Publications

Preprints

• Antar H., Carraro N., Gruber S.*, van der Meer J.R.,* 2024. Orchestrated long-distance gene activation by a ParB-like BisD-CTP DNA clamp in low-frequency transfer competence development in Pseudomonas putida.
  preprint, 2024 [BioRxiv]
• Taschner M., Dickinson J.B., Roisné-Hamelin F., Gruber S.*, 2024. 4G cloning: rapid gene assembly for expression of multisubunit protein complexes in diverse hosts.
  preprint, 2024 [BioRxiv]
• Barth R., Davidson I.F., van der Torre J., Taschner M., Gruber S., Peters J.M., Dekker C.*, 2023. SMC motor proteins extrude DNA asymmetrically and contain a direction switch.
  preprint, 2023 [BioRxiv]

2024

• Roisné-Hamelin F., Liu H. W., Taschner M., Li Y., Gruber S.*, 2024. Structural basis for plasmid restriction by SMC JET nuclease.
  Molecular Cell
  Vol 84, Issue 5 [Pubmed] [DOI]
  preprint 2023 [BioRxiv]
• Tišma M., Bock F.P., Kerssemakkers J., Antar H., Japaridze A., Gruber S., Dekker C.*, 2024. Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells.
  Nature Communications
  Vol 15, 2737 [Pubmed] [DOI]
  preprint 2023 [BioRxiv]
• Liu X., Van Maele L., Matarazzo L., Soulard D., Duarte da Silva V.A., de Bakker V., Dénéréaz J., Bock F.P., Taschner M., Ou J., Gruber S., Nizet V., Sirard J.-C.*, Veening J.-W.*, 2023. A conserved antigen induces respiratory Th17-mediated serotype-independent protection against pneumococcal superinfection.
  Cell Host & Microbe
  Vol 32, 1-11 [Pubmed] [DOI]
  preprint 2023 [BioRxiv]
• Tišma M., Kaljevic J., Gruber S., Le T.B.K., Dekker C.*, 2024. Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies.
  FEMS Microbiol Rev
  Vol 48 (1) [Pubmed] [DOI]
• Gonzalez A.M., Tisma M., Analikwu B.T., Barth A., Janissen R., Antar H., Kemps G., Gruber S., Dekker C.*, 2024. DNA supercoiling enhances DNA condensation by ParB proteins.
  Nucleic Acids Research
  gkae936 [Pubmed] [DOI]
  preprint, 2024 [BioRxiv]

2023

• Taschner M., Gruber S.*, 2023. DNA segment capture by Smc5/6 holo-complexes.
  Nature Structural & Molecular Biology
  10.1038/s41594-023-00956-2 [Pubmed] [DOI]
  preprint 2022 [BioRxiv]
• Liu H. W., Roisné-Hamelin F., Gruber S.*, 2023. SMC-based immunity against extrachromosomal DNA elements.
  Biochemical Society Transactions
  BST20221395 [Pubmed] [DOI]
• Antar H., Gruber S.*, 2023. VirB, a transcriptional activator of virulence in Shigella flexneri, uses CTP as a cofactor.
  Communications Biology
  6:1024 [Pubmed] [DOI]
  preprint 2023 [BioRxiv]
• Tišma M., Janissen R., Antar H., Martin Gonzalez A., Barth R., Beekman T., van der Torre J., Michieletto D., Gruber S., Dekker C.*, 2023. Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation.
  Nucleic Acids Research
  gkad868 [Pubmed][DOI]
  preprint 2023  [BioRxiv]

2022

• Liu H. W., Roisné-Hamelin F., Beckert B., Li Y., Myasnikov A., Gruber S.*, 2022. DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage.
  Molecular Cell
  Vol 82, Issue 24 [Pubmed] [DOI]
  preprint, 2022 [BioRxiv]
• Roberts D. M., Anchimiuk A., Kloosterman T. G., Murray H., Wu L. J, Gruber S., Errington J.*, 2022. Chromosome remodelling by SMC/Condensin in B. subtilis is regulated by Soj/ParA during growth and sporulation.
  PNAS
  Vol 40, Issue 9 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]
• Bock F. P., Liu H. W., Anchimiuk A., Diebold-Durand M.-L., Gruber S.*, 2022. A joint-ParB interface promotes Smc DNA recruitment.
  Cell Reports
  Vol 119, Issue 41 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]
• Tisma M., Panoukidou M., Antar H., Soh Y.-M., Barth R., Pradhan B., van der Torre J., Michieletto D., Gruber S., Dekker C.*, 2022. ParB proteins can bypass DNA-bound roadblocks by dimer-dimer recruitment.
  Science Advances
  Vol 8, Issue 26 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]
• Nomidis S.S., Carlon E., Gruber S., Marko J. F.*, 2022. DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations.
  Nucleic acids research
  gkac268 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]

2021

• Antar H.°, Soh Y.-M.°, Zamuner S., Bock F. P., Anchimiuk A., De Los Rios P., Gruber S.*, 2021. Relief of ParB autoinhibition by parS DNA catalysis and ParB recycling by CTP hydrolysis promote bacterial centromere assembly.
  Science Advances
  Vol 7, Issue 41 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]
• Taschner M., Basquin J., Steigenberger B., Schaefer I., Soh Y.-M., Basquin C., Lorentzen E., Räschle M., Scheltema R. A., Gruber S.*, 2021. Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding.
  EMBO Journal
  e107807 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]
• Anchimiuk A., Lioy V. S., Minnen A., Boccard F., Gruber S.*, 2021. A low Smc flux avoids collisions and facilitates chromosome organization in B. subtilis.
  eLife
  65467 [Pubmed] [DOI]
  preprint, 2020 [BioRxiv]
• Gallay C.°, Sanselicio S.°, Anderson M. E.,  Soh Y.-M., Liu X., Stamsas G. A., Pelliciari S., van Raaphorst R., Dénéréaz J., Kjos M., Murray H., Gruber S., Grossman A. D., Veening J.-W.*, 2021. CcrZ is a pneumococcal spatiotemporal cell cycle regulator that interacts with FtsZ and controls DNA replication.
  Nature Microbiology
  021-00949-1 [Pubmed] [DOI]
  preprint, 2019 [BioRxiv]
• Vazquez Nunez R. J.°, Polyhach Y.°, Soh Y.-M., Jeschke G., Gruber S.*, 2021. Gradual opening of Smc arms in prokaryotic condensin.
  Cell Reports
  35(4) 109051 [Pubmed] [DOI]
  preprint, 2021 [BioRxiv]

2020

• Soh Y.-M., Basquin J., Gruber S.*, 2020. A rod conformation of the Pyrococcus furiosus Rad50 coiled coil.
  Proteins
  prot.26005 [Pubmed] [DOI] [PDB: 6ZFF]
  preprint, 2020 [BioRxiv]
• Metwaly G., Wu Y., Peplowska K., Röhrl J., Soh Y.-M., Bürmann F., Gruber S., Storchova Z.*, 2020. Phospho-regulation of the Shugoshin-Condensin interaction at the centromere in budding yeast.
  PLOS Genetics
  16(8) [Pubmed] [DOI]
  preprint, 2019 [BioRxiv]
• Jeon J.-H., Lee H.-S., Shin H.-C., Kwak M.-J., Kim Y.-G., Gruber S. and Oh B.-H.*, 2020. Evidence for binary Smc complexes lacking kite subunits in archaea.
  IUCrJ
  7(2) [Pubmed] [DOI]
• Prassler J., Simon F., Ecke M., Gruber S. and Gerisch G.* 2020. Decision making in phagocytosis.
  AEMB
  1246:71-81 [Pubmed] [DOI] [PDF]

2019

• Soh Y.-M., Davidson I. F., Zamuner S., Basquin J., Taschner M., Bock F. P., Veening J.-W., De Los Rios P., Peters J.-M., Gruber S.*, 2019. Self-organization of parS centromeres by the ParB CTP hydrolase.
  Science
  360(6469) p. 1129-1133 [Pubmed] [DOI] [Free] [PDB: 6SDK] [PDF] [F1000_recommendations] [Perspective by Barbara Funnell]
• Vazquez Nunez R.°, Ruiz Avila L. B.°, Gruber S.*, 2019. Transient DNA occupancy of the SMC interarm space in prokaryotic condensin.
  Molecular Cell
  75(5) p. 1-15 [Pubmed] [DOI] [Free full-text] [Preview by Tomoko Nishiyama]
  preprint, 2018 [BioRxiv]
• Marko J. F.*, De Los Rios P., Barducci A., Gruber S., 2019. DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes.
  Nucleic Acids Research
  gkz497 [Pubmed] [DOI]
  preprint, 2018 [BioRxiv]
• Diebold-Durand M.-L., Bürmann F., Gruber S.*, 2019. High-throughput allelic replacement screening in Bacillus subtilis.
  Methods in Molecular Biology
  2004 p. 49-61 [Pubmed] [DOI] [PDF]

2018

• Pfeiffer F., Zamora-Lagos M.-A., Blettinger M., Yeroslavic A., Dahl A., Gruber S.*, Habermann B. H.*, 2018. The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains.
  BMC Genomics
  19(1):20 [Pubmed] [DOI]
• Gruber S., 2018. SMC complexes sweeping through the chromosome: Going with the flow and against the tide.
  Current Opinion in Microbiology
  42:96-103 [Pubmed] [DOI] [PDF]
• Stockmar I., Feddersen H., Cramer K., Gruber S., Jung K., Bramkamp M.*, Shin J. Y.* 2018. Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy.
  Scientific Reports
  8(1): 10137 [Pubmed] [DOI]

2017

• Diebold-Durand M.-L.°, Lee H.°, Ruiz Avila L.°, Noh H., Shin H.-C., Im H., Bock F. P., Bürmann F., Durand A., Basfeld A., Ham S., Basquin J., Oh B.-H.*, Gruber S.*, 2017. Structure of full-length SMC and rearrangements required for chromosome organization.
  Molecular Cell
  67(2) p. 334-347 [DOI] [Web of Science] [Pubmed] [PDB: 5NMO, 5NNV]
• Bürmann F., Basfeld A., Vazquez Nunez R., Diebold-Durand M.-L., Wilhelm L., Gruber S.*, 2017. Tuned SMC arms drive chromosomal loading of prokaryotic condensin.
  Molecular Cell
  65(5) p. 861-872 [DOI] [Web of Science] [Pubmed] [F1000 recommendation]
• Gruber S., 2017. Shaping Chromosomes by DNA Capture and Release: Gating the SMC Rings.
  Current Opinion in Cell Biology
  46:87-93 [DOI] [Web of Science] [Pubmed] [PDF]
• Wilhelm L., Gruber S.*, 2017. A Chromosome Co-Entrapment Assay to Study Topological Protein–DNA Interactions.
  Methods in Molecular Biology
  1624 p. 117-126 [DOI] [Web of Science] [Pubmed] [PDF]. An updated version of the protocol (using agarose microbeads instead of agarose plugs) is available here: [DOI].

2016