Dennis Claessen
Professor Molecular Microbiology / Director of Education
- Name
- Prof.dr. D. Claessen
- Telephone
- +31 71 527 5052
- d.claessen@biology.leidenuniv.nl
- ORCID iD
- 0000-0002-0789-2633
The Claessen lab studies morphogenesis and phenotypic heterogeneity in filamentous actinomycetes, which are prolific antibiotic producers. We pursue several research projects that span areas of multicellular growth and development, stress-adaptation and microbial evolution. By using multidisciplinary approaches, we aim to tackle fundamental questions, and use the generated knowledge to improve industrial exploitation of these organisms. Dennis Claessen is also the current head of the cluster Microbial Sciences.
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The cell wall is a shape-defining structure that envelopes almost all bacteria and protects them from environmental stresses. Bacteria can be forced to grow without a cell wall under certain conditions that interfere with cell wall synthesis, yielding wall-less cells known as L-forms. We have shown that several species of filamentous actinomycetes have a natural ability to generate wall-deficient cells in response to hyperosmotic stress. This wall-deficient state is transient and these cells are able to switch to the normal mycelial mode of growth. Interestingly, prolonged exposure to hyperosmotic stress yields variants that are able to proliferate indefinitely without their cell wall, similarly to L-forms. This indicates that the formation of wall-deficient cells in actinomycetes serves as an adaptation to osmotic stress. We are currently studying this remarkable response in more detail, and exploit the unique properties of these cells to obtain fundamental new insight into the plasticity of bacterial life.
Professor Molecular Microbiology / Director of Education
- Science
- Instituut Biologie Leiden
- IBL Microbial Sciences
- Ouyang R., Ongenae V.M.A., Muok A.R., Claessen D. & Briegel A. (2024), Phage fibers and spikes: a nanoscale Swiss army knife for host infection, Current Opinion in Microbiology 77: 102429.
- Guerrero Egio G., Pintado A., Bretscher K.M., Arias-Giraldo L.M., Paulson J.N., Spaink H.P., Claessen D., Ramos C., Cazorla F.M., Medema M.H., Raaijmakers J.M. & Carrion Bravo V.J. (2024), bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria, Nature Communications 15: 2072.
- Zhong X., Nicolardi S., Ouyang R., Wuhrer M., Du C., Wezel G. van, Vijgenboom E., Briegel A. & Claessen D. (2024), CslA and GlxA from Streptomyces lividans form a functional cellulose synthase complex, Applied and Environmental Microbiology 90(4): e02087.
- Britton A.P., Visser K.A., Ongenae V.M.A., Zhang P., Wassink H., Doerksen T.A., Welke C.A., Lynch K.H., Belkum M.J. van, Dennis J.J., Yang X., Claessen D., Briegel A. & Martin-Visscher L.A. (2023), Characterization of bacteriophage cd2, a siphophage infecting Carnobacterium divergens and a representative species of a new genus of phage, Microbiology Spectrum 11(4): e00973-23.
- Ongenae V.M.A., Kempff A., Neer V. van, Shomar H., Tesson F., Rozen D.E., Briegel A. & Claessen D. (2023), Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus, Scientific Reports 13: 20153.
- Zhang L., Willemse J.J., Yagüe Menéndez P., Waal E.C. de, Claessen D. & Wezel G.P. van (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.
- Lubbers M., Wezel G.P. van & Claessen D. (2023), Reproducible switching between a walled and cell wall-deficient lifestyle of actinomycetes using gradient agar plates, Journal of Microbiological Methods 204: 106660.
- Sidi Mabrouk A., Ongenae V.M.A., Claessen D., Brenzinger S. & Briegel A. (2023), A flexible and efficient microfluidics platform for the characterization and isolation of novel bacteriophages, Applied and Environmental Microbiology 89(1): e01596.
- Ongenae V.M.A., Sidi Mabrouk A., Crooijmans M.E., Rozen D.E., Briegel A. & Claessen D. (2022), Reversible bacteriophage resistance by shedding the bacterial cell wall, Open Biology 12(6): 210379.
- Kapteijn R., Shitut S.S., Aschmann D., Zhang L., Beer M. de, Daviran D., Roverts R., Akiva A., Wezel G.P. van, Kros A. & Claessen D. (2022), Endocytosis-like DNA uptake by cell wall-deficient bacteria, Nature Communications 13(1): 5524.
- Anonymous (2022), Genome sequence and characterization of Streptomyces phage Pablito, representing a new species within the genus Janusvirus [Genoom sequentie en karakterisatie van streptomyces faag pablito, een nieuwe soort in de genus Janusvirus] (translation: Ongenae V.M.A., Azeredo J., Kropinski A.M., Rozen D.E., Briegel A. & Claessen D. ), Scientific Reports 12: 17785.
- Shitut S.S., Shen M., 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.
- Zhong X., Zhang L., Wezel G.P. van, Vijgenboom E. & Claessen D. (2022), Role for a lytic polysaccharide monooxygenase in cell wall remodeling in streptomyces coelicolor, mBio 13(2): e00456-22.
- Ultee E., Zhong X.B., Shitut S., Briegel A. & Claessen D. (2021), Formation of wall‐less cells in Kitasatospora viridifaciens requires cytoskeletal protein FilP in oxygen‐limiting conditions, Molecular Microbiology 115(6): 1181-1190.
- Zhang L., Ramijan K., Carrion Bravo V.J., Aart L.T. van der, Willemse J.J., Wezel G.P. van & Claessen D. (2021), An alternative and conserved cell wall enzyme that can substitute for the lipid II synthase MurG, mBio 12(2): e03381.
- Ongenae V., Briegel A & Claessen D (2021), Cell wall deficiency as an escape mechanism from phage infection, Open Biology 11(9): 210199.
- Muok A.R., Claessen D. & Briegel A. (2021), Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria, The ISME Journal 15(9): 2591-2600.
- Zhang Z., Du C., De Barsy F., Liem M., Liakopoulos A., Wezel G.P. van, Choi Y.H., Claessen D. & Rozen D.E. (2020), Antibiotic production in Streptomyces is organized by a division of labor through terminal genomic differentiation, Science Advances 6(3): eaay5781.
- Brink M. van den, Tandar S.T., Akker T.A.P. van den, Jovikj S., Defourt V., Langelaar T.G.B., Delzenne T.O., Strien K. van, Schonk A.W., Beers A.J.A.M., Golov E., Chong L.J., Bergman G.Ö., Meijdam J.J.W.D. Crooijmans M.E., Claessen D. & Winde J.H. de (2020), Rapidemic, a versatile and label-free DNAzyme-based platform for visual nucleic acid detection. bioRxiv. [working paper].
- Ultee E., Aart L.T. van der, Zhang L., Dissel M.D. van, Diebolder C.A., Wezel G.P. van, Claessen D. & Briegel A. (2020), Teichoic acids anchor distinct cell wall lamellae in an apically growing bacterium, Communications Biology 3: 314.
- Zhang L., Willemse J., Yagüe P., Waal E.C. de, Claessen D. & Wezel G.P. van (2020), Branching of sporogenic aerial hyphae in sflA and sflB mutants of Streptomyces coelicolor correlates to ectopic localization of DivIVA and FtsZ in time and space. bioRxiv. [working paper].
- Ramijan Carmiol A.K., Zhang Z., Wezel G.P. van & Claessen D. (2020), Genome rearrangements and megaplasmid loss in the filamentous bacterium Kitasatospora viridifaciens are associated with protoplast formation and regeneration, Antonie van Leeuwenhoek 113(6): 825-837.
- Shitut S., Bergman G.Ö., Kros A., Rozen D.E. & Claessen D. (2020), Use of permanent wall-deficient cells as a system for the discovery of new-to-nature metabolites, Microorganisms 8(12): 1897.
- Ultee E., Zhong X., Shitut S.S., Briegel A. & Claessen D. (2020), Formation of wall‐less cells in Kitasatospora viridifaciens requires cytoskeletal protein FilP in oxygen‐limiting conditions, Molecular Microbiology 115(6): 1181-1190.
- Ultee E., Ramijan K., Dame R.T., Briegel A. & Claessen D. (2019), Stress-induced adaptive morphogenesis in bacteria. In: Poole R.K (Ed.), Advances in Microbial Physiology no. 74: Academic Press. 97-141.
- Claessen D. & Errington J. (2019), Cell Wall Deficiency as a Coping Strategy for Stress, Trends in Microbiology 27(12): 1025-1033.
- López-Goñi I., Giner-Lamia J., Álvarez-Ordoñez A., Alfonso Benitez-Páez, Claessen D., Cortesao M., De Toro M., García-Ruano D., Granato E.T., Kovács A.T., Romalde J.L., Sana T.G., Sánchez-Angulo M., Sangari F.J., Smits W.K., Sturm T., Thomassin J.L., Valdehuesa K.N.G. & Zapotoczna M. (2019), #EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide, FEMS Microbiology Letters 366(11): fnz141.
- Willemse J.J., Büke F., Dissel M.D. van, Grevink S., Claessen D. & Wezel G.P. van (2018), SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures, Antonie van Leeuwenhoek 111: 171-182.
- Ramijan Carmiol A.K., Ultee E., Willemse J.J., Zhang Z., Wondergem A.J., Meij A. van der, Heinrich D.M., Briegel A., Wezel G.P. van & Claessen D. (2018), Stress-induced formation of cell wall-deficient cells in filamentous actinomysetes, Nature Communications 9: 5164.
- Dissel M.D. van, Willemse J.J., Zacchetti B., Claessen D., Pier G.B. & Wezel G.P. van (2018), Production of poly-β-1, 6-N-acetylglucosamine by MatAB is required for hyphal aggregation and hydrophilic surface adhesion by Streptomyces, Microbial Cell 5(6): 269-279.
- Zacchetti B., Wösten H.A.B. & Claessen D. (2018), Multiscale heterogeneity in filamentous microbes, Biotechnology Advances 36(8): 2138-2149.
- Zacchetti B., Andrianos A., Dissel D. van, Ruiter E.M. de, Wezel G.P. van & Claessen D. (2018), Microencapsulation extends mycelial viability of Streptomyces lividans 66 and increases enzyme production, BMC Biotechnology 18: 13.
- Zacchetti B., Smits P. & Claessen D. (2018), Dynamics of pellet fragmentation and aggregation in liquid-grown cultures of Streptomyces lividans, Frontiers in Microbiology 9: 943.
- Dragoš A., Kovács Á.T. & Claessen D. (2017), The role of functional amyloids in multicellular growth and development of Gram-positive bacteria, Biomolecules 7(3): 60.
- Yang W., Willemse J., Sawyer E.B., Lou F., Gong W., Zhang H., Gras S.L., Claessen D. & Perrett S. (2017), The propensity of the bacterial rodlin protein RdlB to form amyloid fibrils determines its function in Streptomyces coelicolor, Scientific Reports 7: 42867.
- Ramijan Carmiol A.K., Wezel G.P. van & Claessen D. (2017), Genome Sequence of the Filamentous Actinomycete Kitasatospora viridifaciens, Genome Announcements 5(6): e01560.
- Dragoš A., Kovács Á.T. & Claessen D. (2017), The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria, Biomolecules 7(3): 60.
- Zhang Z., Claessen D. & Rozen D.E. (2016), Understanding Microbial Divisions of Labor, Frontiers in Microbiology 7: 2070.
- Zacchetti B., Willemse J.J., Recter B., Dissel M.D. van, Wezel G.P. van, Wösten H.A.B. & Claessen D. (2016), Aggregation of germlings is a major contributing factor towards mycelial heterogeneity of Streptomyces, Scientific Reports 6: 27045.
- Zhang L., Willemse J., Claessen D. & Wezel G.P. van (2016), SepG coordinates sporulation-specific cell division and nucleoid organization in Streptomyces coelicolor, Open Biology 6(4): 150164.
- Petrus M.L.C., Vijgenboom E., Chaplin A.K., Worrall J.A.R., Wezel G.P. van & Claessen D. (2016), The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces, Open Biology 6(1): 150149.
- Dissel M.D. van, Claessen D., Roth M. & Wezel G.P. van (2015), A novel locus for mycelial aggregation forms a gateway to improved Streptomyces cell factories, Microbial Cell Factories 14: 44.
- Wu C., Zacchetti B., Ram A.F.J., Wezel G.P. van, Claessen D. & Choi Y.H. (2015), Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation, Scientific Reports 2015(5): 10868.
- Chaplin A.K., Petrus M.L.C., Mangiameli G., Hough M.A., Svistunenko D.A., Nicholls P., Claessen D., Vijgenboom E. & Worrall J.A.R. (2015), GlxA is a new structural member of the radical copper oxidase family and is required for glycan deposition at hyphal tips and morphogenesis of Streptomyces lividans, Biochemical Journal 469(3): 433-444.
- Ekkers D., Claessen D., Galli F. & Stamhuis E.T. (2014), Surface modification using interfacial assembly of the Streptomyces chaplin proteins, Applied Microbiology and Biotechnology 98(10): 4491-4501.
- Gras S.L. & Claessen D. (2014), Functional amyloid fibrils: lessons from microbes. In: , Natural products analysis: instrumentation, methods, and applications.: Wiley. 573-600.
- Girard G.A.O., Willemse J.J., Zhu H., Claessen D., Bukarasam K., Goodfellow M. & Wezel G.P. van (2014), Analysis of novel kitasatosporae reveals significant evolutionary changes in conserved developmental genes between Kitasatospora and Streptomyces, Antonie van Leeuwenhoek 106(2): 365-380.
- Claessen D., Rozen D.E., Kuipers O.P., Søgaard-Andersen L. & Wezel G.P. van (2014), Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies, Nature Reviews Microbiology 12(2): 115-124.
- Dissel M.D. van, Claessen D. & Wezel G.P. van (2014), Morphogenesis of streptomyces in submerged cultures, Advances in Applied Microbiology 89: 1-45.
- Petrus M.L.C. & Claessen D. (2014), Pivotal roles for Streptomyces cell surface polymers in morphological differentiation, attachment and mycelial architecture, Antonie van Leeuwenhoek 106(1): 127-139.
- Petrus M.L.C., Veluw G.J. van, Wösten H.A.B. & Claessen D. (2014), Sorting of Streptomyces cell pellets using a complex object parametric analyzer and sorter, Journal of visualized experiments 84(e51178): .
- Claessen D. & Wezel G.P. van (2014), Bacterial Proliferation: Off the wall, eLife 3: e05427.
- Surdova K., Gamba P., Claessen D., Siersma T., Jonker M.J., Errington J. & Hamoen L.W. (2013), The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis, Journal of Bacteriology Dec;195(24):5450-60(2013): .
- Bokhove M., Claessen D., De Jong W., Dijkhuizen L., Boekema E.J. & Oostergetel G.T. (2013), Chaplins of Streptomyces coelicolor self-assemble into two distinct functional amyloids, Journal of Structural Biology 2013 Nov;184(2):301-9(2013): .
- Veluw G.J. van, Petrus M.L.C., Gubbens J., Graaf R. de, Jong I.P. de, Wezel G.P. van, Wosten H.A. & Claessen D. (2012), Analysis of two distinct mycelial populations in liquid-grown Streptomyces cultures using a flow cytometry-based proteomics approach, Applied Microbiology and Biotechnology 96(5): 1301-1312.
- Jong I.P. de & Claessen D. (2012), A sandwich-culture technique for controlling antibiotic production and morphological development in Streptomyces coelicolor, Journal of Microbiological Methods 91: 318-320.
- Jong W. de, Vijgenboom E., Dijkhuizen L., Wösten H.A.B. & Claessen D. (2012), SapB and the rodlins are required for development of Streptomyces coelicolor in high osmolarity media, FEMS Microbiology Letters 329(2): 154-159.
- Sawyer E.B., Claessen D., Gras S.L. & Perrett S. (2012), Exploiting amyloid: how and why bacteria use cross-beta fibrils, Biochemical Society Transactions 40: 728-734.
- Jong W. de, Wosten H.A.B., Dijkhuizen L. & Claessen D. (2009), Attachment of Streptomyces coelicolor is mediated by amyloidal fimbriae that are anchored to the cell surface via cellulose, Molecular Microbiology 73(6): 1128-1140.
- De Jong Wouter, Manteca Angel, Sanchez Jesus, Bucca Giselda, Smith Colin P., Dijkhuizen Lubbert, Claessen Dennis & Wosten Han A.B. (2009), NepA is a structural cell wall protein involved in maintenance of spore dormancy in Streptomyces coelicolor, Molecular Microbiology 71(6): 1591-1603.
- Claessen D., Emmins R., Hamoen L.W., Daniel R.A., Errington J. & Edwards D.H. (2008), Control of the cell elongation-division cycle by shuttling of PBP1 protein in Bacillus subtilis, Molecular Microbiology 68(4): 1029-1046.
- Manteca Angel, Claessen Dennis, Lopez-Iglesias Carmen & Sanchez Jesus (2007), Aerial hyphae in surface cultures of Streptomyces lividans and Streptomyces coelicolor originate from viable segments surviving an early programmed cell death event, FEMS Microbiology Letters 274(1): 118-125.
- Claessen Dennis, De Jong Wouter, Dijkhuizen Lubbert & Wosten Han A.B. (2006), Regulation of Streptomyces development: reach for the sky!, Trends in Microbiology 14(7): 313-319.
- Gebbink M.F.B.G., Claessen D., Bouma B., Dijkhuizen L. & Wosten H.A.B. (2005), Amyloids - A functional coat for microorganisms, Nature Reviews Microbiology 3(4): 333-341.
- Claessen D., Stokroos I., Deelstra H.J., Penninga N.A., Bormann C., Salas J.A., Dijkhuizen L. & Wosten H.A.B. (2004), The formation of the rodlet layer of streptomycetes is the result of the interplay between rodlins and chaplins, Molecular Microbiology 53(2): 433-443.
- Keulen G. van, Jonkers H.M., Claessen D., Dijkhuizen L. & Wosten H.A.B. (2003), Differentiation and anaerobiosis in standing liquid cultures of Streptomyces coelicolor, Journal of Bacteriology 185(4): 1455-1458.
- Claessen D., Rink R., Jong W. de, Siebring J., Vreugd P. de, Boersma F.G.H., Dijkhuizen L. & Wosten H.A.B. (2003), A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils, Genes & Development 17(14): 1714-1726.
- Claessen D., Wosten H.A.B., Keulen G. van, Faber O.G., Alves A.M.C.R., Meijer W.G. & Dijkhuizen L. (2002), Two novel homologous proteins of Streptomyces coelicolor and Streptomyces lividans are involved in the formation of the rodlet layer and mediate attachment to a hydrophobic surface, Molecular Microbiology 44(6): 1483-1492.