Publication highlights
Research articles
2024
Wong, Sook Yi and Soman, Aghil and Korolev, Nikolay and Surya, Wahyu and Chen, Qinming and Shum, Wayne and van Noort, John and Nordenskiöld, Lars, The shelterin component TRF2 mediates columnar stacking of human telomeric chromatin, The EMBO journal. 2024; 43(1);87-111. doi: 10.1038/s44318-023-00002-3
Severins, Ivo and Bastiaanssen, Carolien and Kim, Sung Hyun and Simons, Roy B and van Noort, John and Joo, Chirlmin, Single-molecule structural and kinetic studies across sequence space, Science. 2024; 385(6711);898-904. doi: 10.1126/science.adn5968
Augustijn, H. E., Karapliafis, D., Joosten, K. M. M., Rigali, S., van Wezel, G. P. & Medema, M. H. LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria. J Mol Biol, 168558 (2024). doi: 10.1016/j.jmb.2024.168558
Li, C., Urem, M., Kotsogianni, I., Lau, J., Elsayed, S.S., Martin, N.I., McNae, I.W., Voskamp, P., Mayer, C., Rigali, S., Pannu, N., Abrahams, J.P., Schada von Borzyskovski, L. and van Wezel, G.P. A new pathway in central metabolism mediates nutrient control of development and antibiotic production by Streptomyces. BioRXiv. doi: 10.1101/2024.1107.1114.603434
Proteolytic activity of surface-exposed HtrA determines its expression level and is needed to survive acidic conditions in Clostridioides difficile.
Corver J, Claushuis B, Shamorkina TM, de Ru AH, van Leeuwen MM, Hensbergen PJ, Smits WK.Mol Microbiol. 2024; 122(4):413-428. doi: 10.1111/mmi.15300
Clostridioides difficile in calves, cattle and humans from Dutch dairy farms: Predominance of PCR ribotype 695 (clade 5, sequence type 11) in cattle. Cuperus T, Wit B, Castelijn G, Hengeveld P, Opsteegh M, van der Giessen J, Harmanus C, van Prehn J, Kuijper EJ, Smits WK.One Health. 2024; 18:100739. doi: 10.1016/j.onehlt.2024.100739
CslA and GlxA from Streptomyces lividans form a functional cellulose synthase complex. Zhong X, Nicolardi S, Ouyang R, Wuhrer M, Du C, van Wezel G, Vijgenboom E, Briegel A, Claessen D.Appl Environ Microbiol. 2024; 90(4):e0208723. doi: 10.1128/aem.02087-23
Phage fibers and spikes: a nanoscale Swiss army knife for host infection. Ouyang R, Ongenae V, Muok A, Claessen D, Briegel A.Curr Opin Microbiol. 2024; 77:102429. doi: 10.1016/j.mib.2024.102429
S. Schwab, Y. Hu, B. van Erp, M.K.M. Cajili, M.D. Hartmann, B. Hernandez Alvarez, V. Alva, A.L. Boyle & R.T. Dame, Novel histones and histone variant families in prokaryotes.
Nature Communications. doi: 10.1038/s41467-024-52337-y
Y. Hu, S. Schwab, S. Deiss, P. Escudeiro, T. van Heesch, J.D. Joiner, J. Vreede, M.D. Hartmann, A.N. Lupas, B. Hernandez Alvarez, V.Alva & R.T. Dame, Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending.
Nucleic Acids Research. 52(14): 8193-8204, 2024 doi: 10.1093/nar/gkae485.
Richter A, Blei F, Hu G, Schwitalla JW, Lozano-Andrade CN, Xie J, Jarmusch SA, Wibowo M, Kjeldgaard B, Surabhi S, Xu X, Jautzus T, Phippen CBW, Tyc O, Arentshorst M, Wang Y, Garbeva P, Larsen TO, Ram AFJ, van den Hondel CAM, Maróti G, Kovács ÁT (2024) Enhanced surface colonisation and competition during bacterial adaptation to a fungus. Nature Communications 15:4486. doi: 10.1038/s41467-024-48812-1
Lyng M, Jørgensen JPB, Schostag MD, Jarmusch SA, Aguilar DKC, Lozano-Andrade CN, Kovács ÁT (2024) Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis. ISME Journal 18:wrad001. doi: 10.1093/ismejo/wrad001
2023
F. Sartor, X. Xu, T. Popp, AN Dodd, Á.T. Kovács & M. Merrow, The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems. Science Adv 9:eadh1308, 2023 doi: 10.1126/sciadv.adh1308.
R. Gallegos-Monterrosa & Á.T. Kovács, Phenotypic plasticity: the role of a phosphatase family Rap in the genetic regulation of Bacilli. Mol Microbiol 120: 20-31, 2023 doi: 10.1111/mmi.15060.
A.M. Erkelens, B. Henneman, R.A. van der Valk, N.C.S. Kirolos & R.T. Dame, Specific DNA binding of archaeal histones HMfA and HMfB from Methanothermus fervidus. Front. Microbiol. 14:1166608, 2023. doi: 10.3389/fmicb.2023.1166608
A.M. Erkelens, L. Qin, B. van Erp, A. Miguel-Arribas, D. Abia, H. Keek, D. Markus, M.K. Cajili, S. Schwab, W.J.J. Meijer & R.T. Dame, The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues. Nucleic Acids Research. 50(21):12166-12185, 2022. doi: 10.1093/nar/gkac1064.
A.R. Muok, K. Kurniyati, C.K. Cassidy, F.A. Olsthoorn, D.R. Ortega, A. Sidi Mabrouk, C. Li, A. Briegel (2023), A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis, mBio. doi: 10.1128/mbio.01598-23.
A. Sidi Mabrouk, V. Ongenae, D. Claessen, S. Brenzinger, A. Briegel (2023), A Flexible and Efficient Microfluidics Platform for the Characterization and Isolation of Novel Bacteriophages, Applied and Environmental Microbiology 89(1). doi: 10.1128/aem.01596-22.
Ducarmon Q.R., van der Bruggen T., Harmanus C., Sanders I.M.J.G., Daenen L.G.M., Fluit A.C., Vossen R.H.A.M., Kloet S.L., Kuijper E.J., Smits W.K. (2023), Clostridioides difficile infection with isolates of cryptic clade C-II: a genomic analysis of polymerase chain reaction ribotype 151, Clin Microbiol Infect 29(4):538.e1-538.e6. doi: 10.1016/j.cmi.2022.12.003.
Roseboom A.M., Ducarmon Q.R., Hornung B.V.H., Harmanus C., Crobach M.J.T., Kuijper E.J., Vossen R.H.A.M., Kloet S.L., Smits W.K. (2023), Carriage of three plasmids in a single human clinical isolate of Clostridioides difficile, Plasmid. 125:102669. doi: 10.1016/j.plasmid.2022.102669.
Etifa P., Rodríguez C., Harmanus C., Sanders I.M.J.G., Sidorov I.A., Mohammed O.A., Savage E., Timms A.R., Freeman J., Smits W.K., Wilcox M.H., Baines S.D. (2023), Non-Toxigenic Clostridioides difficile Strain E4 (NTCD-E4) Prevents Establishment of Primary C. difficile Infection by Epidemic PCR Ribotype 027 in an In Vitro Human Gut Model, Antibiotics 12(3):435. doi: 10.3390/antibiotics12030435.
Zhang L., Willemse J., Yagüe P., de Waal E., Claessen D. & van Wezel G.P. (2023), The SepF-like proteins SflA and SflB prevent ectopic localization of FtsZ and DivIVA during sporulation of Streptomyces coelicolor. Biochemical and Biophysical Research Communications 645:79-87. doi: 10.1016/j.bbrc.2023.01.021.
2022
Shitut S.S., Shen M.J., Claushuis B., Derks R.J.E., Giera M., Rozen D.E., Claessen D. & Kros A. (2022), Generating Heterokaryotic Cells via Bacterial Cell-Cell Fusion. Microbiology Spectrum. 10(4):e0169322. doi: 10.1128/spectrum.01693-22.
Zhong X., Zhang L., van Wezel G.P., Vijgenboom E. & Claessen D. (2022), Role for A lytic polysaccharide monooxygenase in cell wall remodeling in Streptomyces coelicolor. mBio 13(2): e0045622. doi: 10.1128/mbio.00456-22.
Du C., Willemse J., Erkelens A.M., Carrion V.J., Dame R.T. & Wezel G.P. van (2022), System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on Streptomyces Development, mSystems 7(3): e00061-22. doi: 10.1093/nar/gkab993.
Forrest D., Warman E.A., Erkelens A.M., Dame R.T. & Grainger D.C. (2022), Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity, Nature Communications 13(1): 1149. doi: 10.1038/s41467-022-28747-1.
Rashid F.Z.M., Mahlandt E., Vaart M. van der, Boer D.E.C., Valera Alvarez M., Henneman B., Brocken D.J.W., Voskamp P., Blok A.J., Shimizu T.S., Meijer A.H., Luijsterburg M.S., Goedhart J., Cremazy F.G.E. & Dame R.T. (2022), HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein, Nucleic Acids Research 50(2): e10. doi: 10.1093/nar/gkab993.
Ongenae Véronique, Mabrouk Adam Sidi, Crooijmans Marjolein, Rozen Daniel, Briegel Ariane and Claessen Dennis, Reversible bacteriophage resistance by shedding the bacterial cell wall, Open Biol. 12210379210379. doi: 10.1098/rsob.210379.
Smits W.K., Mohammed Y., de Ru A.H., Cordo' V., Friggen A.H., van Veelen P.A., Hensbergen P.J., Clostridioides difficile Phosphoproteomics Shows an Expansion of Phosphorylated Proteins in Stationary Growth Phase, mSphere. 2022 Feb 23;7(1):e0091121. doi: 10.1128/msphere.00911-21. Epub 2022 Jan 5.PMID: 34986318
Oliveira Paiva A.M., Friggen A.H., Douwes R., Wittekoek B., Smits W.K., Practical observations on the use of fluorescent reporter systems in Clostridioides difficile, Antonie Van Leeuwenhoek. 2022 Feb;115(2):297-323. doi: 10.1007/s10482-021-01691-8. Epub 2022 Jan 18.PMID: 35039954.
Garcia-Garcia T., Douché T., Giai Gianetto Q., Poncet S., El Omrani N., Smits W.K., Cuenot E., Matondo M., Martin-Verstraete I. (2022), In-Depth Characterization of the Clostridioides difficile Phosphoproteome to Identify Ser/Thr Kinase Substrates, Mol Cell Proteomics 21(11):100428. doi: 10.1016/j.mcpro.2022.100428.
Kapteijn R., Shitut S., Aschmann D., Zhang L., de Beer M., Daviran D., Roverts R., Akiva A., van Wezel G.P., Kros A., Claessen D., Endocytosis-like DNA uptake by cell wall-deficient bacteria, Nat Commun. (2022) Sep 22;13(1):5524. doi: 10.1038/s41467-022-33054-w.
2021
Gilbert B.R., Thornburg Z.R., Lam V., Rashid F.-Z.M., Glass J.I., Villa E., Dame R.T. & Luthey-Schulten Z., Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps, Frontiers in Molecular Biosciences 8: 644133. doi: 10.3389/fmolb.2021.644133.
Ultee, E., Zhong, X., Shitut, S., Briegel, A. and Claessen, D. Formation of wall-less cells in Kitasatospora viridifaciens requires cytoskeletal protein FilP in oxygen-limiting conditions. Mol Microbiol. doi: 10.1111/mmi.14662.
Zhang, L. Ramijan, K., Carrión, V.J., van der Aart, L.T., Willemse, J., van Wezel, G.P. and Claessen, D. A novel and conserved cell wall enzyme that can substitute for the Lipid II synthase MurG biorXiv. doi: 10.1101/2020.10.12.336396.
Henneman, B., Brouwer, T.B., Erkelens, A.M., Kuijntjes, G.J., van Emmerik, C., van der Valk, R.A., Timmer, M., Kirolos, N.C.S., van Ingen, H., van Noort, J. and Dame, R.T. Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Res. doi: 10.1093/nar/gkaa1196.
Muok, A.R., Claessen, D. & Briegel, A., Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria, ISME J 15, 2591–2600 (2021). doi: 10.1038/s41396-021-00952-8.
Boekhoud I.M., Sidorov I., Nooij S., Harmanus C., Bos-Sanders I.M.J.G., Viprey V., Spittal W., Clark E., Davies K., Freeman J., Kuijper E.J., Smits W.K., Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile, COMBACTE-CDI Consortium.J Antimicrob Chemother. 2021 Jun 18;76(7):1731-1740. doi: 10.1093/jac/dkab097.PMID: 33876817.
2020
Kloosterman, A.M., Cimermancic, P., Elsayed, S.S., Du, C., Hadjithomas, M., Donia, M.S., Fischbach, M.A., van Wezel, G.P. and Medema, M.H. Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PLoS Biol. 18(12):e3001026. doi: 10.1371/journal.pbio.3001026.
Zhang, Z., Du, C., de Barsy, F., Liem, M., Liakopoulos, A., van Wezel, G.P., Choi, Y.H., Claessen, D. and Rozen, D.E. Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation. Sci Adv. 6(3):eaay5781. doi: 10.1126/sciadv.aay5781.
Muok, A.R., Ortega, D.R., Kurniyati, K., Yang, W., Maschmann, Z.A., Mabrouk, A.S., Li, C., Crane, B.R. and Briegel, A. Atypical chemoreceptor arrays accommodate high membrane curvature. Nature Comm. 11(1):5763. doi: 10.1038/s41467-020-19628-6.
Oliveira Paiva, A.M., van Eijk, E., Friggen, A.H., Weigel, C. and Smits, W.K. Identification of the Unwinding Region in the Clostridioides difficile Chromosomal Origin of Replication. Front Microbiol. 11:581401. doi: 10.3389/fmicb.2020.581401.
Boekhoud, I.M., Hornung, B.V.H., Sevilla, E., Harmanus, C., Bos-Sanders, I.M.J.G., Terveer, E.M., Bolea, R., Corver, J., Kuijper, E.J. and Smits W.K. Plasmid-mediated metronidazole resistance in Clostridioides difficile. Nature Comm. 11(1):598. doi: 10.1038/s41467-020-14382-1.
Qin, L., Bdira, F.B., Sterckx, Y.G.J., Volkov, A.N., Vreede, J., Giachin, G., van Schaik, P., Ubbink, M. and Dame, R.T. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Res. 48(4):2156-2172. doi: 10.1093/nar/gkz1226.
2019
van Eijk E., Boekhoud .IM., Kuijper E.J., Bos-Sanders I.M.J.G., Wright G. and Smits W.K. Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile. Antimicrob. Agents Chemother. 63(2). pii: e01363-18. doi: 10.1128/AAC.01363-18.
Oliveira Paiva, A.M., Friggen, A.H., Qin L., Douwes, R., Dame, R.T. and Smits W.K. The Bacterial Chromatin Protein HupA Can Remodel DNA and Associates with the Nucleoid in Clostridium difficile. J. Mol. Biol. 431(4):653-672. doi: 10.1016/j.jmb.2019.01.001.
Wu, C., van der Heul, H.U., Melnik, A.V., Luebben, J., Dorrestein, P.C., Minnaard, A.J., Choi, Y.H. and van Wezel, G.P. Lugdunomycin, an angucycline-derived molecule with unprecedented chemical architecture. Angew. Chem. Int. Ed. Engl. doi:10.1002/anie.201814581.
2018
Dissel, D., Willemse, J., Zacchetti, B., Claessen, D., Pier, G.B., and van Wezel, G.P. Production of poly-beta-1,6-N-acetylglucosamine by MatAB is required for hyphal aggregation and hydrophilic surface adhesion by Streptomyces. Microb. cell 5: 269-279.
Henneman, B., van Emmerik, C.L., van Ingen, H. and Dame, R.T.
Structure and function of archaeal histones. PLOS Gen. 14(9):e1007582. doi: 10.1371/journal.pgen.1007582.
Ramijan, K, E. Ultee, J. Willemse, Z. Zhang, J.A.J. Wondergem, A. van der Meij, D. Heinrich, A. Briegel, G.P. van Wezel & D. Claessen. Stress-induced formation of cell wall-deficient cells in filamentous actinomycetes. Nature Comm. 9: 5164.
Yang, W., Alvarado, A., Glatter, T., Ringgaard, S., and Briegel, A.
Baseplate variability of Vibrio choleraechemoreceptor arrays, Proc. Natl. Acad. Sci. USA. 115, 13365-13370.
2017
van der Valk, R.A, Vreede, J., Moolenaar, G.F., Hofmann, A., Goosen, N. and Dame, R.T. Environmentally driven conformational changes modulate the function of H-NS. eLife. 6: 27369.
2016
Briegel, A., Ortega, D. R., Mann, P., Kjaer, A., Ringgaard, S., and Jensen, G. J. Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio choleraeand are stabilized by a double signaling domain receptor DosM Proc. Natl. Acad. Sci. USA. 113, 10412-10417.
Celler, K., Koning, R.I., Willemse, J., Koster, A.J. and van Wezel, G.P. Cross-membranes orchestrate compartmentalization and morphogenesis in Streptomyces. Nature Communications 7: 11836.
Petrus, M.L.C., E. Vijgenboom, A.K. Chaplin, J.A.R. Worrall, G.P. van Wezel and Claessen, D. The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces. Open Biology 6: 150149.
Zacchetti, B., Willemse, J., Recter, B., van Dissel, D., van Wezel, G.P., Wösten, H.A.B. and Claessen, D. Aggregation of germlings is a major contributing factor towards mycelial heterogeneity of Streptomyces. Scientific Reports 6: 27045.
Authoritative review articles
F-Z. M. Rashid & R.T. Dame, Interplay between local chromosome structure and gene activity. Mol. Microbiol. 120 (1): 60-70, 2023. doi: 10.1111/mmi.15062.
Smits W.K., Roseboom A.M., Corver J., Plasmids of Clostridioides difficile, Curr Opin Microbiol. 2022 Feb;65:87-94. doi: 10.1016/j.mib.2021.10.016. Epub 2021 Nov 11.PMID: 34775173
Yang, W. and Briegel, A. Diversity of Bacterial Chemosensory Arrays. Trends Microbiol. 2020.28(1):68-80. doi: 10.1016/j.tim.2019.08.002.
Dame, R.T., Rashid, F.M. and Grainger, D.C. Chromosome organization in bacteria: mechanistic insights into genome structure and function. Nature Reviews Gen. 2020. doi: 10.1038/s41576-019-0185-4.
Claessen, D. and Errington, J. Cell Wall Deficiency as a Coping Strategy for Stress. Trends Microbiol. 2019. 27(12):1025-1033. doi: 10.1016/j.tim.2019.07.008.
Ultee, E., Ramijan, K., Dame, R.T., Briegel, A. and Claessen, D. Stress-induced adaptive morphogenesis in bacteria. Adv. Microb. Physiol. 2019. 74:97-141. doi: 10.1016/bs.ampbs.2019.02.001.
Smits, W.K., Lyras, D., Lacy, D.B., Wilcox, M.H. and Kuijper, E.J. Clostridium difficile infection. Nature Reviews Dis Primers. 2016. 2:16020. doi: 10.1038/nrdp.2016.20
Driessen, R.P.C., Peeters, E., Werner, F. and Dame, R.T. The interplay between nucleoid organization and transcription in archaeal genomes. Nature Reviews Microbiol. 2015. 13(6), 333-341.
Claessen, D., Rozen, D.E., Kuipers, O.P., Søgaard-Andersen, L. and G.P. van Wezel. Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies. Nature Reviews Microbiol. 2014. 12: 115-124.