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...
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...
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...
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...
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...
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...