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Publication highlights

Research articles


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.


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 DevelopmentmSystems 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 promiscuityNature 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 proteinNucleic 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 bacteriaNat Commun. (2022) Sep 22;13(1):5524. doi: 10.1038/s41467-022-33054-w.



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 mapsFrontiers 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 bacteriaISME 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.



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.KPlasmid-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.TStructural 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.



van Eijk E., Boekhoud .IM., Kuijper E.J., Bos-Sanders I.M.J.G., Wright G. and Smits W.KGenome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficileAntimicrob. 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.KThe 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.



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 StreptomycesMicrob. 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. ClaessenStress-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.



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.



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, ADiversity 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.CChromosome 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, DStress-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.

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