1128/AAC.01206-12
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. https://doi.org/10.1002/cbic.201200437
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.

2011

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. https://doi.org/10.1007/978-1-61779-433-9_8
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. https://doi.org/10.1111/j.1751-7915.2011.00270.x
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. https://doi.org/10.1016/j.copbio.2010.11.009
Kuipers, O. (2011). Bacteriele bendes: samen sterk door Quorum sensing. In H. Smit, & P. Willemsen (Eds.), De Microcanon [Hoofdstuk 19] VBK Media.
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. https://doi.org/10.1002/bies.201000127
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. https://doi.org/10.1016/j.copbio.2010.10.016
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]. https://doi.org/10.1371/journal.pone.0026707
Shafeeq, S., Kloosterman, T. G., & Kuipers, O. P. (2011). CeIR-mediated activation of the cellobiose-utilization gene cluster in Streptococcus pneumoniae. Microbiology-Sgm, 157(10), 2854-2861. https://doi.org/10.1099/mic.0.051359-0
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.
Neef, J., Farshchi Andisi, V., Kim, K. S., Kuipers, O. P., & Bijlsma, J. J. E. (2011). Deletion of a Cation Transporter Promotes Lysis in Streptococcus pneumoniae. Infection and Immunity, 79(6), 2314-2323. https://doi.org/10.1128/IAI.00677-10
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. https://doi.org/10.1111/j.1365-2958.2011.07846.x
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]. https://doi.org/10.1371/journal.pone.0021859
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]. https://doi.org/10.1371/journal.pone.0021873
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. https://doi.org/10.1517/17425255.2011.573478
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. https://doi.org/10.1007/978-1-4419-7692-5_5
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. https://doi.org/10.3791/3145
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., 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. https://doi.org/10.1128/AEM.05196-11
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. https://doi.org/10.1074/jbc.M111.295832
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. https://doi.org/10.1128/JB.00264-11
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. https://doi.org/10.1007/978-0-387-92771-8_8
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. https://doi.org/10.1128/JB.01170-10
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. https://doi.org/10.1517/14712598.2011.542138
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. https://doi.org/10.1111/j.1365-2958.2011.07758.x
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. https://doi.org/10.1128/AEM.06107-11
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]. https://doi.org/10.1371/journal.pone.0024060
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]. https://doi.org/10.1371/journal.pone.0027160
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. https://doi.org/10.1039/c1mt00030f
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]. https://doi.org/10.1371/journal.pone.0024304
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. https://doi.org/10.1016/j.copbio.2011.02.001

2010

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). https://doi.org/10.1186/1471-2164-11-1
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. https://doi.org/10.1093/nar/gkq365
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. https://doi.org/10.1128/JB.00058-10
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. https://doi.org/10.1111/j.1365-2958.2010.07113.x
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. https://doi.org/10.1128/AAC.00769-09
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. https://doi.org/10.1128/AEM.03060-09
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. https://doi.org/10.1128/JB.01484-09
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. https://doi.org/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. https://doi.org/10.1111/j.1365-2958.2010.07188.x
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. https://doi.org/10.1128/AAC.00883-09
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. https://doi.org/10.1093/bioinformatics/btq535
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. https://doi.org/10.1128/AEM.01195-10

2009

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. https://doi.org/10.1111/j.1365-2958.2008.06564.x
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. https://doi.org/10.1128/JB.01616-08
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. https://doi.org/10.1074/jbc.M109.026690
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. https://doi.org/10.1099/mic.0.027987-0
Leenhouts, C., Ramasamy, R., Steen, A., KOK, JAAM., 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)).
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. https://doi.org/10.1128/MMBR.00037-08
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. https://doi.org/10.1093/bioinformatics/btn588
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. https://doi.org/10.1093/bioinformatics/btp013
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. https://doi.org/10.1128/JB.01264-08
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]. https://doi.org/10.1186/1471-2180-9-227
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. https://doi.org/10.1099/mic.0.025072-0
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. https://doi.org/10.1128/JB.00215-09
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. https://doi.org/10.1111/j.1742-4658.2008.06776.x
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. https://doi.org/10.1111/j.1462-2920.2009.01937.x

2008

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. https://doi.org/10.1016/j.jmb.2007.11.002
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. https://doi.org/10.1074/jbc.M708134200
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]. https://doi.org/10.1186/1471-2180-8-62
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. https://doi.org/10.1073/pnas.0700463105
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. https://doi.org/10.1007/s00018-007-7171-2
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. https://doi.org/10.1146/annurev.micro.62.081307.163002
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. https://doi.org/10.1128/JB.00917-07
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]. https://doi.org/10.1186/1471-2105-9-535
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. https://doi.org/10.1128/AEM.00136-08
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. https://doi.org/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. https://doi.org/10.1111/j.1751-7915.2008.00023.x
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. https://doi.org/10.1128/AEM.00112-08
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.
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. https://doi.org/10.1128/JB.01151-07
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. https://doi.org/10.1111/j.1365-2958.2008.06211.x
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. https://doi.org/10.1128/JB.00307-08
Nijland, R., & Kuipers, O. P. (2008). Optimization of protein secretion by Bacillus subtilis. Recent patents on biotechnology, 2, 79 - 87. https://doi.org/10.2174/187220808784619694
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.
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]. https://doi.org/10.1186/1471-2164-9-495
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. https://doi.org/10.1128/AEM.00103-08
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. https://doi.org/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]. https://doi.org/10.1186/1471-2105-9-93
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. https://doi.org/10.1128/JB.00485-08
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. https://doi.org/10.1016/j.jmb.2007.09.087
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. https://doi.org/10.1093/bib/bbn019
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. https://doi.org/10.1128/AEM.00117-08
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]. https://doi.org/10.1038/msb.2008.18
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. https://doi.org/10.1111/j.1467-8659.2008.01221.x
Kuipers, O. P., Poolman, B., & Hugenholtz, J. (2008). 9th International Symposium on Lactic Acid Bacteria. Applied and environmental microbiology, 74(15), 4589.
Kuipers, O. P., Poolman, B., & Hugenholtz, J. (2008). 9th International Symposium on lactic acid bacteria. Applied and environmental microbiology, 74(15), 4589-4589. https://doi.org/10.1128/AEM.01384-08

2007

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. https://doi.org/10.1128/AEM.02266-06
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. https://doi.org/10.1128/JB.00281-07
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. https://doi.org/10.1111/j.1365-2958.2007.05662.x
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. https://doi.org/10.1111/j.1365-2958.2007.05668.x
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. https://doi.org/10.1128/AEM.02356-06
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. https://doi.org/10.1128/AEM.01273-07
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. https://doi.org/10.1128/JB.01768-06
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. https://doi.org/10.1128/AEM.01900-06
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. https://doi.org/10.1128/AEM.01104-07
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. https://doi.org/10.1016/j.idairyj.2006.05.013
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. https://doi.org/10.1093/bioinformatics/btl658
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. https://doi.org/10.1016/j.jbiotec.2006.07.014
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. https://doi.org/10.1128/JB.00473-07
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. https://doi.org/10.1016/j.idairyj.2006.12.007
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.
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. https://doi.org/10.1021/bi700106z
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. https://doi.org/10.1128/AEM.02751-06
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. https://doi.org/10.1128/AEM.00472-07
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. https://doi.org/10.1128/AEM.02350-06
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. https://doi.org/10.1128/JB.01144-06
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. https://doi.org/10.1128/jb.00573-07
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. https://doi.org/10.1074/jbc.M611308200
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. https://doi.org/10.1111/j.1365-2958.2007.05776.x
Romero, D., de Vicente, A., Rakotoaly, R. H., Dufour, S. E., Veening, J-W., Arrebola, E., ... Perez-Garcia, A. (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. https://doi.org/10.1094/MPMI-20-4-0430
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.
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. https://doi.org/10.1111/j.1365-2958.2007.05849.x
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. https://doi.org/10.1128/JB.01013-06
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. https://doi.org/10.1159/000096463

2006

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. https://doi.org/10.1128/AEM.01176-06
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. https://doi.org/10.1126/science.1129818
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. https://doi.org/10.1093/nar/gkl237
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. https://doi.org/10.1099/mic.0.29113-0
Veening, JW., Kuipers, OP., Brul, S., Hellingwerf, KJ., & 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. https://doi.org/10.1128/JB.188.8.3099-3109.2006
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. https://doi.org/10.1128/AEM.72.1.404-411.2006
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. https://doi.org/10.1099/mic.0.28357-0
Westenberg, M. A., van Hijum, S. A. F. T., Kuipers, O. P., & Roerdink, J. B. T. M. (2006, May 29). Gene expression and network visualization.
Westenberg, M. A., van Hijum, S. A. F. T., Kuipers, O. P., & Roerdink, J. B. T. M. (2006, Apr 24). GENeVis: Gene expression and network visualization.
Larsen, R., Kloosterman, TG., Kok, J., & Kuipers, OP. (2006). GlnR-mediated regulation of nitrogen metabolism in Lactococcus lactis. Journal of Bacteriology, 188(13), 4978-4982. https://doi.org/10.1128/JB.00025-06
den Hengst, CD., Groeneveld, M., Kuipers, OP., 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. https://doi.org/10.1128/JB.188.9.3280-3289.2006
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. https://doi.org/10.1128/JB.01049-06
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. https://doi.org/10.1111/j.1365-2958.2006.05267.x
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).
van Roosmalen, ML., 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. https://doi.org/10.1016/j.ymeth.2005.09.015
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. https://doi.org/10.1016/j.ymben.2006.05.003
Bosma, T., Kanninga, R., Neef, J., Audouy, SAL., van Roosmalen, ML., 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. https://doi.org/10.1128/AEM.72.1.880-889.2006
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. https://doi.org/10.1038/nrmicro1381
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. https://doi.org/10.1074/jbc.M601661200
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. https://doi.org/10.1128/AEM.01802-06
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]. https://doi.org/10.1186/1471-2105-7-205
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. https://doi.org/10.1111/j.1365-2672.2006.02911.x
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. https://doi.org/10.1074/jbc.M607044200
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.
Kloosterman, TG., Bijlsma, J. J. E., Kok, J., & Kuipers, OP. (2006). To have neighbour's fare: extending the molecular toolbox for Streptococcus pneumoniae. Microbiology, 152, 351-359. https://doi.org/10.1099/mic.0.28521-0
Kramer, NE., Van Hijum, SAFT., Knol, J., Kok, J., Kuipers, OP., & Kramer, N. E. (2006). Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance. Antimicrobial Agents and Chemotherapy, 50(5), 1753-1761. https://doi.org/10.1128/AAC.50.5.1753-1761.2006
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. https://doi.org/10.1016/j.mimet.2006.01.005

2005

van Hijum, SAFT., de Jong, A., Baerends, RJS., Karsens, HA., Kramer, NE., 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]. https://doi.org/10.1186/1471-2164-6-77
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). https://doi.org/10.1186/gb-2005-6-4-p4
Steen, A., Buist, G., Horsburgh, GJ., Venema, G., Kuipers, OP., Foster, SJ., ... 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. https://doi.org/10.1111/j.1742-4658.2005.04706.x
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. https://doi.org/10.1128/JB.187.1.114-124.2005
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. https://doi.org/10.1016/j.fmrre.2005.04.004
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. https://doi.org/10.1128/AEM.71.12.8818-8824.2005
Barrière, C., Veiga-da-Cunha, M., Pons, N., Guédon, 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. Journal of Bacteriology, 187(11), 3752-3761. https://doi.org/10.1128/JB.187.11.3752-3761.2005
Larsen, R., Kok, J., & Kuipers, OP. (2005). Interaction between ArgR and AhrC controls regulation of arginine metabolism in Lactococcus lactis. The Journal of Biological Chemistry, 280(19), 19319-19330. https://doi.org/10.1074/jbc.M413983200
de Vos, W. M., Kleerebezem, M., & Kuipers, O. P. (2005). Lactic acid bacteria - Genetics, metabolism and application. FEMS Microbiol.Rev., 29(3), 391.
Rink, R., Kuipers, A., de Boef, E., Leenhouts, KJ., Driessen, AJM., Moll, GN., ... 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. https://doi.org/10.1021/bi050081h
den Hengst, C., Gajic, O., Kuipers, O., Kok, J., Sikkema, J., Geurts, JMW., & Nauta, A. (2005). IPC No. C12N 15/ 74 A I. Methods and means for regulating gene expression. (Patent No. WO2005003354).
Neves, AR., Pool, WA., Kok, J., Kuipers, OP., 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. https://doi.org/10.1016/j.fmrre.2005.04.005
Veening, JW., Hamoen, LW., & Kuipers, OP. (2005). Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis. Molecular Microbiology, 56(6), 1481-1494. https://doi.org/10.1111/j.1365-2958.2005.04659.x
Kluskens, LD., Kuipers, A., Rink, R., de Boef, E., Fekken, S., Driessen, AJM., ... Moll, GN. (2005). Post-translational modification of therapeutic peptides by NisB, the dehydratase of the lantibiotic nisin. Biochemistry, 44(38), 12827-12834. https://doi.org/10.1021/bi050805p
den Hengst, CD., 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. https://doi.org/10.1128/JB.187.2.512-521.2005
van Hijum, SAFT., Zomer, AL., Kuipers, OP., & 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. https://doi.org/10.1093/nar/gki356
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. https://doi.org/10.1111/j.1365-2958.2005.04488.x
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. https://doi.org/10.1074/jbc.M502349200
Albano, M., Smits, WK., Ho, LTY., Kraigher, B., Mandic-Mulec, N. V., Kuipers, OP., ... 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. https://doi.org/10.1128/JB.187.6.2010-2019.2005
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. https://doi.org/10.1128/JB.187.12.3921-3930.2005

2004

Larsen, R., Buist, G., Kuipers, OP., & Kok, J. (2004). ArgR and AhrC are both required for regulation of arginine metabolism in Lactococcus lactis. Journal of Bacteriology, 186(4), 1147-1157. https://doi.org/10.1128/JB.186.4.1147-1157.2004
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. https://doi.org/10.1016/j.peptides.2003.11.025
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. https://doi.org/10.1128/JB.186.4.1097-1105.2004
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. https://doi.org/10.1111/j.1365-2672.2004.02179.x
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]. https://doi.org/10.1186/gb-2004-5-5-r37
Kuipers, OP. (2004). Genomics and bioinformatics enhance research on food and gut bacteria - Editorial overview. Current Opinion in Biotechnology, 15(2), 83-85. https://doi.org/10.1016/j.copbio.2004.03.003
Susanna, KA., van der Werff, AF., den Hengst, CD., Calles, B., Salas, M., Venema, G., ... Kuipers, OP. (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. https://doi.org/10.1128/JB.186.4.1120-1128.2004
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. https://doi.org/10.1093/bioinformatics/bth206
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. https://doi.org/10.1074/jbc.M312789200
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. https://doi.org/10.1128/mmbr.68.2.207-233.2004
Kramer, NE., Smid, EJ., Kok, J., de Kruijff, B., Kuipers, OP., 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. https://doi.org/10.1016/j.femsle.2004.08.033
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. https://doi.org/10.1111/j.1365-2958.2004.04278.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. https://doi.org/10.1078/0723-2020-00258
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. https://doi.org/10.1111/j.1472-765X.2004.01539.x
Veening, JW., Smits, WK., Hamoen, LW., Jongbloed, JDH., Kuipers, OP., & 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. https://doi.org/10.1128/AEM.70.11.6809-6815.2004

2003

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).
Steen, A., Buist, G., Leenhouts, KJ., El Khattabi, M., Grijpstra, F., Zomer, AL., ... 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. https://doi.org/10.1074/jbc.M211055200
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). https://doi.org/10.1073/pnas.0337704100
Hamoen, LW., Venema, G., & Kuipers, OP. (2003). Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology-Sgm, 149(1), 9-17. https://doi.org/10.1099/mic.0.26003-0
Kemperman, R., Jonker, M., Nauta, A., Kuipers, OP., & 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. https://doi.org/10.1128/AEM.69.10.5839-5848.2003
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. https://doi.org/10.1093/molbev/msg219
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. https://doi.org/10.1128/AEM.69.3.1589-1597.2003
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, OP., & 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. https://doi.org/10.1074/jbc.M211100200
van Hijum, SAFT., Zomer, AL., Kuipers, OP., & Kok, J. (2003). Projector: automatic contig mapping for gap closure purposes. Nucleic Acids Research, 31(22), [144]. https://doi.org/10.1093/nar/gng144
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. https://doi.org/10.1046/j.1365-2958.2003.03565.x
van Hijum, SAFT., de Jong, A., Buist, G., Kok, J., & Kuipers, OP. (2003). UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons. Bioinformatics, 19(12), 1580-1582. https://doi.org/10.1093/bioinformatics/btg203

2002

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. https://doi.org/10.1128/JB.184.20.5661-5671.2002
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. https://doi.org/10.1023/A:1020638309912
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, LW., Smits, WK., de Jong, A., Holsappel, S., Kuipers, OP., & 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. https://doi.org/10.1093/nar/gkf698
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. https://doi.org/10.1128/JB.184.1.82-90.2002
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. https://doi.org/10.1023/A:1020691801251

2001

Kleerebezem, M., Kuipers, OP., de Vos, WM., Stiles, ME., Quadri, LEN., 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. https://doi.org/10.1016/S0196-9781(01)00494-6
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). https://doi.org/10.1128/JB.183.4.1184-1194.2001
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). https://doi.org/10.1007/s00203-001-0361-7
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). https://doi.org/10.1128/AEM.67.11.5171-5178.2001
Kuipers, O. P. (2001). Complete DNA sequence of Lactococcus lactis adds flavor to genomics. Genome Research, 11(5), 673-674. https://doi.org/10.1101/gr.188501
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.
Kuipers, O. (2001). Leven in een notendop: een genomische benadering van bacteriën. s.n.
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).
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). https://doi.org/10.1128/JB.183.11.3391-3398.2001
Wiedemann, N. V., Breukink, E., van Kraaij, C., Kuipers, O. P., Bierbaum, G., de Kruijff, B., & Sahl, HA. (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. https://doi.org/10.1074/jbc.M006770200

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). https://doi.org/10.1128/AEM.66.9.3686-3691.2000
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. Applied Environmental Microbiology, 66(4), 1360-1368.
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). https://doi.org/10.1128/JB.182.21.5982-5989.2000
Kuipers, O. P., Buist, G., & Kok, J. (2000). Current strategies for improving food bacteria. Research in Microbiology, 151(10), 815-822. https://doi.org/10.1016/S0923-2508(00)01147-5
van Kraaij, C., Breukink, E., Rollema, HS., Bongers, RS., Kosters, HA., 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. https://doi.org/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. https://doi.org/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. Applied Environmental Microbiology, 6(1), 42-48. https://doi.org/10.1128/aem.66.1.42-48.2000
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). https://doi.org/10.1128/AEM.66.9.3756-3763.2000
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). https://doi.org/10.1128/JB.182.17.4738-4743.2000
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. https://doi.org/10.1016/S0723-2020(00)80001-6

1999

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. Microbiology, 145(11), 3185–3194. https://doi.org/10.1099/00221287-145-11-3185
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. Journal of Bacteriology, 181(6), 1924–1926.
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. Applied Environmental Microbiology, 65(10), 4436–4442.
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. https://doi.org/10.1023/A:1002021812783
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). https://doi.org/10.1099/13500872-145-5-1227
Kuipers, OP. (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. https://doi.org/10.1016/S0958-1669(99)00019-1
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.
van Kraaij, C., de Vos, WM., Siezen, RJ., Kuipers, OP., Vos, W. M. D., & Siezen, R. J. (1999). Lantibiotics: biosynthesis, mode of action and applications. Natural product reports, 16(5), 575-587. https://doi.org/10.1039/a804531c
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. Journal of Bacteriology, 181(3), 764–771. https://doi.org/10.1128/JB.181.3.764-771.1999
Konings, WN., in't Veld, JHJH., & Kuipers, OP. (1999). The sixth symposium on Lactic Acid Bacteria. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 76(1-4), 1-1.
Breukink, E., Wiedemann, N. V., van Kraaij, C., Kuipers, OP., Sahl, HG., 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. https://doi.org/10.1126/science.286.5448.2361

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. https://doi.org/10.1099/00221287-144-10-2885
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). https://doi.org/10.1016/S0958-6946(98)00049-1
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). https://doi.org/10.1021/bi980931b
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). https://doi.org/10.1016/S0168-1656(98)00100-X
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). https://doi.org/10.1021/bi972797l
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). https://doi.org/10.1046/j.1365-2958.1998.01111.x
Eichenbaum, Z., Federle, MJ., Marra, D., De Vos, WM., Kuipers, OP., Kleerebezem, M., & Scott, J. A. (1998). Use of the lactococcal nisA promoter to regulate gene expression in gram-positive bacteria: Comparison of induction level and promoter strength. Applied and environmental microbiology, 64(8), 2763-2769.

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. Journal of Bacteriology, 179(19), 6163–6171. https://doi.org/10.1128/jb.179.19.6163-6171.1997
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). https://doi.org/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). https://doi.org/10.1016/S0958-1669(97)80027-4
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). https://doi.org/10.1038/nbt1097-976
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). https://doi.org/10.1111/j.1432-1033.1997.00114.x
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). https://doi.org/10.1046/j.1365-2958.1997.4251782.x
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). https://doi.org/10.1021/bi9713106
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). https://doi.org/10.1021/bi970008u

1996

Siezen, R. J., Kuipers, O. P., & Vos, W. M. D. (1996). Comparison of lantibiotic gene clusters and encoded proteins. Antonie van Leeuwenhoek, 69(2). https://doi.org/10.1007/BF00399422
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. Applied Environmental Microbiology, 62(10), 3662–3667. https://doi.org/10.1128/AEM.62.10.3662-3667.1996
deRuyter, PGGA., Kuipers, OP., Beerthuyzen, MM., vanAlenBoerrigter, IJ., & deVos, WM. (1996). Functional analysis of promoters in the nisin gene cluster of Lactococcus lactis. Journal of Bacteriology, 178(12), 3434-3439. https://doi.org/10.1128/jb.178.12.3434-3439.1996
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). https://doi.org/10.1111/j.1432-1033.1996.00267.x
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. https://doi.org/10.1007/BF00399421
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). https://doi.org/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). https://doi.org/10.1016/0014-5793(96)00771-5

1995

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). https://doi.org/10.1074/jbc.270.45.27299
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). https://doi.org/10.1111/j.1432-1033.1995.tb20600.x
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). https://doi.org/10.1093/protein/8.2.117
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).
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). https://doi.org/10.1111/j.1365-2958.1995.mmi_17030427.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). https://doi.org/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. The Journal of Biological Chemistry, 269(5), 3555-3562.

1993

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). https://doi.org/10.1016/0014-5793(93)80911-D
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. Journal of Bacteriology, 175(9), 2578-2588. https://doi.org/10.1128/JB.175.9.2578-2588.1993
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). https://doi.org/10.1111/j.1432-1033.1993.tb18143.x
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). https://doi.org/10.1093/nar/21.3.777
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. The Journal of Biological Chemistry, 268(22), 16361-16368.

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. The Journal of Biological Chemistry, 267(34), 24340-24346.

1991

Kuipers, O. P., Boot, H. J., & Vos, W. M. D. (1991). Improved site-directed mutagenesis method using PCR. Nucleic Acids Research, 19(16). https://doi.org/10.1093/nar/19.16.4558
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). https://doi.org/10.1021/bi00100a008

1990

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). https://doi.org/10.1021/bi00477a029
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). https://doi.org/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). https://doi.org/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).
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. https://doi.org/10.1038/347689a0

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. https://doi.org/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). https://doi.org/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). https://doi.org/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). https://doi.org/10.1016/0882-4010(86)90030-6
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