Grande Burgos, María J, Kovács, Ákos T, Mirończuk, Aleksandra M, Abriouel, Hikmate, Gálvez, Antonio, Kuipers, Oscar P
Abstract Background Enterocin AS-48 is produced by Enterococcus faecalis S48 to compete with other bacteria in their environment. Due to its activity against various Gram positive and some Gram...
Castro, Rute, Neves, Ana R., Fonseca, Luís L., Pool, Wietske A., Kok, Jan, Kuipers, Oscar P., ...
According to previous reports, Lactococcus lactis imports glucose via two distinct phosphoenolpyruvate:phosphotransferase systems (mannose-PTS and cellobiose-PTS) and one or more unknown non-PTS...
Barnett, James P., Ploeg, René Van Der, Eijlander, Robyn T., Nenninger, Anja, Mendel, Sharon, Rozeboom, Rense, ...
The twin arginine translocation (Tat) system transports folded proteins across the bacterial plasma membrane. In Gram-negative bacteria, membrane-bound TatABC subunits are all essential for activity,...
Hendriksen, Wouter T., Bootsma, Hester J., Diepen, Angela Van, Estevão, Silvia, Kuipers, Oscar P., Groot, Ronald De, ...
Previous studies have indicated that PsaR of Streptococcus pneumoniae is a manganese-dependent regulator, negatively affecting the expression of at least seven genes. Here, we extended these...
Copper Acquisition Is Mediated by YcnJ and Regulated by YcnK and CsoR in Bacillus subtilis (2009)
Chillappagari, Shashi, Miethke, Marcus, Trip, Hein, Kuipers, Oscar P., Marahiel, Mohamed A.
Copper is an essential cofactor for many enzymes, and at over a threshold level, it is toxic for all organisms. To understand the mechanisms underlying copper homeostasis of the gram-positive...
Blom, Evert-Jan, Kuipers, Oscar P.
Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify...
Eijlander, Robyn T., Jongbloed, Jan D.H., Kuipers, Oscar P.
Protein translocation via the twin arginine translocation (TAT) pathway is characterized by the translocation of prefolded proteins across the hydrophobic lipid bilayer of the membrane. In Bacillus...
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context (2009)
Brouwer, Rutger W.W., Kuipers, Oscar P.
We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive...
Eijlander, Robyn T., Kolbusz, Magdalena A., Berendsen, Erwin M., Kuipers, Oscar P.
Protein translocation via the Tat machinery in thylakoids and bacteria occurs through a cooperation between the TatA, TatB and TatC subunits, of which the TatC protein forms the initial Tat...
Jong, Esther J. De, Jongbloed, Jan D.H., Kuipers, Oscar P.
The gram-positive bacterium Bacillus subtilis contains two minimal Tat translocases, TatAdCd and TatAyCy, which are each involved in the secretion of one or more specific protein substrates. We have...
Lubelski, Jacek, Khusainov, Rustem, Kuipers, Oscar P.
The lantibiotic nisin is a potent antimicrobial substance, which contains unusual lanthionine rings and dehydrated amino acid residues and is produced by Lactococcus lactis. Recently, the nisin...
Blom, Evert-Jan, Kuipers, Oscar P.
Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications...
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context (2009)
Brouwer, Rutger W. W., Kuipers, Oscar P.
Summary: We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates...
Blom, Evert-Jan, Van Hijum, Sacha AFT, Hofstede, Klaas J, Silvis, Remko, Roerdink, Jos BTM, Kuipers, Oscar P
Abstract Background A typical step in the analysis of gene expression data is the determination of clusters of genes that exhibit similar expression patterns. Researchers are confronted with the...
Blom, Evert, Breitling, Rainer, Hofstede, Klaas, Roerdink, Jos BTM, Van Hijum, Sacha AFT, Kuipers, Oscar P
Abstract Background Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows...
Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, (2008)
Helga Westers, Ronald Dorenbos, Jorrit Kabel, Tony Flanagan, Kevin M. Devine, ...
Reconstructing the Bacillus genome (Westers et al.) Bacterial genomes contain 250 to 500 essential genes as suggested by single gene disruptions and theoretical considerations. If this view is...
Van Der Voort, Menno, Kuipers, Oscar P, Buist, Girbe, De Vos, Willem M, Abee, Tjakko
Abstract Background The catabolite control protein CcpA is a transcriptional regulator conserved in many Gram-positives, controlling the efficiency of glucose metabolism. Here we studied the role of...
Van Hijum, Sacha AFT, Baerends, Richard JS, Zomer, Aldert L, Karsens, Harma A, Martin-Requena, Victoria, Trelles, Oswaldo, ...
Abstract Background Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome...
Michel A. Westenberg, Andrzej T. Lulko, Oscar P. Kuipers
Summary. We present GENeVis, an application to visualize gene expression time series data in a gene regulatory network context. This is a network of regulator proteins that regulate the expression of...
Agustiandari, Herfita, Lubelski, Jacek, Kuipers, Oscar P., Driessen, Arnold J.M.
LmrCD is an ABC-type multidrug transporter in Lactococcus lactis. LmrR encodes a putative transcriptional regulator. In a ΔlmrR strain, lmrCD is up-regulated. LmrR binds the promoter region of lmrCD...
Bet-hedging and epigenetic inheritance in bacterial cell development (2008)
Veening, Jan-Willem, Stewart, Eric J., Berngruber, Thomas W., Taddei, François, Kuipers, Oscar P., Hamoen, Leendert W.
Upon nutritional limitation, the bacterium Bacillus subtilis has the capability to enter the irreversible process of sporulation. This developmental process is bistable, and only a subpopulation of...
Barnett, James P., Eijlander, Robyn T., Kuipers, Oscar P., Robinson, Colin
The Tat system transports folded proteins across bacterial and thylakoid membranes. In Gram-negative organisms, a TatABC substrate-binding complex and separate TatA complex are believed to coalesce...
Mendel, Sharon, McCarthy, Andrew, Barnett, James P., Eijlander, Robyn T., Nenninger, Anja, Kuipers, Oscar P., ...
The Tat system transports folded proteins across bacterial and thylakoid membranes. In Gram-negative organisms, it is encoded by tatABC genes and the system recognizes substrates bearing signal...
Widdick, David A., Eijlander, Robyn T., Dijl, Jan Maarten Van, Kuipers, Oscar P., Palmer, Tracy
We have developed a reporter protein system for the experimental verification of twin-arginine signal peptides. This reporter system is based on the Streptomyces coelicolor agarase protein, which is...
Hendriksen, Wouter T., Kloosterman, Tomas G., Bootsma, Hester J., Estevão, Silvia, Groot, Ronald De, Kuipers, Oscar P., ...
The transcriptional regulator GlnR of Streptococcus pneumoniae is involved in the regulation of glutamine and glutamate metabolism, controlling the expression of the glnRA and glnPQ-zwf operons, as...
CodY of Streptococcus pneumoniae: Link between Nutritional Gene Regulation and Colonization (2008)
Hendriksen, Wouter T., Bootsma, Hester J., Estevão, Silvia, Hoogenboezem, Theo, Jong, Anne De, Groot, Ronald De, ...
CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillus subtilis and Lactococcus lactis. We investigated the role of CodY in gene...
LysM, a widely distributed protein motif for binding to (peptido)glycans (2008)
Buist, Girbe, Steen, Anton, Kok, Jan, Kuipers, Oscar P.
Bacteria retain certain proteins at their cell envelopes by attaching them in a non-covalent manner to peptidoglycan, using specific protein domains, such as the prominent LysM (Lysin Motif) domain....
Kramer, Naomi E., Hasper, Hester E., Morath, Siegfried, Kruijff, Ben De, Hartung, Thomas, ...
Nisin is a post-translationally modified antimicrobial peptide produced by Lactococcus lactis which binds to lipid II in the membrane to form pores and inhibit cell-wall synthesis. A nisin-resistant...
Transient heterogeneity in extracellular protease production by Bacillus subtilis (2008)
Veening, Jan-Willem, Igoshin, Oleg A., Eijlander, Robyn T., Nijland, Reindert, Hamoen, Leendert W., Kuipers, Oscar P.
The most sophisticated survival strategy Bacillus subtilis employs is the differentiation of a subpopulation of cells into highly resistant endospores. To examine the expression patterns of...
Baerends, Richard J.S., Zomer, Aldert L., Karsens, Harma A., Martin-Requena, Victoria, Trelles, Oswaldo, ...
Background: Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome...
Voort, Menno Van Der, Kuipers, Oscar P., Buist, Girbe, Vos, Willem M. De, Abee, Tjakko
Background: The catabolite control protein CcpA is a transcriptional regulator conserved in many Gram-positives, controlling the efficiency of glucose metabolism. Here we studied the role of Bacillus...
Kloosterman, Tomas G., Witwicki, Robert M., Bijlsma, Jetta J.E., Kuipers, Oscar P.
Homeostasis of Zn2+ and Mn2+ is important for the physiology and virulence of the human pathogen Streptococcus pneumoniae. Here, transcriptome analysis was used to determine the response of S....
Induction of natural competence in Bacillus cereus ATCC14579 (2008)
Mirończuk, Aleksandra M., Kovács, Ákos T., Kuipers, Oscar P.
Natural competence is the ability of certain microbes to take up exogenous DNA from the environment and integrate it in their genome. Competence development has been described for a variety of...
Zaidi, Arsalan Haseeb, Bakkes, Patrick J., Lubelski, Jacek, Agustiandari, Herfita, Kuipers, Oscar P., Driessen, Arnold J.M.
Upon prolonged exposure to cholate and other toxic compounds, Lactococcus lactis develops a multidrug resistance phenotype that has been attributed to an elevated expression of the heterodimeric...
Transcriptome Analysis of the Lactococcus lactis ArgR and AhrC Regulons (2008)
Larsen, Rasmus, Martinussen, Jan, Kuipers, Oscar P., Kok, Jan
In previous studies, we have shown that direct protein-protein interaction between the two regulators ArgR and AhrC in Lactococcus lactis is required for arginine-dependent repression of the...
Steen, Anton, Buist, Girbe, Kramer, Naomi E., Jalving, Ruud, Venema, Gerard, ...
When Lactococcus lactis subsp. lactis IL1403 or L. lactis subsp. cremoris MG1363 is grown in a medium with galactose as the carbon source, the culture lyses to a lesser extent in stationary phase...
Lubelski, Jacek, Overkamp, Wout, Kluskens, Leon D., Moll, Gert N., Kuipers, Oscar P.
Since the recent discovery that the nisin modification and transport machinery can be used to produce and modify peptides unrelated to nisin, specific questions arose concerning the specificity of...
Stevens, Marc J.A., Wiersma, Anne, Vos, Willem M. De, Kuipers, Oscar P., Smid, Eddy J., Molenaar, Douwe, ...
An aerobic Lactobacillus plantarum culture displayed growth stagnation during early growth. Transcriptome analysis revealed that resumption of growth after stagnation correlated with activation of...
Kloosterman, Tomas G., Witwicki, Robert M., Bijlsma, Jetta J.E., Kuipers, Oscar P.
Homeostasis of Zn2+ and Mn2+ is important for the physiology and virulence of the human pathogen Streptococcus pneumoniae. Here, transcriptome analysis was used to determine the response of S....
The relative value of operon predictions (2008)
Kuipers, Oscar P., Brouwer, Rutger W.W.
For most organisms, computational operon predictions are the only source of genome-wide operon information. Operon prediction methods described in literature are based on (a combination of) the...
Bistability, Epigenetics, and Bet-Hedging in Bacteria (2008)
Veening, Jan-Willem, Smits, Wiep Klaas, Kuipers, Oscar P.
Clonal populations of microbial cells often show a high degree of phenotypic variability under homogeneous conditions. Stochastic fluctuations in the cellular components that determine cellular...
Silvis, Remko, Hofstede, Klaas J., Blom, Evert-Jan, Kuipers, Oscar P.
Background: A typical step in the analysis of gene expression data is the determination of clusters of genes that exhibit similar expression patterns. Researchers are confronted with the seemingly...
Blom, Evert Jan, Breitling, Rainer, Hofstede, Klaas Jan, Kuipers, Oscar P.
Background: Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows...
Westenberg, Michel A., Lulko, Andrzej T., Kuipers, Oscar P.
We present GENeVis, an application to visualize gene expression time series data in a gene regulatory network context. This is a network of regulator proteins that regulate the expression of their...
Phenotypic Variation and Bistable Switching in Bacteria (2008)
Smits, Wiep Klaas, Veening, Jan-Willem, Kuipers, Oscar P.
Microbial research generally focuses on clonal populations. However, bacterial cells with identical genotypes frequently display different phenotypes under identical conditions. This microbial cell...
The relative value of operon predictions (2008)
Brouwer, Rutger W. W., Kuipers, Oscar P.
For most organisms, computational operon predictions are the only source of genome-wide operon information. Operon prediction methods described in literature are based on (a combination of) the...
Bmc Bioinformatics, Richard Js Baerends, Aldert L Zomer, Oscar P Kuipers
Research article Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons
Bmc Microbiology, Oscar P Kuipers, Girbe Buist, Tjakko Abee
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Blom, Evert-Jan, Bosman, Dinne W. J., Breitling, Rainer, Tijsma, Lars, Silvis, Remko, ...
Summary: FIVA (Function Information Viewer and Analyzer) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software...
Production of Dehydroamino Acid-Containing Peptides by Lactococcus lactis (2007)
Rink, Rick, Wierenga, Jenny, Kuipers, Anneke, Kluskens, Leon D., Driessen, Arnold J.M., Kuipers, Oscar P., ...
Nisin is a pentacyclic peptide antibiotic produced by some Lactococcus lactis strains. Nisin contains dehydroresidues and thioether rings that are posttranslationally introduced by a...
Rink, Rick, Kluskens, Leon D., Kuipers, Anneke, Driessen, Arnold J.M., Kuipers, Oscar P., Moll, Gert N.
Nisin is a pentacyclic peptide antibiotic active against Gram-positive bacteria. Its thioether rings are formed by two enzymatic steps: nisin dehydratase (NisB)-mediated dehydration of serines and...
SIMAGE: simulation of DNA-microarray gene expression data. Software (2006)
Albers, Casper J., Jansen, Ritsert C., Kok, Jan, Kuipers, Oscar P.
Background: Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing...
LmrCD is a major multidrug resistance transporter in Lactococcus lactis (2006)
Lubelski, Jacek, Jong, Anne De, Merkerk, Ronald Van, Agustiandari, Herfita, Kuipers, Oscar P., Kok, Jan, ...
When Lactococcus lactis is challenged with drugs it displays a multidrug resistance (MDR) phenotype. In silico analysis of the genome of L. lactis indicates the presence of at least 40 putative MDR...
Sec-Mediated Transport of Posttranslationally Dehydrated Peptides in Lactococcus lactis (2006)
Kuipers, Anneke, Wierenga, Jenny, Rink, Rick, Kluskens, Leon D., Driessen, Arnold J.M., Kuipers, Oscar P., ...
Nisin is a lanthionine-containing antimicrobial peptide produced by Lactococcus lactis. Its (methyl)lanthionines are introduced by two posttranslational enzymatic steps involving the dehydratase...
Kuipers, Oscar P., Hamoen, Leendert W., Fusetti, Fabrizia, Susanna, Kim A.
The competence transcription factor ComK is the master regulator of competence development in Bacillus subtilis. In the regulatory pathway, ComK is involved in different interactions: (i)...
Bosman, Diederik W.J., Blom, Evert-Jan, Ogao, Patrick J., Kuipers, Oscar P.
Among the various research areas that comprise bioinformatics, systems biology is gaining increasing attention. An important goal of systems biology is the unraveling of dynamic interactions between...
Novel Surface Display System for Proteins on Non-Genetically Modified Gram-Positive Bacteria (2006)
Robillard, George, Kuipers, Oscar P., Kok, Jan, Buist, Girbe, Steen, Anton, Roosmalen, Maarten L. Van, ...
A novel display system is described that allows highly efficient immobilization of heterologous proteins on bacterial surfaces in applications for which the use of genetically modified bacteria is...
Leenhouts, Kees, Robillard, George, Kuipers, Oscar P., Buist, Girbe, Kok, Jan, Steen, Anton, ...
Mucosal immunization with subunit vaccines requires new types of antigen delivery vehicles and adjuvants for optimal immune responses. We have developed a non-living and non-genetically modified...
Complete Genome Sequence of the Prototype Lactic Acid Bacterium (2006)
Udo Wegmann, Aldert Zomer, Girbe Buist, Claire Shearman, Carlos Canchaya, Marco Ventura, ...
Lactococcus lactis is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of Lactococcus lactis subsp. cremoris MG1363, the...
BAGEL: a web-based bacteriocin genome mining tool. Nucleic Acids Res (2006)
Anne De Jong, Jan Kok, Oscar P. Kuipers
A common problem in the annotation of open reading frames (ORFs) is the identification of genes that are functionally similar but have limited or no sequence homology. This is particularly the case...
Bmc Bioinformatics, Casper J Albers, Ritsert C Jansen, Jan Kok, Oscar P Kuipers, Biomed Central
Software SIMAGE: simulation of DNA-microarray gene expression data
BAGEL: a web-based bacteriocin genome mining tool (2006)
De Jong, Anne, Bijlsma, Jetta J. E., Kok, Jan, Kuipers, Oscar P.
A common problem in the annotation of open reading frames (ORFs) is the identification of genes that are functionally similar but have limited or no sequence homology. This is particularly the case...
A novel scheme to assess factors involved in the reproducibility of DNA-microarray data (2005)
Jong, Anne De, Baerends, Richard J.S., Karsens, Harma A., Kramer, Naomi E., Larsen, Rasmus, ...
Background: In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust...
Metabolism, and Cellular Differentiation in Bacillus subtilis† (2005)
Oxidative Stress, Wiep Klaas Smits, Sierd Bron, ...
Thioredoxins are important thiol-reactive proteins. Most knowledge about this class of proteins is derived from proteome studies, and little is known about the global transcriptional response of...
Zomer, Aldert L., Kuipers, Oscar P., Kok, Jan
With genome sequencing efforts increasing exponentially, valuable information accumulates on genomic content of the various organisms sequenced. Projector 2 uses (un)finished genomic sequences of an...
Swertz, Morris A., Brock, E.O. (Bert) De, Jong, Anne De, Buist, Girbe, Baerends, Richard J.S., ...
Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of...
Kuipers, Anneke, Boef, Esther De, Rink, Rick, Fekken, Susan, Kluskens, Leon D., Driessen, Arnold J.M., ...
Lantibiotics are lanthionine-containing peptide antibiotics. Nisin, encoded by nisA, is a pentacyclic lantibiotic produced by some Lactococcus lactis strains. Its thioether rings are...
Rational: UML Semantics Appendix M4 -Relationship to OMG Technologies (2004)
Morris A. Swertz, Anne De Jong, Girbe Buist, Jan Kok, Oscar P. Kuipers, ...
*To whom correspondence should be addressed.
Swertz, Morris A., De Brock, E. O., De Jong, Anne, Buist, Girbe, Baerends, Richard J. S., ...
Motivation: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of...
Swertz, Morris A., (Bert) De Brock, E. O., De Jong, Anne, Buist, Girbe, Baerends, Richard J. S., ...
Motivation: Genomic research laboratories need an adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? Lack of...
Swertz, Morris A., (Bert) De Brock, E. O., De Jong, Anne, Buist, Girbe, Baerends, Richard J. S., ...
Motivation: Genomic research laboratories need an adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? Lack of...
Genome Engineering Reveals Large Dispensable Regions in Bacillus subtilis (2003)
Westers, Helga, Dorenbos, Ronald, Van Dijl, Jan Maarten, Kabel, Jorrit, Flanagan, Tony, Devine, Kevin M., ...
Bacterial genomes contain 250 to 500 essential genes as suggested by single gene disruptions and theoretical considerations. If this view is correct, the remaining non-essential genes of an organism,...
Projector: automatic contig mapping for gap closure purposes (2003)
Zomer, Aldert L., Kuipers, Oscar P., Kok, Jan
Projector was designed for automatic positioning of contigs from an unfinished prokaryotic genome onto a template genome of a closely related strain or species. Projector mapped 84 contigs of...
Genome Engineering Reveals Large Dispensable Regions in Bacillus subtilis (2003)
Westers, Helga, Dorenbos, Ronald, Van Dijl, Jan Maarten, Kabel, Jorrit, Flanagan, Tony, Devine, Kevin M., ...
Bacterial genomes contain 250 to 500 essential genes, as suggested by single gene disruptions and theoretical considerations. If this view is correct, the remaining nonessential genes of an organism,...
Genome Engineering Reveals Large Dispensable Regions in Bacillus subtilis (2003)
Westers, Helga, Dorenbos, Ronald, Van Dijl, Jan Maarten, Kabel, Jorrit, Flanagan, Tony, Devine, Kevin M., ...
Bacterial genomes contain 250 to 500 essential genes as suggested by single gene disruptions and theoretical considerations. If this view is correct, the remaining non-essential genes of an organism,...
Hamoen, Leendert W., Smits, Wiep Klaas, Jong, Anne De, Holsappel, Siger, Kuipers, Oscar P.
Generally, the presence of a consensus sequence in the promoter of a gene is taken as indication for regulation by the transcription factor that binds to this sequence. In light of the recent...
Lactic acid bacteria: the bugs of the new millennium (2000)
Kuipers, Oscar P., Kok, Jan, Konings, Wil N., Poolman, Bert
Lactic acid bacteria (LABs) are widely used in the manufacturing of fermented food and are among the best-studied microorganisms. Detailed knowledge of a number of physiological traits has opened new...
Siezen, Roland J., Rollema, Harry S., Kuipers, Oscar P., De Vos, Willem M.
A model is presented for the 3-D structure of the catalytic domain of the putative leader peptidase NisP of Lactococcus lactis, and the interaction with its specific substrate, the precursor of the...
Efficient random mutagenesis method with adjustable mutation frequency by use of PCR and dITP (1993)
X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor (1990)
Kalk, Kor H., AB, Eiso, Drenth, Jan, Dijkstra, Bauke W., Kuipers, Oscar P., ...
Phospholipases A2 play a part in a number of physiologically important cellular processes such as inflammation, blood platelet aggregation and acute hypersensitivity. These processes are all...
Kuipers, Oscar P., Kerver, Jana, Van Meersbergen, Joop, Vis, Roel, Dijkman, Ruud, Verheij, Hubertus M., ...
Residue 31 of porcine pancreatic phospholipase A2 (PLA2) is located at the entrance to the active site. To study the role of residue 31 in PLA2, six mutant enzymes were produced by site-directed...
Function of the fully conserved residues Asp99, Tyr52 and Tyr73 in phospholipase A2 (1990)
Kuipers, Oscar P., Franken, Peet A., Hendriks, Rob, Verheji, Hubertus M., De Haas, Gerard H.
In the active centre of pancreatic phospholipase A2 His48 is at hydrogen-bonding distance to Asp99. This Asp-His couple is assumed to act together with a water molecule as a catalytic triad. Asp99 is...
Enhanced Activity and Altered Specificity of Phospholipase A2 by Deletion of a Surface Loop (1989)
Dijkstra, Bauke W., Geus, Pieter De, Kuipers, Oscar P., Drenth, Jan, Verheij, Hubertus M., ...
Protein engineering and x-ray crystallography have been used to study the role of a surface loop that is present in pancreatic phospholipases but is absent in snake venom phospholipases. Removal of...
Kuipers, Oscar P., Dijkman, Ruud, Verheij, Hubertus M., Haas, Gerard H.de
We have studied the role of Tyr-69 of porcine pancreatic phospholipase A2 in catalysis and substrate binding, using site-directed mutagenesis. A mutant was constructed containing Phe at position 69....
Burghout, Peter, Bootsma, Hester J., Kloosterman, Tomas G., Bijlsma, Jetta J. E., De Jongh, Christa E., Kuipers, Oscar P., ...
We applied a novel negative selection strategy called genomic array footprinting (GAF) to identify genes required for genetic transformation of the gram-positive bacterium Streptococcus pneumoniae....
Rink, Rick, Wierenga, Jenny, Kuipers, Anneke, Kluskens, Leon D., Driessen, Arnold J. M., Kuipers, Oscar P., ...
Nisin A is a pentacyclic antibiotic peptide produced by various Lactococcus lactis strains. Nisin displays four different activities: (i) it autoinduces its own synthesis; (ii) it inhibits the growth...
Van Hijum, Sacha AFT, Baerends, Richard JS, Zomer, Aldert L, Karsens, Harma A, Martin-Requena, Victoria, Trelles, Oswaldo, ...
Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereus ATCC 14579
Van Der Voort, Menno, Kuipers, Oscar P, Buist, Girbe, De Vos, Willem M, Abee, Tjakko
Agustiandari, Herfita, Lubelski, Jacek, Kuipers, Oscar P., Driessen, Arnold J. M.
LmrCD is an ABC-type multidrug transporter in Lactococcus lactis. LmrR encodes a putative transcriptional regulator. In a ΔlmrR strain, lmrCD is up-regulated. LmrR binds the promoter region of lmrCD...
CodY of Streptococcus pneumoniae: Link between Nutritional Gene Regulation and Colonization▿
Hendriksen, Wouter T., Bootsma, Hester J., Estevão, Silvia, Hoogenboezem, Theo, De Jong, Anne, De Groot, Ronald, ...
CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillus subtilis and Lactococcus lactis. We investigated the role of CodY in gene...
Transient heterogeneity in extracellular protease production by Bacillus subtilis
Veening, Jan-Willem, Igoshin, Oleg A, Eijlander, Robyn T, Nijland, Reindert, Hamoen, Leendert W, Kuipers, Oscar P
The most sophisticated survival strategy Bacillus subtilis employs is the differentiation of a subpopulation of cells into highly resistant endospores. To examine the expression patterns of...
Hendriksen, Wouter T., Kloosterman, Tomas G., Bootsma, Hester J., Estevão, Silvia, De Groot, Ronald, Kuipers, Oscar P., ...
The transcriptional regulator GlnR of Streptococcus pneumoniae is involved in the regulation of glutamine and glutamate metabolism, controlling the expression of the glnRA and glnPQ-zwf operons, as...
Bet-hedging and epigenetic inheritance in bacterial cell development
Veening, Jan-Willem, Stewart, Eric J., Berngruber, Thomas W., Taddei, François, Kuipers, Oscar P., Hamoen, Leendert W.
Upon nutritional limitation, the bacterium Bacillus subtilis has the capability to enter the irreversible process of sporulation. This developmental process is bistable, and only a subpopulation of...
Blom, Evert Jan, Breitling, Rainer, Hofstede, Klaas Jan, Roerdink, Jos BTM, Van Hijum, Sacha AFT, Kuipers, Oscar P
Kloosterman, Tomas G., Witwicki, Robert M., Bijlsma, Jetta J. E., Kuipers, Oscar P.
Homeostasis of Zn2+ and Mn2+ is important for the physiology and virulence of the human pathogen Streptococcus pneumoniae. Here, transcriptome analysis was used to determine the response of S....
Steen, Anton, Buist, Girbe, Kramer, Naomi E., Jalving, Ruud, Venema, Gerard, ...
When Lactococcus lactis subsp. lactis IL1403 or L. lactis subsp. cremoris MG1363 is grown in a medium with galactose as the carbon source, the culture lyses to a lesser extent in stationary phase...
Stevens, Marc J. A., Wiersma, Anne, De Vos, Willem M., Kuipers, Oscar P., Smid, Eddy J., Molenaar, Douwe, ...
An aerobic Lactobacillus plantarum culture displayed growth stagnation during early growth. Transcriptome analysis revealed that resumption of growth after stagnation correlated with activation of...
Transcriptome Analysis of the Lactococcus lactis ArgR and AhrC Regulons▿
Larsen, Rasmus, Martinussen, Jan, Kuipers, Oscar P., Kok, Jan
In previous studies, we have shown that direct protein-protein interaction between the two regulators ArgR and AhrC in Lactococcus lactis is required for arginine-dependent repression of the...
Lubelski, Jacek, Overkamp, Wout, Kluskens, Leon D., Moll, Gert N., Kuipers, Oscar P.
Since the recent discovery that the nisin modification and transport machinery can be used to produce and modify peptides unrelated to nisin, specific questions arose concerning the specificity of...
Blom, Evert-Jan, Van Hijum, Sacha AFT, Hofstede, Klaas J, Silvis, Remko, Roerdink, Jos BTM, Kuipers, Oscar P
Zaidi, Arsalan Haseeb, Bakkes, Patrick J., Lubelski, Jacek, Agustiandari, Herfita, Kuipers, Oscar P., Driessen, Arnold J. M.
Upon prolonged exposure to cholate and other toxic compounds, Lactococcus lactis develops a multidrug resistance phenotype that has been attributed to an elevated expression of the heterodimeric...
Relaxed Specificity of the Bacillus subtilis TatAdCd Translocase in Tat-Dependent Protein Secretion▿
Eijlander, Robyn T., Jongbloed, Jan D. H., Kuipers, Oscar P.
Protein translocation via the twin arginine translocation (TAT) pathway is characterized by the translocation of prefolded proteins across the hydrophobic lipid bilayer of the membrane. In Bacillus...
Copper Acquisition Is Mediated by YcnJ and Regulated by YcnK and CsoR in Bacillus subtilis▿
Chillappagari, Shashi, Miethke, Marcus, Trip, Hein, Kuipers, Oscar P., Marahiel, Mohamed A.
Copper is an essential cofactor for many enzymes, and at over a threshold level, it is toxic for all organisms. To understand the mechanisms underlying copper homeostasis of the gram-positive...