Publications
2023
Morawska,
L. P., & Kuipers, O. P. (2023).
Cell-to-cell non-conjugative plasmid transfer between
Bacillus subtilis and lactic acid bacteria.
Microbial Biotechnology, 16(4),
784-798. https://doi.org/10.1111/1751-7915.14195
2022
Arias-Orozco,
P., Yi, Y., Ruijne, F., Cebrián, R.,
& Kuipers, OP. (2023). Investigating the
Specificity of the Dehydration and Cyclization Reactions in
Engineered Lanthipeptides by Synechococcal SyncM.
ACS Synthetic Biology, 12,
164–177. https://doi.org/10.1021/acssynbio.2c00455
Muñoz,
C. Y., Zhou, L., Yi, Y.,
& Kuipers, O. P. (2022). Biocontrol properties
from phyllospheric bacteria isolated from Solanum lycopersicum and
Lactuca sativa and genome mining of antimicrobial gene
clusters. BMC Genomics,
23(1), [152]. https://doi.org/10.1186/s12864-022-08392-0
Cebrián,
R., Li, Q., Peñalver, P., Belmonte-Reche, E.,
Andrés-Bilbao, M., Lucas, R., de Paz, M. V., Kuipers, O.
P., & Morales, J. C. (2022). Chemically Tuning
Resveratrol for the Effective Killing of Gram-Positive
Pathogens. Journal of Natural
Products, 85(6), 1459-1473. [1c01107]. https://doi.org/10.1021/acs.jnatprod.1c01107
Farooq,
S. A., de Jong, A., Khaliq, S., & Kuipers,
O. P. (2022). Draft Genome Sequences of Bacillus
velezensis Strains AF_3B and OS2, Bacillus amyloliquefaciens Strain
BS9, Bacillus halotolerans Strain A1, and Bacillus sp. Strain BS3,
Producing Biosurfactants with Antimicrobial Potential.
Microbiology resource announcements,
11(10), [e0048222]. https://doi.org/10.1128/mra.00482-22
Bustamante
Ordonez, M., van Doorn, S., Weissing,
F., Daras, I., Kuipers, O.,
& de Vos, M. (2022). Eco-evolutionary
interactions and the spread of antimicrobial resistance in
pathogenic microbial communities. Poster session
presented at Netherlands Society for Evolutionary Biology Meeting
2022, Ede, Netherlands.
Mordhorst,
S., Ruijne, F., Vagstad, A. L., Kuipers, O.
P., & Piel, J. (2022). Emulating nonribosomal
peptides with ribosomal biosynthetic strategies.
RSC Chemical Biology, 4, 7-36. https://doi.org/10.1039/d2cb00169a
de
Jong, A., Kuipers, O. P., & Kok,
J. (2022). FUNAGE-Pro: comprehensive web server for
gene set enrichment analysis of prokaryotes.
Nucleic Acids Research, 50(W1),
330-336. [gkac441]. https://doi.org/10.1093/nar/gkac441
Liu,
F., van Heel, A. J., Chen,
J., & Kuipers, O. P. (2022).
Functional production of clostridial circularin A in
Lactococcus lactis NZ9000 and mutational analysis of its aromatic
and cationic residues. Frontiers in
Microbiology, 13, [1026290]. https://doi.org/10.3389/fmicb.2022.1026290
Pinto,
J. P. C., Brouwer, R., Zeyniyev, A., Kuipers, O.
P., & Kok, J. (2022). High-Resolution
Chrono-Transcriptome of Lactococcus lactis Reveals That It
Expresses Proteins with Adapted Size and pI upon Acidification and
Nutrient Starvation. Applied and environmental
microbiology, 88(9), [e0247621]. https://doi.org/10.1128/aem.02476-21
Viel,
J. H., & Kuipers, O. P. (2022).
Modular Use of the Uniquely Small Ring A of Mersacidin
Generates the Smallest Ribosomally Produced Lanthipeptide.
ACS Synthetic Biology, 11(9),
3078-3087. [2c00343]. https://doi.org/10.1021/acssynbio.2c00343
Viel,
J. H., & Kuipers, O. P. (2022).
Mutational Studies of the Mersacidin Leader Reveal the
Function of Its Unique Two-Step Leader Processing Mechanism.
ACS Synthetic Biology, 11(5),
1949–1957 . https://doi.org/10.1021/acssynbio.2c00088
Schouten,
G. K., Paulussen, F. M., Kuipers, O. P., Bitter, W.,
Grossmann, T. N., & van Ulsen, P. (2022). Stapling of
Peptides Potentiates the Antibiotic Treatment of Acinetobacter
baumannii In Vivo. Antibiotics ,
11(2), [11020273]. https://doi.org/10.3390/antibiotics11020273
Morawska,
L. P., Detert Oude Weme, R. G. J., Frenzel, E., Dirkzwager,
M., Hoffmann, T., Bremer, E., & Kuipers, O. P.
(2022). Stress-induced activation of the proline biosynthetic
pathway in Bacillus subtilis: A population-wide and single-cell
study of the osmotically controlled proHJ promoter.
Microbial Biotechnology, 15(9),
2411-2425. https://doi.org/10.1111/1751-7915.14073
Ekkers,
D. M., Tusso, S., Moreno-Gamez, S., Rillo, M.
C., Kuipers, O. P., & van Doorn, G.
S. (2022). Trade-offs predicted by metabolic network
structure give rise to evolutionary specialization and phenotypic
diversification. Molecular Biology and
Evolution, 39(6), [msac124]. https://doi.org/10.1093/molbev/msac124
Morawska,
L. P., & Kuipers, O. P. (2022).
Transcriptome analysis and prediction of the metabolic state
of stress-induced viable but non-culturable Bacillus subtilis
cells. Scientific Reports,
12(1), [18015]. https://doi.org/10.1038/s41598-022-21102-w
Yu,
Y., van der Zwaag, M., Wedman, J.
J., Permentier, H., Plomp,
N., Jia, X., Kanon, B.,
Eggens-Meijer, E., Buist, G., Harmsen,
H., Kok, J., Salles, J. F.,
Wertheim, B., Hayflick, S. J., Strauss,
E., Grzeschik, N. A., Schepers, H.,
& Sibon, O. C. M. (2022). Coenzyme A precursors
flow from mother to zygote and from microbiome to host.
Molecular Cell, 82(14),
2650-2665.e12. https://doi.org/10.1016/j.molcel.2022.05.006
Kong,
C., de Jong, A., de Haan, B.
J., Kok, J., & de Vos, P.
(2022). Human milk oligosaccharides and non-digestible
carbohydrates reduce pathogen adhesion to intestinal epithelial
cells by decoy effects or by attenuating bacterial
virulence. Food Research
International, 151, [110867]. https://doi.org/10.1016/j.foodres.2021.110867
2021
Chen,
J., & Kuipers, O. P. (2022). Analysis
of cross-functionality within LanBTC synthetase complexes from
different bacterial sources with respect to production of fully
modified lanthipeptides. Applied and environmental
microbiology, 88(2), [AEM0161821]. https://doi.org/10.1128/AEM.01618-21
Morawska,
L. P., Hernandez-Valdes, J. A., &
Kuipers, O. P. (2022). Diversity of bet-hedging
strategies in microbial communities-Recent cases and
insights. Wires mechanisms of disease,
14(2), [e1544]. https://doi.org/10.1002/wsbm.1544
Cebrián,
R., Belmonte-Reche, E., Pirota, V., de Jong,
A., Morales, J. C., Freccero, M., Doria, F., &
Kuipers, O. P. (2022). G-Quadruplex DNA as a Target in
Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide
Ligand and Its Mode of Action. Journal of
Medicinal Chemistry, 65(6), 4752-4766. https://doi.org/10.1021/acs.jmedchem.1c01905
van
Tilburg, A. Y., Warmer, P., van Heel, A. J.,
Sauer, U., & Kuipers, O. P. (2022). Membrane
composition and organization of Bacillus subtilis 168 and its
genome-reduced derivative miniBacillus PG10.
Microbial Biotechnology, 15(5),
1633-1651. [13978]. https://doi.org/10.1111/1751-7915.13978
Zhou,
L., Song, C., Li, Z., & Kuipers, O. P.
(2021). Antimicrobial activity screening of rhizosphere soil
bacteria from tomato and genome-based analysis of their
antimicrobial biosynthetic potential. BMC
Genomics, 22(1), [29]. https://doi.org/10.1186/s12864-020-07346-8
Fu,
Y., Jaarsma, A. H., & Kuipers, O. P.
(2021). Antiviral activities and applications of ribosomally
synthesized and post-translationally modified peptides
(RiPPs). Cellular and molecular life
sciences, 78, 3921–3940 . https://doi.org/10.1007/s00018-021-03759-0
Zhou,
L., Song, C., Muñoz, C. Y., &
Kuipers, O. P. (2021). Bacillus cabrialesii BH5
Protects Tomato Plants Against Botrytis cinerea by Production of
Specific Antifungal Compounds. Frontiers in
Microbiology, 12, [707609]. https://doi.org/10.3389/fmicb.2021.707609
Zhao,
X., Wang, X., Shukla, R., Kumar, R., Weingarth, M.,
Breukink, E., & Kuipers, O. P. (2021).
Brevibacillin 2V, a Novel Antimicrobial Lipopeptide With an
Exceptionally Low Hemolytic Activity. Frontiers in
Microbiology, 12, [693725]. https://doi.org/10.3389/fmicb.2021.693725
Zhao,
X., Wang, X., Shukla, R., Kumar, R., Weingarth, M.,
Breukink, E., & Kuipers, O. P. (2021).
Brevibacillin 2V Exerts Its Bactericidal Activity via Binding
to Lipid II and Permeabilizing Cellular Membranes.
Frontiers in Microbiology, 12,
[694847]. https://doi.org/10.3389/fmicb.2021.694847
Zhao,
X., & Kuipers, O. P. (2021).
BrevicidineB, a New Member of the Brevicidine Family,
Displays an Extended Target Specificity. Frontiers
in Microbiology, 12, [693117]. https://doi.org/10.3389/fmicb.2021.693117
Viel,
J. H., van Tilburg, A. Y., & Kuipers,
O. P. (2021). Characterization of Leader Processing
Shows That Partially Processed Mersacidin Is Activated by AprE
After Export. Frontiers in
Microbiology, 12, [765659]. https://doi.org/10.3389/fmicb.2021.765659
Ruijne,
F., & Kuipers, O. P. (2021).
Combinatorial biosynthesis for the generation of
new-to-nature peptide antimicrobials. Biochemical
Society Transactions, 49(1), 203-215. [
BST20200425]. https://doi.org/10.1042/BST20200425
Muñoz,
C. Y., de Jong, A., & Kuipers, O.
P. (2021). Draft Genome Sequences of a Bacillus
subtilis Strain, a Bacillus velezensis Strain, a Paenibacillus
Strain, and an Acinetobacter baumannii Strain, All Isolated from
the Phyllosphere of Lactuca sativa or Solanum lycopersicum.
Microbiology resource announcements,
10(4), [e01092-20]. https://doi.org/10.1128/MRA.01092-20
Arias-Orozco,
P., Yi, Y., & Kuipers, O. P.
(2021). Draft Genome Sequences of Four Bacterial Strains of
Heterotrophic Alteromonas macleodii and Marinobacter, Isolated from
a Nonaxenic Culture of Two Marine Synechococcus Strains.
Microbiology resource announcements,
10(19), [e00116-21]. https://doi.org/10.1128/MRA.00116-21
Xia,
Y., Cebrián, R., Xu, C., Jong, A.
D., Wu, W., & Kuipers, O. P. (2021).
Elucidating the mechanism by which synthetic helper peptides
sensitize Pseudomonas aeruginosa to multiple antibiotics.
PLoS Pathogens, 17(9), [e1009909].
https://doi.org/10.1371/journal.ppat.1009909
Arias-Orozco,
P., Inklaar, M., Lanooij, J., Cebrián,
R., & Kuipers, O. P. (2021).
Functional Expression and Characterization of the Highly
Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production
of Lanthipeptides with a Broad Range of Ring Topologies.
ACS Synthetic Biology, 10(10),
2579-2591. [acssynbio.1c00224]. https://doi.org/10.1021/acssynbio.1c00224
Gazioglu,
O., Kareem, B. O., Afzal, M., Shafeeq, S., Kuipers, O.
P., Ulijasz, A. T., Andrew, P. W., & Yesilkaya, H.
(2021). Glutamate Dehydrogenase (GdhA) of Streptococcus
pneumoniae Is Required for High Temperature Adaptation.
Infection and Immunity, 89(12),
[IAI0040021]. https://doi.org/10.1128/IAI.00400-21
Viel,
J. H., Jaarsma, A. H., & Kuipers, O. P.
(2021). Heterologous Expression of Mersacidin in Escherichia
coli Elucidates the Mode of Leader Processing. ACS
Synthetic Biology, 10(3), 600-608.
[acssynbio.0c00601]. https://doi.org/10.1021/acssynbio.0c00601
Zhou,
L., de Jong, A., Yi, Y.,
& Kuipers, O. P. (2021). Identification,
Isolation, and Characterization of Medipeptins, Antimicrobial
Peptides From Pseudomonas mediterranea EDOX.
Frontiers in Microbiology, 12,
[732771]. https://doi.org/10.3389/fmicb.2021.732771
Chen,
J., & Kuipers, O. P. (2021).
Isolation and Analysis of the Nisin Biosynthesis Complex
NisBTC: Further Insights into Their Cooperative Action.
Mbio, 12(5), [e02585-21]. https://doi.org/10.1128/mBio.02585-21
Lauxen,
A. I., Kobauri, P., Wegener, M., Hansen, M.
J., Galenkamp, N. S., Maglia, G.,
Szymanski, W., Feringa, B. L., &
Kuipers, O. P. (2021). Mechanism of Resistance
Development in E. coli against TCAT, a Trimethoprim-Based
Photoswitchable Antibiotic.
Pharmaceuticals, 14(5),
[ph14050392]. https://doi.org/10.3390/ph14050392
Zhao,
X., & Kuipers, O. P. (2021). Nisin-
and Ripcin-Derived Hybrid Lanthipeptides Display Selective
Antimicrobial Activity against Staphylococcus aureus.
ACS Synthetic Biology, 10(7),
1703–1714. https://doi.org/10.1021/acssynbio.1c00080
Li,
Q., Cebrián, R., Montalbán-López, M., Ren, H., Wu,
W., & Kuipers, O. P. (2021).
Outer-membrane-acting peptides and lipid II-targeting
antibiotics cooperatively kill Gram-negative pathogens.
Communications biology, 4(1), [31].
https://doi.org/10.1038/s42003-020-01511-1
Luo,
Y., Korza, G., DeMarco, A. M., Kuipers, O. P., Li,
Y-Q., & Setlow, P. (2021). Properties of spores of
Bacillus subtilis with or without a transposon that decreases spore
germination and increases spore wet heat resistance.
Journal of Applied Microbiology,
131(6), 2918-2928. https://doi.org/10.1111/jam.15163
Fernandez-Cantos,
M. V., Garcia-Morena, D., Iannone, V.,
El-Nezami, H., Kolehmainen, M., & Kuipers, O. P.
(2021). Role of microbiota and related metabolites in
gastrointestinal tract barrier function in NAFLD.
Tissue Barriers, 9(3), [e1879719].
https://doi.org/10.1080/21688370.2021.1879719
Zhao,
X., Xu, Y., Viel, J. H.,
& Kuipers, O. P. (2021). Semisynthetic Macrocyclic
Lipo-lanthipeptides Display Antimicrobial Activity Against
Bacterial Pathogens. ACS Synthetic
Biology, 10(8), 1980-1991. https://doi.org/10.1021/acssynbio.1c00161
Zhao,
X., & Kuipers, O. P. (2021).
Synthesis of silver-nisin nanoparticles with low cytotoxicity
as antimicrobials against biofilm-forming pathogens.
Colloids and Surfaces B: Biointerfaces,
206, [111965]. https://doi.org/10.1016/j.colsurfb.2021.111965
Michalik,
S., Reder, A., Richts, B., Faßhauer, P., Mäder, U.,
Pedreira, T., Poehlein, A., van Heel, A. J., van
Tilburg, A. Y., Altenbuchner, J., Klewing, A., Reuß, D.
R., Daniel, R., Commichau, F. M., Kuipers, O. P.,
Hamoen, L. W., Völker, U., & Stülke, J. (2021).
The Bacillus subtilis Minimal Genome Compendium.
ACS Synthetic Biology, 10(10),
2767-2771. [acssynbio.1c00339]. https://doi.org/10.1021/acssynbio.1c00339
Cebrián,
R., Xu, C., Xia, Y., Wu, W., &
Kuipers, O. P. (2021). The cathelicidin-derived
close-to-nature peptide D-11 sensitizes Klebsiella pneumoniae to a
range of antibiotics in vitro, ex vivo and in vivo.
International journal of antimicrobial
agents, 58(5), [106434]. https://doi.org/10.1016/j.ijantimicag.2021.106434
Shlla,
B., Gazioglu, O., Shafeeq, S., Manzoor, I., Kuipers, O.
P., Ulijasz, A., Hiller, N. L., Andrew, P. W., &
Yesilkaya, H. (2021). The Rgg1518 transcriptional regulator
is a necessary facet of sugar metabolism and virulence in
Streptococcus pneumoniae. Molecular
Microbiology, 116(3), 996-1008. https://doi.org/10.1111/mmi.14788
van
Tilburg, A. Y., Fülleborn, J. A., Reder,
A., Völker, U., Stülke, J., van Heel, A.
J., & Kuipers, O. P. (2021).
Unchaining miniBacillus PG10: Relief of FlgM-mediated
repression of autolysin genes. Applied and
environmental microbiology, 87(18),
[e01123-21]. https://doi.org/10.1128/AEM.01123-21
Chen,
J., van Heel, A. J., & Kuipers, O.
P. (2021). Visualization and Analysis of the Dynamic
Assembly of a Heterologous Lantibiotic Biosynthesis Complex in
Bacillus subtilis. Mbio,
12(4), [e01219-21]. https://doi.org/10.1128/mBio.01219-21
Hernández-Ortega,
E. P., van der Meulen, S., Kuijpers, L. J., & Kok,
J. (2022). Riboswitch RSthiT as a molecular tool in
Lactococcus lactis. Applied and environmental
microbiology, 88(4), [e01764-21]. https://doi.org/10.1128/AEM.01764-21
Wakai,
T., Kano, C., Karsens, H., Kok, J., &
Yamamoto, N. (2021). Functional role of surface layer
proteins of Lactobacillus acidophilus L-92 in stress tolerance and
binding to host cell proteins. Bioscience of
Microbiota, Food and Health, 40(1), 33-42. https://doi.org/10.12938/BMFH.2020-005
2020
van
Tatenhove-Pel, R. J., Rijavec, T., Lapanje, A., van Swam, I.,
Zwering, E., Hernandez-Valdes, J. A., Kuipers,
O. P., Picioreanu, C., Teusink, B., & Bachmann, H.
(2021). Microbial competition reduces metabolic interaction
distances to the low µm-range. The ISME
journal, 15, 688–701. https://doi.org/10.1038/s41396-020-00806-9
Montalbán-López,
M., Scott, T. A., Ramesh, S., Rahman, I. R., van Heel, A.
J., Viel, J. H., Bandarian, V., Dittmann, E.,
Genilloud, O., Goto, Y., Grande Burgos, M. J., Hill, C., Kim, S.,
Koehnke, J., Latham, J. A., Link, A. J., Martínez, B., Nair,
S. K., Nicolet, Y., ... van der Donk, W. A. (2021). New
developments in RiPP discovery, enzymology and engineering.
Natural product reports, 38(1),
130-239. [D0NP00027B]. https://doi.org/10.1039/d0np00027b
de
Vries, R. H., Viel, J. H., Kuipers, O.
P., & Roelfes, G. (2021). Rapid and
selective chemical editing of Ribosomally synthesized and
Post-translationally modified Peptides (RiPPs) via Cu(II)-catalyzed
β-borylation of dehydroamino acids.
Angewandte Chemie (International ed. in
English), 60(8), 3946-3950. https://doi.org/10.1002/anie.202011460
Teusink,
B., Kuipers, O. P., & Moineau, S. (2021).
Symposium on Lactic Acid Bacteria-reading while waiting for a
meeting. FEMS Microbiology Reviews,
45(2), [fuaa049]. https://doi.org/10.1093/femsre/fuaa049
Xia,
Y., Xu, C., Wang, D., Weng, Y., Jin, Y., Bai,
F., Cheng, Z., Kuipers, O. P., & Wu, W. (2021).
YbeY controls the type III and type VI secretion systems and
biofilm formation through RetS in Pseudomonas aeruginosa.
Applied and environmental microbiology,
87(5). https://doi.org/10.1128/AEM.02171-20
Boonstra,
M., Schaffer, M., Sousa, J., Morawska, L.,
Holsappel, S., Hildebrandt, P., Sappa, P. K., Rath,
H., de Jong, A., Lalk, M., Mäder, U.,
Völker, U., & 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
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
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), 1-14. [e00903-20]. https://doi.org/10.1128/AEM.00903-20
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
Caro-Astorga,
J., Frenzel, E., Perkins, J. R., Álvarez-Mena, A., de Vicente,
A., Ranea, J. A. G., Kuipers, O. P., & 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.,
Scheffers, D-J., & 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, 22(12), 5125-5136. 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
Deng,
J., Viel, J. H., Kubyshkin, V., Budisa, N.,
& Kuipers, O. P. (2020). Conjugation of Synthetic
Polyproline Moietes to Lipid II Binding Fragments of Nisin Yields
Active and Stable Antimicrobials. Frontiers in
Microbiology, 11, [575334]. https://doi.org/10.3389/fmicb.2020.575334
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 of
Lactococcus lactis Biosensors 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]. 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., Xia, B.,
Li, H., Chen, R., Liu, C., Jin, Y., Bai, F., Cheng, Z.,
Kuipers, O. P., & 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., Bachmann,
H., & 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 a
Lactococcus lactis dipeptidase mutant and rescue by mutation in the
pleiotropic regulator cody. Applied and
environmental microbiology, 86(8), [2937]. 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,
27(10), 1262-1271. 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
Li,
Z., de Vries, R. H., Chakraborty, P.,
Song, C., Zhao, X., Scheffers,
D-J., Roelfes, G., & Kuipers, O.
P. (2020). Novel modifications of nonribosomal
peptides from Brevibacillus laterosporus MG64 and investigation of
their mode of action. Applied and environmental
microbiology, 86(24), 1-14. [e01981-20]. https://doi.org/10.1128/AEM.01981-20
Chen,
J., van Heel, A. J., & Kuipers, O.
P. (2020). Subcellular Localization and Assembly
Process of the Nisin Biosynthesis Machinery in Lactococcus
lactis. Mbio, 11(6), 1-22.
[e02825-20]. https://doi.org/10.1128/mBio.02825-20
Deng,
J., Viel, J. H., Chen, J., &
Kuipers, O. P. (2020). Synthesis and Characterization
of Heterodimers and Fluorescent Nisin Species by Incorporation of
Methionine Analogues and Subsequent Click Chemistry.
ACS Synthetic Biology, 9(9),
2525-2536. https://doi.org/10.1021/acssynbio.0c00308
Vaishampayan,
A., Ahmed, R., Wagner, O., de Jong, A., Haag,
R., Kok, J., & Grohmann, E. (2021).
Transcriptomic analysis of stress response to novel
antimicrobial coatings in a clinical MRSA strain.
Materials science & engineering c-Biomimetic and
supramolecular systems, 119, [111578]. https://doi.org/10.1016/j.msec.2020.111578
Huang,
C., & Kok, J. (2020). Editing of the
proteolytic system of Lactococcus lactis increases its bioactive
potential. Applied and environmental
microbiology, 86(18), [e01319]. https://doi.org/10.1128/AEM.01319-20
Papadimitriou,
K., Kline, K., Renault, P., & Kok, J. (2020).
Editorial: Omics and Systems Approaches to Study the Biology
and Applications of Lactic Acid Bacteria.
Frontiers in Microbiology, 11,
[1786]. https://doi.org/10.3389/fmicb.2020.01786
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
Price,
C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J.,
Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F.
J., Marrink, S-J., Montalban-Lopez, M., de Jong,
A., Kok, J., Molenaar, D., Poolman,
B., Teusink, B., & 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., Kuipers, O. P., & 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
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
Skirl,
A-M., Kuipers, O. P., & van Doorn, G.
S. (2019). Characterization of controllable
mutator strains. Poster session presented at
Netherlands Society for Evolutionary Biology Meeting 2019, Ede,
Netherlands.
Perez,
M., Calles-Enríquez, M., Del Rio, B., Redruello, B., de
Jong, A., Kuipers, O. P., Kok, J.,
Martin, M. C., Ladero, V., Fernandez, M., & 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
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
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
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., Hiller, N. L., Andrew, P. W.,
& 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
Kasuga,
G., Tanaka, M., Harada, Y., Nagashima, H., Yamato, T., Wakimoto,
A., Arakawa, K., Ito, Y., Kawai, Y., Kok, J., &
Masuda, T. (2019). Homologous expression and characterization
of gassericin T and gassericin S, a novel class IIb bacteriocin
produced by LA327. Applied and environmental
microbiology, 85(6), [e02815-18]. https://doi.org/10.1128/AEM.02815-18
Omony,
J., de Jong, A., Kok, J., & van
Hijum, S. A. F. T. (2019). Reconstruction and inference of
the Lactococcus lactis MG1363 gene co-expression network.
PLoS ONE, 14(5), [e0214868]. https://doi.org/10.1371/journal.pone.0214868
van
der Meulen, S. B., Hesseling-Meinders, A., de Jong,
A., & Kok, J. (2019). The protein
regulator ArgR and the sRNA derived from the 3'-UTR region of its
gene, ArgX, both regulate the arginine deiminase pathway in
Lactococcus lactis. PLoS ONE,
14(6), [e0218508]. https://doi.org/10.1371/journal.pone.0218508
Tarazanova,
M., Starrenburg, M., Todt, T., van Hijum, S., Kok, J.,
& Bachmann, H. (2019). Transcriptional response of
Lactococcus lactis during bacterial emulsification.
PLoS ONE, 14(7), [e0220048]. https://doi.org/10.1371/journal.pone.0220048
2018
Bron,
P. A., Marcelli, B., Mulder, J., van der Els, S., Morawska,
L. P., Kuipers, O. P., Kok, J.,
& 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). https://worldwide.espacenet.com/publicationDetails/originalDocument?CC=WO&NR=2018231058A2&KC=A2&FT=D&ND=3&date=20181220&DB=&locale=en_EP
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., Bassard, J-E., Benkoulouche, M., Bott, M., Braga, A., Breitel,
D., Brennan, R., Bulteau, L., Chanforan, C., Costa, I., Costa, R.
S., Doostmohammadi, M., Faria, N., Feng, C., ... 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., Xu, H., Saris,
P., Kuipers, O. P., & 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
Tarazanova,
M., Huppertz, T., Kok, J., & Bachmann, H. (2018).
Altering textural properties of fermented milk by using
surface-engineered Lactococcus lactis. Microbial
Biotechnology, 11(4), 770-780. https://doi.org/10.1111/1751-7915.13278
Vaishampayan,
A., de Jong, A., Wight, D. J., Kok, J.,
& Grohmann, E. (2018). A Novel Antimicrobial Coating
Represses Biofilm and Virulence-Related Genes in
Methicillin-Resistant Staphylococcus aureus.
Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.00221
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
Tarazanova,
M., Huppertz, T., Kok, J., & Bachmann, H. (2018).
Influence of lactococcal surface properties on cell retention
and distribution in cheese curd. International
Dairy Journal, 85, 73-78. https://doi.org/10.1016/j.idairyj.2018.05.003
Siroli,
L., Braschi, G., de Jong, A., Kok, J.,
Patrignani, F., & Lanciotti, R. (2018). Transcriptomic
approach and membrane fatty acid analysis to study the response
mechanisms of Escherichia coli to thyme essential oil, carvacrol,
2-(E)-hexanal and citral exposure. Journal of
Applied Microbiology, 125(5), 1308-1320.
[jam.14048]. https://doi.org/10.1111/jam.14048
2017
Clauss-Lendzian,
E., Vaishampayan, A., de Jong, A., Landau, U., Meyer,
C., Kok, J., & Grohmann, E. (2018). Stress
response of a clinical Enterococcus faecalis isolate subjected to a
novel antimicrobial surface coating.
Microbiological Research, 207,
53-64. https://doi.org/10.1016/j.micres.2017.11.006
Tarazanova,
M., Huppertz, T., Beerthuyzen, M., van Schalkwijk, S., Janssen, P.,
Wels, M., Kok, J., & Bachmann, H. (2017).
Cell Surface Properties of Lactococcus lactis Reveal Milk
Protein Binding Specifically Evolved in Dairy Isolates.
Frontiers in Microbiology, 8,
[1691]. https://doi.org/10.3389/fmicb.2017.01691
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
van
der Meulen, S. B., de Jong, A., & Kok,
J. (2017). Early Transcriptome Response of Lactococcus
lactis to Environmental Stresses Reveals Differentially Expressed
Small Regulatory RNAs and tRNAs. Frontiers in
Microbiology, 8, [1704]. https://doi.org/10.3389/fmicb.2017.01704
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
Gijtenbeek, L. A., & Kok, J. (2017).
Illuminating Messengers: An Update and Outlook on RNA
Visualization in Bacteria. Frontiers in
Microbiology, 8, [1161]. https://doi.org/10.3389/fmicb.2017.01161
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., Kok, J., Martin,
M. C., Fernandez, M., & 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
2016
Solopova,
A., Formosa-Dague, C., Courtin, P., Furlan, S., Veiga, P.,
Péchoux, C., Armalyte, J., Sadauskas, M., Kok,
J., Hols, P., Dufrêne, Y. F., Kuipers, O.
P., Chapot-Chartier, M-P., & 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
Papadimitriou,
K., Alegría, Á., Bron, P. A., de Angelis, M., Gobbetti,
M., Kleerebezem, M., Lemos, J. A., Linares, D. M., Ross, P.,
Stanton, C., Turroni, F., van Sinderen, D., Varmanen, P., Ventura,
M., Zúñiga, M., Tsakalidou, E., & Kok,
J. (2016). Stress Physiology of Lactic Acid
Bacteria. Microbiology and Molecular Biology
Reviews, 80(3), 837-890. https://doi.org/10.1128/MMBR.00076-15
van
der Meulen, S. B., de Jong, A., & Kok,
J. (2016). Transcriptome landscape of Lactococcus
lactis reveals many novel RNAs including a small regulatory RNA
involved in carbon uptake and metabolism. RNA
Biology, 13(3), 353-366. https://doi.org/10.1080/15476286.2016.1146855
Perez,
M., Ladero, V., Del Rio, B., Redruello, B., Jong, de,
A., Kuipers, O. P., Kok, J.,
Martin, M. C., Fernandez, M., & 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
Goel,
A., Eckhardt, T. H., Puri, P., de Jong, A., Branco dos
Santos, F., Giera, M., Fusetti, F., de Vos, W. M., Kok,
J., Poolman, B., Molenaar, D., Kuipers,
O. P., & 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
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
2014
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
C.
Abrantes, M., Kok, J., & de Fatima Silva Lopes, M.
(2014). Enterococcus faecalis zinc-responsive proteins
mediate bacterial defence against zinc overload, lysozyme and
oxidative stress. Microbiology,
160(12), 2755-2762. https://doi.org/10.1099/mic.0.080341-0
Visweswaran,
G. R. R., Leenhouts, K., van Roosmalen, M., Kok,
J., & Buist, G. (2014). Exploiting
the peptidoglycan-binding motif, LysM, for medical and industrial
applications. Applied Microbiology and
Biotechnology, 98(10), 4331-4345. https://doi.org/10.1007/s00253-014-5633-7
Kok,
J., Johansen, E., Kleerebezem, M., & Teusink, B. (2014).
Lactic Acid Bacteria: embarking on 30 more years of
research. Microbial Cell Factories,
13(Suppl 1), [l1]. https://doi.org/10.1186/1475-2859-13-S1-I1
Puri,
P., Eckhardt, T. H., Franken, L. E., Fusetti, F., Stuart, M.
C. A., Boekema, E. J., Kuipers, O. P.,
Kok, 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
2013
Visweswaran,
G. R. R., Steen, A., Leenhouts, K., Szeliga, M.,
Ruban, B., Hesseling-Meinders, A., Dijkstra, B. W., Kuipers,
O. P., Kok, J., & 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., Kok, J., Kuipers, O.
P., & 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
Abrantes,
M. C., Kok, J., & Lopes, M. D. F. (2013).
EfaR Is a Major Regulator of Enterococcus faecalis Manganese
Transporters and Influences Processes Involved in Host Colonization
and Infection. Infection and Immunity,
81(3), 935-944. https://doi.org/10.1128/IAI.06377-11
Steele,
J., Broadbent, J., & Kok, J. (2013).
Perspectives on the contribution of lactic acid bacteria to
cheese flavor development. Current Opinion in
Biotechnology, 24(2), 135-141. https://doi.org/10.1016/j.copbio.2012.12.001
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
2012
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2012).
A genetically engineered protein domain binding to bacterial
murein, archaeal pseudomurein, and fungal chitin cell wall
material. Applied Microbiology and
Biotechnology, 96(3), 729-737. https://doi.org/10.1007/s00253-012-3871-0
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
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
Tariq,
M., Bruijs, C., Kok, J., & Krom, B. P. (2012).
Link between Culture Zeta Potential Homogeneity and Ebp in
Enterococcus faecalis. Applied and environmental
microbiology, 78(7), 2282-2288. https://doi.org/10.1128/AEM.07618-11
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
Honda,
H., Nagaoka, S., Kawai, Y., Kemperman, R., Kok, J.,
Yamazaki, Y., Tateno, Y., Kitazawa, H., & Saito, T. (2012).
Purification and characterization of two
phospho-β-galactosidases, LacG1 and LacG2, from Lactobacillus
gasseri ATCC33323T. The Journal of General and
Applied Microbiology, 58(1), 11-17. https://doi.org/10.2323/jgam.58.11
Roces,
C., Pérez, V., Campelo, A. B., Blanco, D., Kok,
J., Kuipers, O. P., Rodríguez, A., &
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
Puri,
P., Eckhardt, T., Franken, L., Fusetti, F., Stuart,
M., Boekema, E., Kok, J., Kuipers,
O., & 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
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2011).
A minimum of three motifs is essential for optimal binding of
pseudomurein cell wall-binding domain of Methanothermobacter
thermautotrophicus. PLoS ONE,
6(6), [21582]. https://doi.org/10.1371/journal.pone.0021582
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.
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
Papadimitriou,
K., & Kok, J. (2011). Future Challenges in
Lactic Acid Bacteria Stress Physiology Research. In K.
Papadimitriou, & E. Tsakalidou (Eds.), Stress Responses of
Lactic Acid Bacteria (pp. 507-518). (Food Microbiology and
Food Safety). Springer. https://doi.org/10.1007/978-0-387-92771-9_21
Kabuki,
T., Kawai, Y., Uenishi, H., Seto, Y., Kok, J.,
Nakajima, H., & Saito, T. (2011). Gene cluster for
biosynthesis of thermophilin 1277-a lantibiotic produced by
Streptococcus thermophilus SBT1277, and heterologous expression of
TepI, a novel immunity peptide. Journal of Applied
Microbiology, 110(3), 641-649. https://doi.org/10.1111/j.1365-2672.2010.04914.x
Abrantes,
M. C., Lopes, M. D. F., & Kok, J. (2011).
Impact of manganese, copper and zinc ions on the
transcriptome of the nosocomial pathogen Enterococcus faecalis
V583. PLoS ONE, 6(10),
[e26519]. https://doi.org/10.1371/journal.pone.0026519
Rigottier-Gois,
L., Alberti, A., Houel, A., Taly, J-F., Palcy, P., Manson, J.,
Pinto, D., Matos, R. C., Carrilero, L., Montero, N., Tariq,
M., Karsens, H., Repp, C., Kropec, A., Budin-Verneuil,
A., Benachour, A., Sauvageot, N., Bizzini, A., Gilmore, M. S., ...
Serror, P. (2011). Large-Scale Screening of a Targeted
Enterococcus faecalis Mutant Library Identifies Envelope Fitness
Factors. PLoS ONE, 6(12),
[29023]. https://doi.org/10.1371/journal.pone.0029023
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2011).
Murein and pseudomurein cell wall binding domains of bacteria
and archaea-a comparative view. Applied
Microbiology and Biotechnology, 92(5),
921-928. https://doi.org/10.1007/s00253-011-3637-0
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
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).
Springer. https://doi.org/10.1007/978-0-387-92771-8_8
Campelo,
A. B., Gaspar, P., Roces, C., Rodriguez, A., Kok,
J., Kuipers, O. P., Neves, A. R., &
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
Hill,
C., Kleerebezem, M., & Kok, J. (2011). The
proceedings of the Tenth Symposium on Lactic Acid Bacteria.
Microbial Cell Factories, 10((Suppl.
1) : S1), S1-S1. https://doi.org/10.1186/1475-2859-10-S1-S1
2010
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
Linares,
D. M., Kok, J., & Poolman, B. (2010).
Genome Sequences of Lactococcus lactis MG1363 (Revised) and
NZ9000 and Comparative Physiological Studies.
Journal of Bacteriology, 192(21),
5806 - 5812. https://doi.org/10.1128/JB.00533-10
Chikindas,
M., Emond, E., Haandrikman, A. J., Kok, J., Leenhouts,
K., Pandian, S., Venema, G., & Venema, K. (2010).
Heterologous Processing and Export of the Bacteriocins
Pediocin PA-1 and Lactococcin A in Lactococcus Lactis: A Study with
Leader Exchange. Probiotics and Antimicrobial
Proteins, 2(2), 66-76. https://doi.org/10.1007/s12602-009-9023-x
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
Visweswaran,
G. R. R., Dijkstra, B. W., & Kok, J. (2010).
Two Major Archaeal Pseudomurein Endoisopeptidases: PeiW and
PeiP. Archaea-An international microbiological
journal, 2010(3), 1-4. [480492]. https://doi.org/10.1155/2010/480492
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
Kawai,
Y., Kusnadi, J., Kemperman, R., Kok, J., Ito, Y.,
Endo, M., Arakawa, K., Uchida, H., Nishimura, J., Kitazawa, H.,
& Saito, T. (2009). DNA Sequencing and Homologous
Expression of a Small Peptide Conferring Immunity to Gassericin A,
a Circular Bacteriocin Produced by Lactobacillus gasseri
LA39. Applied Environmental
Microbiology, 75(5), 1324-1330. https://doi.org/10.1128/AEM.02485-08
2008
Kramer,
N. E., Hasper, H. E., van den Bogaard, P. T. C., Morath, S., de
Kruijff, B., Hartung, T., Smid, E. J., Breukink, E., Kok,
J., & 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
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
Steen,
A., Buist, G., Kramer, N. E., Jalving, R.,
Benus, G. F. J. D., Venema, G., Kuipers, O. P.,
& 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
van
Hijum, S. A. F. T., Baerends, R. J. S., Zomer, A. L.,
Karsens, H. A., Martin-Requena, V., Trelles, O., Kok,
J., & 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
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
2007
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
Ventura,
M., Zomer, A., Canchaya, C., O'Connell-Motherway, M.,
Kuipers, O., Turroni, F., Ribbera, A., Foroni, E.,
Buist, G., Wegmann, U., Shearman, C., Gasson, M. J.,
Fitzgerald, G. F., Kok, J., van Sinderen, D., &
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., Ventura, M., Goesmann, A., Gasson, M.
J., Kuipers, O. P., van Sinderen, D., & 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
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
Steen,
A., van Schalkwijk, S., Buist, G., Twigt, M.,
Szeliga, M., Meijer, W., Kuipers, O. P., Kok,
J., & 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
Veiga,
P., Bulbarela-Sampieri, C., Furlan, S., Maisons, A.,
Chapot-Chartier, M-P., Erkelenz, M., Mervelet, P., Noirot, P.,
Frees, D., Kuipers, O. P., Kok, J.,
Gruss, A., Buist, G., & 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
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
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
Kenny,
JG., Leach, S., de la Hoz, AB., Venema, G., Kok, J.,
Fitzgerald, GF., Nauta, A., Alonso, JC., van Sinderen, D., Kenny,
J. G., Hoz, A. B. D. L., Fitzgerald, G. F., & Alonso, J. C.
(2006). Characterization of the lytic-lysogenic switch of the
lactococcal bacteriophage Tuc2009.
Virology, 347(2), 434-446. https://doi.org/10.1016/j.virol.2005.11.041
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
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
Gutierrez,
J., Larsen, R., Cintas, L. M., Kok, J., &
Hernandez, P. E. (2006). High-level heterologous production
and functional expression of the sec-dependent enterocin P from
Enterococcus faecium P13 in Lactococcus lactis.
Applied Microbiology and Biotechnology,
72(1), 41-51. https://doi.org/10.1007/s00253-005-0233-1
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
Last modified: | 07 March 2016 11.42 a.m. |