1
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Letzkus M, Trela C, Mera PE. Three factors ParA, TipN, and DnaA-mediated chromosome replication initiation are contributors of centromere segregation in Caulobacter crescentus. Mol Biol Cell 2024; 35:ar68. [PMID: 38568781 DOI: 10.1091/mbc.e23-12-0503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The ability of bacteria to maintain chromosomal integrity throughout their life cycle is crucial for survival. In Caulobacter crescentus, the polar factor TipN has been proposed to be involved with the partitioning system ParABS. Cells with tipN knocked out display subtle segregation defects of the centromere-like region parS. We hypothesized that TipN's role with parS segregation is obscured by other forces that are ParABS-independent. To test our hypothesis, we removed one of those forces - chromosome replication - and analyzed the role of TipN with ParA. We first confirm that ParA retains its ability to transport the centromeric region parS from the stalked pole to the opposite pole in the absence of chromosome replication. Our data revealed that in the absence of chromosome replication, TipN becomes essential for ParA's ability to transport parS. Furthermore, we identify a potential connection between the replication initiator DnaA and TipN. Although TipN is not essential for viability, tipN knockout cells lose viability when the regulation of DnaA levels is altered. Our data suggest that the DnaA-dependent susceptibility of tipN knockout cells is connected to parS segregation. Collectively, this work provides insights into the complex regulation involved in the coordination of chromosome replication and segregation in bacteria.
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Affiliation(s)
- Morgan Letzkus
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Corey Trela
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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2
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Köhler R, Murray SM. Plasmid partitioning driven by collective migration of ParA between nucleoid lobes. Proc Natl Acad Sci U S A 2024; 121:e2319205121. [PMID: 38652748 PMCID: PMC11067062 DOI: 10.1073/pnas.2319205121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
The ParABS system is crucial for the faithful segregation and inheritance of many bacterial chromosomes and low-copy-number plasmids. However, despite extensive research, the spatiotemporal dynamics of the ATPase ParA and its connection to the dynamics and positioning of the ParB-coated cargo have remained unclear. In this study, we utilize high-throughput imaging, quantitative data analysis, and computational modeling to explore the in vivo dynamics of ParA and its interaction with ParB-coated plasmids and the nucleoid. As previously observed, we find that F-plasmid ParA undergoes collective migrations ("flips") between cell halves multiple times per cell cycle. We reveal that a constricting nucleoid is required for these migrations and that they are triggered by a plasmid crossing into the cell half with greater ParA. Using simulations, we show that these dynamics can be explained by the combination of nucleoid constriction and cooperative ParA binding to the DNA, in line with the behavior of other ParA proteins. We further show that these ParA flips act to equally partition plasmids between the two lobes of the constricted nucleoid and are therefore important for plasmid stability, especially in fast growth conditions for which the nucleoid constricts early in the cell cycle. Overall, our work identifies a second mode of action of the ParABS system and deepens our understanding of how this important segregation system functions.
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Affiliation(s)
- Robin Köhler
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and Centre for Synthetic Microbiology (SYNMIKRO), Marburg35043, Germany
| | - Seán M. Murray
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and Centre for Synthetic Microbiology (SYNMIKRO), Marburg35043, Germany
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3
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Harju J, Broedersz CP. Physical models of bacterial chromosomes. Mol Microbiol 2024. [PMID: 38578226 DOI: 10.1111/mmi.15257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can be theoretically challenging. In this minireview, we discuss how connecting experimental observations to biophysical theory and modeling can give rise to new insights on bacterial chromosome organization. We consider three flavors of models of increasing complexity: simple polymer models that explore how physical constraints, such as confinement or plectoneme branching, can affect bacterial chromosome organization; bottom-up mechanistic models that connect these constraints to their underlying causes, for instance, chromosome compaction to macromolecular crowding, or supercoiling to transcription; and finally, data-driven methods for inferring interpretable and quantitative models directly from complex experimental data. Using recent examples, we discuss how biophysical models can both deepen our understanding of how bacterial chromosomes are structured and give rise to novel predictions about bacterial chromosome organization.
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Affiliation(s)
- Janni Harju
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilian-University Munich, Munich, Germany
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4
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Tišma M, Kaljević J, Gruber S, Le TBK, Dekker C. Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies. FEMS Microbiol Rev 2024; 48:fuad067. [PMID: 38142222 PMCID: PMC10786196 DOI: 10.1093/femsre/fuad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 12/25/2023] Open
Abstract
Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system - partition protein B (ParB) - regulates chromosome organization and chromosome segregation during the bacterial cell cycle. Over the past decades, research has greatly advanced our knowledge of the ParABS system. However, many intricate details of the mechanism of ParB proteins were only recently uncovered using in vitro single-molecule techniques. These approaches allowed the exploration of ParB proteins in precisely controlled environments, free from the complexities of the cellular milieu. This review covers the early developments of this field but emphasizes recent advances in our knowledge of the mechanistic understanding of ParB proteins as revealed by in vitro single-molecule methods. Furthermore, we provide an outlook on future endeavors in investigating ParB, ParB-like proteins, and their interaction partners.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands
| | - Jovana Kaljević
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, United Kingdom
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, UNIL-Sorge, Biophore, CH-1015 Lausanne, Switzerland
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, United Kingdom
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology; Van der Maasweg 9, Delft, the Netherlands
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5
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Jakob S, Steinchen W, Hanßmann J, Rosum J, Langenfeld K, Osorio-Valeriano M, Steube N, Giammarinaro PI, Hochberg GKA, Glatter T, Bange G, Diepold A, Thanbichler M. The virulence regulator VirB from Shigella flexneri uses a CTP-dependent switch mechanism to activate gene expression. Nat Commun 2024; 15:318. [PMID: 38182620 PMCID: PMC10770331 DOI: 10.1038/s41467-023-44509-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
The transcriptional antisilencer VirB acts as a master regulator of virulence gene expression in the human pathogen Shigella flexneri. It binds DNA sequences (virS) upstream of VirB-dependent promoters and counteracts their silencing by the nucleoid-organizing protein H-NS. However, its precise mode of action remains unclear. Notably, VirB is not a classical transcription factor but related to ParB-type DNA-partitioning proteins, which have recently been recognized as DNA-sliding clamps using CTP binding and hydrolysis to control their DNA entry gate. Here, we show that VirB binds CTP, embraces DNA in a clamp-like fashion upon its CTP-dependent loading at virS sites and slides laterally on DNA after clamp closure. Mutations that prevent CTP-binding block VirB loading in vitro and abolish the formation of VirB nucleoprotein complexes as well as virulence gene expression in vivo. Thus, VirB represents a CTP-dependent molecular switch that uses a loading-and-sliding mechanism to control transcription during bacterial pathogenesis.
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Affiliation(s)
- Sara Jakob
- Department of Biology, University of Marburg, Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, Marburg, Germany
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Rosum
- Department of Biology, University of Marburg, Marburg, Germany
| | - Katja Langenfeld
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Niklas Steube
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, Marburg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Georg K A Hochberg
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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6
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Cornet F, Blanchais C, Dusfour-Castan R, Meunier A, Quebre V, Sekkouri Alaoui H, Boudsoq F, Campos M, Crozat E, Guynet C, Pasta F, Rousseau P, Ton Hoang B, Bouet JY. DNA Segregation in Enterobacteria. EcoSal Plus 2023; 11:eesp00382020. [PMID: 37220081 DOI: 10.1128/ecosalplus.esp-0038-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/13/2023] [Indexed: 01/28/2024]
Abstract
DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.
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Affiliation(s)
- François Cornet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Corentin Blanchais
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Romane Dusfour-Castan
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Alix Meunier
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Valentin Quebre
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Hicham Sekkouri Alaoui
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - François Boudsoq
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Manuel Campos
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Estelle Crozat
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Franck Pasta
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Bao Ton Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
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7
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Tišma M, Janissen R, Antar H, Martin-Gonzalez A, Barth R, Beekman T, van der Torre J, Michieletto D, Gruber S, Dekker C. Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation. Nucleic Acids Res 2023; 51:11856-11875. [PMID: 37850647 PMCID: PMC10681803 DOI: 10.1093/nar/gkad868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex for Bacillus subtilis ParB, using single-molecule fluorescence microscopy and AFM imaging to show that transient ParB-ParB bridges are essential for forming DNA condensates. Molecular Dynamics simulations confirm that condensation occurs abruptly at a critical concentration of ParB and show that multimerization is a prerequisite for forming the partition complex. Magnetic tweezer force spectroscopy on mutant ParB proteins demonstrates that CTP hydrolysis at the N-terminal domain is essential for DNA condensation. Finally, we show that transcribing RNA polymerases can steadily traverse the ParB-DNA partition complex. These findings uncover how ParB forms a stable yet dynamic partition complex for chromosome segregation that induces DNA condensation and segregation while enabling replication and transcription.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Hammam Antar
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alejandro Martin-Gonzalez
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Twan Beekman
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stephan Gruber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
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8
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Abstract
VirB is a transcriptional activator of virulence in the gram-negative bacterium Shigella flexneri encoded by the large invasion plasmid, pINV. It counteracts the transcriptional silencing by the nucleoid structuring protein, H-NS. Mutations in virB lead to loss of virulence. Studies suggested that VirB binds to specific DNA sequences, remodels the H-NS nucleoprotein complexes, and changes DNA supercoiling. VirB belongs to the superfamily of ParB proteins which are involved in plasmid and chromosome partitioning often as part of a ParABS system. Like ParB, VirB forms discrete foci in Shigella flexneri cells harbouring pINV. Our results reveal that purified preparations of VirB specifically bind the ribonucleotide CTP and slowly but detectably hydrolyse it with mild stimulation by the virS targeting sequences found on pINV. We show that formation of VirB foci in cells requires a virS site and CTP binding residues in VirB. Curiously, DNA stimulation of clamp closure appears efficient even without a virS sequence in vitro. Specificity for entrapment of virS DNA is however evident at elevated salt concentrations. These findings suggest that VirB acts as a CTP-dependent DNA clamp and indicate that the cellular microenvironment contributes to the accumulation of VirB specifically at virS sites.
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Affiliation(s)
- Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015, Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015, Lausanne, Switzerland.
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9
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Gerson TM, Ott AM, Karney MMA, Socea JN, Ginete DR, Iyer LM, Aravind L, Gary RK, Wing HJ. VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities. mBio 2023; 14:e0151923. [PMID: 37728345 PMCID: PMC10653881 DOI: 10.1128/mbio.01519-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Shigella species cause bacillary dysentery, the second leading cause of diarrheal deaths worldwide. There is a pressing need to identify novel molecular drug targets. Shigella virulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, plasmid-borne clade of the ParB superfamily, which has diverged from versions with a distinct cellular role-DNA partitioning. We report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB, likely because these mutants cannot engage DNA. This study (i) reveals that VirB binds CTP, (ii) provides a link between VirB-CTP interactions and Shigella virulence phenotypes, (iii) provides new insight into VirB-CTP-DNA interactions, and (iv) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many bacteria.
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Affiliation(s)
- Taylor M. Gerson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Audrey M. Ott
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Monika M. A. Karney
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Jillian N. Socea
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Daren R. Ginete
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | | | - L. Aravind
- Computational Biology Branch, National Library of Medicine, Bethesda, Maryland, USA
| | - Ronald K. Gary
- Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Helen J. Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
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10
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Molina M, Way LE, Ren Z, Liao Q, Guerra B, Shields B, Wang X, Kim H. A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments. Cell Rep Methods 2023; 3:100614. [PMID: 37832544 PMCID: PMC10626211 DOI: 10.1016/j.crmeth.2023.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK tag substantially altered ParB's DNA compaction rates and its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.
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Affiliation(s)
- Miranda Molina
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Lindsey E Way
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Qin Liao
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Bianca Guerra
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Brandon Shields
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA.
| | - HyeongJun Kim
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA.
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11
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Kaljević J, Tesseur C, Le TBK, Laloux G. Cell cycle-dependent organization of a bacterial centromere through multi-layered regulation of the ParABS system. PLoS Genet 2023; 19:e1010951. [PMID: 37733798 PMCID: PMC10547168 DOI: 10.1371/journal.pgen.1010951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/03/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023] Open
Abstract
The accurate distribution of genetic material is crucial for all organisms. In most bacteria, chromosome segregation is achieved by the ParABS system, in which the ParB-bound parS sequence is actively partitioned by ParA. While this system is highly conserved, its adaptation in organisms with unique lifestyles and its regulation between developmental stages remain largely unexplored. Bdellovibrio bacteriovorus is a predatory bacterium proliferating through polyploid replication and non-binary division inside other bacteria. Our study reveals the subcellular dynamics and multi-layered regulation of the ParABS system, coupled to the cell cycle of B. bacteriovorus. We found that ParA:ParB ratios fluctuate between predation stages, their balance being critical for cell cycle progression. Moreover, the parS chromosomal context in non-replicative cells, combined with ParB depletion at cell division, critically contribute to the unique cell cycle-dependent organization of the centromere in this bacterium, highlighting new levels of complexity in chromosome segregation and cell cycle control.
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Affiliation(s)
| | | | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Norwich, United Kingdom
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12
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Biswas S, Kang K, Ng KP, Radivoyevitch T, Schalper K, Zhang H, Lindner DJ, Thomas A, MacPherson D, Gastman B, Schrump DS, Wong KK, Velcheti V, Saunthararajah Y. Neuroendocrine lineage commitment of small cell lung cancers can be leveraged into p53-independent non-cytotoxic therapy. Cell Rep 2023; 42:113016. [PMID: 37597186 PMCID: PMC10528072 DOI: 10.1016/j.celrep.2023.113016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/10/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023] Open
Abstract
Small cell lung cancers (SCLCs) rapidly resist cytotoxic chemotherapy and immune checkpoint inhibitor (ICI) treatments. New, non-cross-resistant therapies are thus needed. SCLC cells are committed into neuroendocrine lineage then maturation arrested. Implicating DNA methyltransferase 1 (DNMT1) in the maturation arrests, we find (1) the repression mark methylated CpG, written by DNMT1, is retained at suppressed neuroendocrine-lineage genes, even as other repression marks are erased; (2) DNMT1 is recurrently amplified, whereas Ten-Eleven-Translocation 2 (TET2), which functionally opposes DNMT1, is deleted; (3) DNMT1 is recruited into neuroendocrine-lineage master transcription factor (ASCL1, NEUROD1) hubs in SCLC cells; and (4) DNMT1 knockdown activated ASCL1-target genes and released SCLC cell-cycling exits by terminal lineage maturation, which are cycling exits that do not require the p53/apoptosis pathway used by cytotoxic chemotherapy. Inhibiting DNMT1/corepressors with clinical compounds accordingly extended survival of mice with chemorefractory and ICI-refractory, p53-null, disseminated SCLC. Lineage commitment of SCLC cells can hence be leveraged into non-cytotoxic therapy able to treat chemo/ICI-refractory SCLC.
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Affiliation(s)
- Sudipta Biswas
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kai Kang
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kwok Peng Ng
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kurt Schalper
- Department of Pathology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Hua Zhang
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Daniel J Lindner
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anish Thomas
- Experimental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Brian Gastman
- Department of Plastic Surgery, Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kwok-Kin Wong
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA
| | - Vamsidhar Velcheti
- Thoracic Oncology Program, Langone-Laura and Isaac Perlmutter Cancer Center, New York University, New York, NY 10016, USA.
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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13
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Kawalek A, Bartosik AA, Jagura-Burdzy G. Robust ParB Binding to Half- parS Sites in Pseudomonas aeruginosa-A Mechanism for Retaining ParB on the Nucleoid? Int J Mol Sci 2023; 24:12517. [PMID: 37569892 PMCID: PMC10419367 DOI: 10.3390/ijms241512517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Chromosome segregation in Pseudomonas aeruginosa is assisted by the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB) and its target parS sequence(s). ParB forms a nucleoprotein complex around four parSs (parS1-parS4) that overlaps oriC and facilitates relocation of newly synthesized ori domains inside the cells by ParA. Remarkably, ParB of P. aeruginosa also binds to numerous heptanucleotides (half-parSs) scattered in the genome. Here, using chromatin immunoprecipitation-sequencing (ChIP-seq), we analyzed patterns of ParB genome occupancy in cells growing under conditions of coupling or uncoupling between replication and cell division processes. Interestingly, a dissipation of ParB-parS complexes and a shift of ParB to half-parSs were observed during the transition from the exponential to stationary phase of growth on rich medium, suggesting the role of half-parSs in retaining ParB on the nucleoid within non-dividing P. aeruginosa cells. The ChIP-seq analysis of strains expressing ParB variants unable to dislocate from parSs showed that the ParB spreading ability is not required for ParB binding to half-parSs. Finally, a P. aeruginosa strain with mutated 25 half-parSs of the highest affinity towards ParB was constructed and analyzed. It showed altered ParB coverage of the oriC region and moderate changes in gene expression. Overall, this study characterizes a novel aspect of conserved bacterial chromosome segregation machinery.
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Affiliation(s)
- Adam Kawalek
- Laboratory of DNA Segregation and Life Cycle of Proteobacteria, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Grazyna Jagura-Burdzy
- Laboratory of DNA Segregation and Life Cycle of Proteobacteria, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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14
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Connolley L, Schnabel L, Thanbichler M, Murray SM. Partition complex structure can arise from sliding and bridging of ParB dimers. Nat Commun 2023; 14:4567. [PMID: 37516778 PMCID: PMC10387095 DOI: 10.1038/s41467-023-40320-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
In many bacteria, chromosome segregation requires the association of ParB to the parS-containing centromeric region to form the partition complex. However, the structure and formation of this complex have been unclear. Recently, studies have revealed that CTP binding enables ParB dimers to slide along DNA and condense the centromeric region through the formation of DNA bridges. Using semi-flexible polymer simulations, we demonstrate that these properties can explain partition complex formation. Transient ParB bridges organize DNA into globular states or hairpins and helical structures, depending on bridge lifetime, while separate simulations show that ParB sliding reproduces the multi-peaked binding profile observed in Caulobacter crescentus. Combining sliding and bridging into a unified model, we find that short-lived ParB bridges do not impede sliding and can reproduce both the binding profile and condensation of the nucleoprotein complex. Overall, our model elucidates the mechanism of partition complex formation and predicts its fine structure.
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Affiliation(s)
- Lara Connolley
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany
| | - Lucas Schnabel
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Martin Thanbichler
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany
- Department of Biology, University of Marburg, 35043, Marburg, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, 35043, Marburg, Germany.
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15
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Siguier P, Campos M, Cornet F, Bouet JY, Guynet C. Atypical low-copy number plasmid segregation systems, all in one? Plasmid 2023; 127:102694. [PMID: 37301314 DOI: 10.1016/j.plasmid.2023.102694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Plasmid families harbor different maintenances functions, depending on their size and copy number. Low copy number plasmids rely on active partition systems, organizing a partition complex at specific centromere sites that is actively positioned using NTPase proteins. Some low copy number plasmids lack an active partition system, but carry atypical intracellular positioning systems using a single protein that binds to the centromere site but without an associated NTPase. These systems have been studied in the case of the Escherichia coli R388 and of the Staphylococcus aureus pSK1 plasmids. Here we review these two systems, which appear to be unrelated but share common features, such as their distribution on plasmids of medium size and copy number, certain activities of their centromere-binding proteins, StbA and Par, respectively, as well as their mode of action, which may involve dynamic interactions with the nucleoid-packed chromosome of their hosts.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Manuel Campos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - François Cornet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France.
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16
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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genet 2023; 19:e1010857. [PMID: 37494383 PMCID: PMC10406323 DOI: 10.1371/journal.pgen.1010857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/07/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Hugo B. Brandão
- Illumina Inc., 5200 Illumina Way, San Diego, California, United States of America
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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17
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Chodha SS, Brooks AC, Davis PJ, Ramachandran R, Chattoraj D, Hwang L. Kinetic principles of ParA2-ATP cycling guide dynamic subcellular localizations in Vibrio cholerae. Nucleic Acids Res 2023; 51:5603-5620. [PMID: 37140034 PMCID: PMC10287910 DOI: 10.1093/nar/gkad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
Dynamic protein gradients are exploited for the spatial organization and segregation of replicated chromosomes. However, mechanisms of protein gradient formation and how that spatially organizes chromosomes remain poorly understood. Here, we have determined the kinetic principles of subcellular localizations of ParA2 ATPase, an essential spatial regulator of chromosome 2 segregation in the multichromosome bacterium, Vibrio cholerae. We found that ParA2 gradients self-organize in V. cholerae cells into dynamic pole-to-pole oscillations. We examined the ParA2 ATPase cycle and ParA2 interactions with ParB2 and DNA. In vitro, ParA2-ATP dimers undergo a rate-limiting conformational switch, catalysed by DNA to achieve DNA-binding competence. This active ParA2 state loads onto DNA cooperatively as higher order oligomers. Our results indicate that the midcell localization of ParB2-parS2 complexes stimulate ATP hydrolysis and ParA2 release from the nucleoid, generating an asymmetric ParA2 gradient with maximal concentration toward the poles. This rapid dissociation coupled with slow nucleotide exchange and conformational switch provides for a temporal lag that allows the redistribution of ParA2 to the opposite pole for nucleoid reattachment. Based on our data, we propose a 'Tug-of-war' model that uses dynamic oscillations of ParA2 to spatially regulate symmetric segregation and positioning of bacterial chromosomes.
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Affiliation(s)
- Satpal S Chodha
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Adam C Brooks
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Peter J Davis
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Revathy Ramachandran
- Basic Research Laboratory, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4260, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4260, USA
| | - Ling Chin Hwang
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Medical Technology Research Centre, School of Medicine, Faculty of Health, Education, Medicine & Social Care, Anglia Ruskin University, Chelmsford, UK
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18
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Abstract
Next to Escherichia coli, Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of time, B. subtilis has attracted much scientific interest. Another feature of B. subtilis is its genetic competence, a developmental state in which B. subtilis actively takes up exogenous DNA. This makes B. subtilis amenable to genetic manipulation and investigation. The bacterium was one of the first with a fully sequenced genome, and it has been subject to a wide variety of genome- and proteome-wide studies that give important insights into many aspects of the biology of B. subtilis. Due to its ability to secrete large amounts of proteins and to produce a wide range of commercially interesting compounds, B. subtilis has become a major workhorse in biotechnology. Here, we review the development of important aspects of the research on B. subtilis with a specific focus on its cell biology and biotechnological and practical applications from vitamin production to concrete healing. The intriguing complexity of the developmental programs of B. subtilis, paired with the availability of sophisticated tools for genetic manipulation, positions it at the leading edge for discovering new biological concepts and deepening our understanding of the organization of bacterial cells.
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Affiliation(s)
- Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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19
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Gerson TM, Ott AM, Karney MMA, Socea JN, Ginete DR, Iyer LM, Aravind L, Gary RK, Wing HJ. VirB, a key transcriptional regulator of Shigella virulence, requires a CTP ligand for its regulatory activities. bioRxiv 2023:2023.05.16.541010. [PMID: 37293012 PMCID: PMC10245682 DOI: 10.1101/2023.05.16.541010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The VirB protein, encoded by the large virulence plasmid of Shigella spp., is a key transcriptional regulator of virulence genes. Without a functional virB gene, Shigella cells are avirulent. On the virulence plasmid, VirB functions to offset transcriptional silencing mediated by the nucleoid structuring protein, H-NS, which binds and sequesters AT-rich DNA, making it inaccessible for gene expression. Thus, gaining a mechanistic understanding of how VirB counters H-NS-mediated silencing is of considerable interest. VirB is unusual in that it does not resemble classic transcription factors. Instead, its closest relatives are found in the ParB superfamily, where the best-characterized members function in faithful DNA segregation before cell division. Here, we show that VirB is a fast-evolving member of this superfamily and report for the first time that the VirB protein binds a highly unusual ligand, CTP. VirB binds this nucleoside triphosphate preferentially and with specificity. Based on alignments with the best-characterized members of the ParB family, we identify amino acids of VirB likely to bind CTP. Substitutions in these residues disrupt several well-documented activities of VirB, including its anti-silencing activity at a VirB-dependent promoter, its role in generating a Congo red positive phenotype in Shigella , and the ability of the VirB protein to form foci in the bacterial cytoplasm when fused to GFP. Thus, this work is the first to show that VirB is a bona fide CTP-binding protein and links Shigella virulence phenotypes to the nucleoside triphosphate, CTP. Importance Shigella species cause bacillary dysentery (shigellosis), the second leading cause of diarrheal deaths worldwide. With growing antibiotic resistance, there is a pressing need to identify novel molecular drug targets. Shigella virulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, primarily plasmid-borne clade of the ParB superfamily, which has diverged from versions that have a distinct cellular role - DNA partitioning. We are the first to report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB. This study i) reveals that VirB binds CTP, ii) provides a link between VirB-CTP interactions and Shigella virulence phenotypes, and iii) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many different bacteria.
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Affiliation(s)
- Taylor M. Gerson
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Audrey M. Ott
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Monika MA. Karney
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Jillian N. Socea
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Daren R. Ginete
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
| | - Lakshminarayan M. Iyer
- Computational Biology Branch, 8600 Rockville Pike, Building 38A, Room 5N505, National Library of Medicine, Bethesda, MD 20894
| | - L. Aravind
- Computational Biology Branch, 8600 Rockville Pike, Building 38A, Room 5N505, National Library of Medicine, Bethesda, MD 20894
| | - Ronald K. Gary
- Department of Chemistry and Biochemistry, University of Nevada Las Vegas, Las Vegas, NV 89154-4003
| | - Helen J. Wing
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154-4004, USA
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20
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Molina M, Way LE, Ren Z, Liao Q, Wang X, Kim H. Using DNA flow-stretching assay as a tool to validate the tagging of DNA-binding proteins for single-molecule experiments. bioRxiv 2023:2023.03.19.533373. [PMID: 36993356 PMCID: PMC10055205 DOI: 10.1101/2023.03.19.533373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParB's DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.
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Affiliation(s)
- Miranda Molina
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- These authors contributed equally
| | - Lindsey E. Way
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
- These authors contributed equally
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
| | - Qin Liao
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, Indiana, United States of America
| | - HyeongJun Kim
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, Texas, United States of America
- Lead contact
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21
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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. bioRxiv 2023:2023.03.19.532819. [PMID: 37066390 PMCID: PMC10103936 DOI: 10.1101/2023.03.19.532819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Borrelia burgdorferi , a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/SMC. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that SMC and the SMC-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC . Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford, CA 94305, USA
- Corresponding authors: ;
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Corresponding authors: ;
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22
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McLean TC, Le TB. CTP switches in ParABS-mediated bacterial chromosome segregation and beyond. Curr Opin Microbiol 2023; 73:102289. [PMID: 36871427 DOI: 10.1016/j.mib.2023.102289] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 03/06/2023]
Abstract
Segregation of genetic material is a fundamental process in biology. In many bacterial species, segregation of chromosomes and low-copy plasmids is facilitated by the tripartite ParA-ParB-parS system. This system consists of a centromeric parS DNA site and interacting proteins ParA and ParB that are capable of hydrolyzing adenosine triphosphate and cytidine triphosphate (CTP), respectively. ParB first binds to parS before associating with adjacent DNA regions to spread outward from parS. These ParB-DNA complexes bind to ParA and, through repetitive cycles of ParA-ParB binding and unbinding, move the DNA cargo to each daughter cell. The recent discovery that ParB binds and hydrolyzes CTP as it cycles on and off the bacterial chromosome has dramatically changed our understanding of the molecular mechanism used by the ParABS system. Beyond bacterial chromosome segregation, CTP-dependent molecular switches are likely to be more widespread in biology than previously appreciated and represent an opportunity for new and unexpected avenues for future research and application.
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23
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Sukhoverkov KV, Jalal ASB, Ault JR, Sobott F, Lawson DM, Le TBK. The CTP-binding domain is disengaged from the DNA-binding domain in a cocrystal structure of Bacillus subtilis Noc-DNA complex. J Biol Chem 2023; 299:103063. [PMID: 36841481 PMCID: PMC10060749 DOI: 10.1016/j.jbc.2023.103063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
In Bacillus subtilis, a ParB-like nucleoid occlusion protein (Noc) binds specifically to Noc-binding sites (NBSs) on the chromosome to help coordinate chromosome segregation and cell division. Noc does so by binding to CTP to form large membrane-associated nucleoprotein complexes to physically inhibit the assembly of the cell division machinery. The site-specific binding of Noc to NBS DNA is a prerequisite for CTP-binding and the subsequent formation of a membrane-active DNA-entrapped protein complex. Here, we solve the structure of a C-terminally truncated B. subtilis Noc bound to NBS DNA to reveal the conformation of Noc at this crucial step. Our structure reveals the disengagement between the N-terminal CTP-binding domain and the NBS-binding domain of each DNA-bound Noc subunit; this is driven, in part, by the swapping of helices 4 and 5 at the interface of the two domains. Site-specific crosslinking data suggest that this conformation of Noc-NBS exists in solution. Overall, our results lend support to the recent proposal that parS/NBS binding catalyzes CTP binding and DNA entrapment by preventing the reengagement of the CTP-binding domain and the DNA-binding domain from the same ParB/Noc subunit.
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Affiliation(s)
- Kirill V Sukhoverkov
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom; Section of Structural and Synthetic Biology, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom.
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24
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Kawalek A, Glabski K, Bartosik AA, Wozniak D, Kusiak M, Gawor J, Zuchniewicz K, Jagura-Burdzy G. Diverse Partners of the Partitioning ParB Protein in Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0428922. [PMID: 36622167 DOI: 10.1128/spectrum.04289-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In the majority of bacterial species, the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target parS sequence(s), assists in the chromosome partitioning. ParB forms large nucleoprotein complexes at parS(s), located in the vicinity of origin of chromosomal replication (oriC), which after replication are subsequently positioned by ParA in cell poles. Remarkably, ParA and ParB participate not only in the chromosome segregation but through interactions with various cellular partners they are also involved in other cell cycle-related processes, in a species-specific manner. In this work, we characterized Pseudomonas aeruginosa ParB interactions with the cognate ParA, showing that the N-terminal motif of ParB is required for these interactions, and demonstrated that ParAB-parS-mediated rapid segregation of newly replicated ori domains prevented structural maintenance of chromosome (SMC)-mediated cohesion of sister chromosomes. Furthermore, using proteome-wide techniques, we have identified other ParB partners in P. aeruginosa, which encompass a number of proteins, including the nucleoid-associated proteins NdpA(PA3849) and NdpA2, MinE (PA3245) of Min system, and transcriptional regulators and various enzymes, e.g., CTP synthetase (PA3637). Among them are also NTPases PA4465, PA5028, PA3481, and FleN (PA1454), three of them displaying polar localization in bacterial cells. Overall, this work presents the spectrum of P. aeruginosa ParB partners and implicates the role of this protein in the cross-talk between chromosome segregation and other cellular processes. IMPORTANCE In Pseudomonas aeruginosa, a Gram-negative pathogen causing life-threatening infections in immunocompromised patients, the ParAB-parS system is involved in the precise separation of newly replicated bacterial chromosomes. In this work, we identified and characterized proteins interacting with partitioning protein ParB. We mapped the domain of interactions with its cognate ParA partner and showed that ParB-ParA interactions are crucial for the chromosome segregation and for proper SMC action on DNA. We also demonstrated ParB interactions with other DNA binding proteins, metabolic enzymes, and NTPases displaying polar localization in the cells. Overall, this study uncovers novel players cooperating with the chromosome partition system in P. aeruginosa, supporting its important regulatory role in the bacterial cell cycle.
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25
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Roberts DM. A new role for monomeric ParA/Soj in chromosome dynamics in Bacillus subtilis. Microbiologyopen 2023; 12:e1344. [PMID: 36825885 PMCID: PMC9841721 DOI: 10.1002/mbo3.1344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
ParABS (Soj-Spo0J) systems were initially implicated in plasmid and chromosome segregation in bacteria. However, it is now increasingly understood that they play multiple roles in cell cycle events in Bacillus subtilis, and possibly other bacteria. In a recent study, monomeric forms of ParA/Soj have been implicated in regulating aspects of chromosome dynamics during B. subtilis sporulation. In this commentary, I will discuss the known roles of ParABS systems, explore why sporulation is a valuable model for studying these proteins, and the new insights into the role of monomeric ParA/Soj. Finally, I will touch upon some of the future work that remains.
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26
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Picker MA, Karney MMA, Gerson TM, Karabachev AD, Duhart JC, McKenna JA, Wing HJ. Localized modulation of DNA supercoiling, triggered by the Shigella anti-silencer VirB, is sufficient to relieve H-NS-mediated silencing. bioRxiv 2023:2023.01.09.523335. [PMID: 36711906 PMCID: PMC9882051 DOI: 10.1101/2023.01.09.523335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In Bacteria, nucleoid structuring proteins govern nucleoid dynamics and regulate transcription. In Shigella spp ., at ≤ 30 °C, the histone-like nucleoid structuring protein (H-NS) transcriptionally silences many genes on the large virulence plasmid. Upon a switch to 37 °C, VirB, a DNA binding protein and key transcriptional regulator of Shigella virulence, is produced. VirB functions to counter H-NS-mediated silencing in a process called transcriptional anti-silencing. Here, we show that VirB mediates a loss of negative DNA supercoils from our plasmid-borne, VirB-regulated PicsP-lacZ reporter, in vivo . The changes are not caused by a VirB-dependent increase in transcription, nor do they require the presence of H-NS. Instead, the VirB-dependent change in DNA supercoiling requires the interaction of VirB with its DNA binding site, a critical first step in VirB-dependent gene regulation. Using two complementary approaches, we show that VirB:DNA interactions in vitro introduce positive supercoils in plasmid DNA. Subsequently, by exploiting transcription-coupled DNA supercoiling, we reveal that a localized loss of negative supercoils is sufficient to alleviate H-NS-mediated transcriptional silencing, independently of VirB. Together, our findings provide novel insight into VirB, a central regulator of Shigella virulence and more broadly, a molecular mechanism that offsets H-NS-dependent silencing of transcription in bacteria.
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27
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Takacs CN, Wachter J, Xiang Y, Ren Z, Karaboja X, Scott M, Stoner MR, Irnov I, Jannetty N, Rosa PA, Wang X, Jacobs-Wagner C. Polyploidy, regular patterning of genome copies, and unusual control of DNA partitioning in the Lyme disease spirochete. Nat Commun 2022; 13:7173. [PMID: 36450725 PMCID: PMC9712426 DOI: 10.1038/s41467-022-34876-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Borrelia burgdorferi, the tick-transmitted spirochete agent of Lyme disease, has a highly segmented genome with a linear chromosome and various linear or circular plasmids. Here, by imaging several chromosomal loci and 16 distinct plasmids, we show that B. burgdorferi is polyploid during growth in culture and that the number of genome copies decreases during stationary phase. B. burgdorferi is also polyploid inside fed ticks and chromosome copies are regularly spaced along the spirochete's length in both growing cultures and ticks. This patterning involves the conserved DNA partitioning protein ParA whose localization is controlled by a potentially phage-derived protein, ParZ, instead of its usual partner ParB. ParZ binds its own coding region and acts as a centromere-binding protein. While ParA works with ParZ, ParB controls the localization of the condensin, SMC. Together, the ParA/ParZ and ParB/SMC pairs ensure faithful chromosome inheritance. Our findings underscore the plasticity of cellular functions, even those as fundamental as chromosome segregation.
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Affiliation(s)
- Constantin N Takacs
- Department of Biology, Stanford University, Palo Alto, CA, USA
- Sarafan ChEM-H Institute, Stanford University, Palo Alto, CA, USA
- The Howard Hughes Medical Institute, Palo Alto, CA, USA
| | - Jenny Wachter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Bacterial Vaccine Development Group, Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yingjie Xiang
- Department of Mechanical Engineering, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale West Campus, West Haven, CT, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Xheni Karaboja
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Molly Scott
- Microbial Sciences Institute, Yale West Campus, West Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Matthew R Stoner
- The Howard Hughes Medical Institute, Palo Alto, CA, USA
- Microbial Sciences Institute, Yale West Campus, West Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Irnov Irnov
- Department of Biology, Stanford University, Palo Alto, CA, USA
- Sarafan ChEM-H Institute, Stanford University, Palo Alto, CA, USA
- The Howard Hughes Medical Institute, Palo Alto, CA, USA
| | - Nicholas Jannetty
- The Howard Hughes Medical Institute, Palo Alto, CA, USA
- Microbial Sciences Institute, Yale West Campus, West Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Patricia A Rosa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN, USA.
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Palo Alto, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Palo Alto, CA, USA.
- The Howard Hughes Medical Institute, Palo Alto, CA, USA.
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28
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Köhler R, Kaganovitch E, Murray SM. High-throughput imaging and quantitative analysis uncovers the nature of plasmid positioning by ParABS. eLife 2022; 11:78743. [PMID: 36374535 PMCID: PMC9662831 DOI: 10.7554/elife.78743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/23/2022] [Indexed: 11/16/2022] Open
Abstract
The faithful segregation and inheritance of bacterial chromosomes and low-copy number plasmids requires dedicated partitioning systems. The most common of these, ParABS, consists of ParA, a DNA-binding ATPase and ParB, a protein that binds to centromeric-like parS sequences on the DNA cargo. The resulting nucleoprotein complexes are believed to move up a self-generated gradient of nucleoid-associated ParA. However, it remains unclear how this leads to the observed cargo positioning and dynamics. In particular, the evaluation of models of plasmid positioning has been hindered by the lack of quantitative measurements of plasmid dynamics. Here, we use high-throughput imaging, analysis and modelling to determine the dynamical nature of these systems. We find that F plasmid is actively brought to specific subcellular home positions within the cell with dynamics akin to an over-damped spring. We develop a unified stochastic model that quantitatively explains this behaviour and predicts that cells with the lowest plasmid concentration transition to oscillatory dynamics. We confirm this prediction for F plasmid as well as a distantly-related ParABS system. Our results indicate that ParABS regularly positions plasmids across the nucleoid but operates just below the threshold of an oscillatory instability, which according to our model, minimises ATP consumption. Our work also clarifies how various plasmid dynamics are achievable in a single unified stochastic model. Overall, this work uncovers the dynamical nature of plasmid positioning by ParABS and provides insights relevant for chromosome-based systems.
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Affiliation(s)
- Robin Köhler
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Eugen Kaganovitch
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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29
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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30
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Roberts DM, Anchimiuk A, Kloosterman TG, Murray H, Wu LJ, Gruber S, Errington J. Chromosome remodelling by SMC/Condensin in B. subtilis is regulated by monomeric Soj/ParA during growth and sporulation. Proc Natl Acad Sci U S A 2022; 119:e2204042119. [PMID: 36206370 PMCID: PMC9564211 DOI: 10.1073/pnas.2204042119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
SMC complexes, loaded at ParB-parS sites, are key mediators of chromosome organization in bacteria. ParA/Soj proteins interact with ParB/Spo0J in a pathway involving adenosine triphosphate (ATP)-dependent dimerization and DNA binding, facilitating chromosome segregation in bacteria. In Bacillus subtilis, ParA/Soj also regulates DNA replication initiation and along with ParB/Spo0J is involved in cell cycle changes during endospore formation. The first morphological stage in sporulation is the formation of an elongated chromosome structure called an axial filament. Here, we show that a major redistribution of SMC complexes drives axial filament formation in a process regulated by ParA/Soj. Furthermore, and unexpectedly, this regulation is dependent on monomeric forms of ParA/Soj that cannot bind DNA or hydrolyze ATP. These results reveal additional roles for ParA/Soj proteins in the regulation of SMC dynamics in bacteria and yet further complexity in the web of interactions involving chromosome replication, segregation and organization, controlled by ParAB and SMC.
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Affiliation(s)
- David M. Roberts
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Anna Anchimiuk
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 015 Lausanne, Switzerland
| | - Tomas G. Kloosterman
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 015 Lausanne, Switzerland
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
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31
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Koh A, Strahl H, Murray H. Regulation of DNA replication initiation by ParA is independent of parS location in Bacillus subtilis. Microbiology (Reading) 2022; 168:10.1099/mic.0.001259. [PMID: 36301085 PMCID: PMC7614844 DOI: 10.1099/mic.0.001259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Replication and segregation of the genetic information is necessary for a cell to proliferate. In Bacillus subtilis, the Par system (ParA/Soj, ParB/Spo0J and parS) is required for segregation of the chromosome origin (oriC) region and for proper control of DNA replication initiation. ParB binds parS sites clustered near the origin of replication and assembles into sliding clamps that interact with ParA to drive origin segregation through a diffusion-ratchet mechanism. As part of this dynamic process, ParB stimulates ParA ATPase activity to trigger its switch from an ATP-bound dimer to an ADP-bound monomer. In addition to its conserved role in DNA segregation, ParA is also a regulator of the master DNA replication initiation protein DnaA. We hypothesized that in B. subtilis the location of the Par system proximal to oriC would be necessary for ParA to properly regulate DnaA. To test this model, we constructed a range of genetically modified strains with altered numbers and locations of parS sites, many of which perturbed chromosome origin segregation as expected. Contrary to our hypothesis, the results show that regulation of DNA replication initiation by ParA is maintained when a parS site is separated from oriC. Because a single parS site is sufficient for proper control of ParA, the results are consistent with a model where ParA is efficiently regulated by ParB sliding clamps following loading at parS.
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Affiliation(s)
- Alan Koh
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
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32
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Volante A, Alonso JC, Mizuuchi K. Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery. eLife 2022; 11:79480. [PMID: 36062913 PMCID: PMC9499535 DOI: 10.7554/elife.79480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP-dependent nonspecific DNA-binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParBpSM of the ribbon-helix-helix (RHH) family. We show that parSpSM with four or more contiguous ParBpSM-binding sequence repeats is required to assemble a stable ParApSM-ParBpSM complex and efficiently activate the ParApSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parSpSM sequence array destabilizes the ParApSM-ParBpSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParApSM-ATP.
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Affiliation(s)
- Andrea Volante
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, United States
| | - Juan Carlos Alonso
- Department of Microbial Biotechnology, National Center for Biotechnology, Madrid, Spain
| | - Kiyoshi Mizuuchi
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, United States
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33
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Bock FP, Liu HW, Anchimiuk A, Diebold-Durand ML, Gruber S. A joint-ParB interface promotes Smc DNA recruitment. Cell Rep 2022; 40:111273. [PMID: 36044845 PMCID: PMC9449133 DOI: 10.1016/j.celrep.2022.111273] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/21/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomes readily unlink and segregate to daughter cells during cell division, highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes promote DNA organization by loop extrusion. In most bacteria, chromosome folding initiates at dedicated start sites marked by the ParB/parS partition complexes. Whether SMC complexes recognize a specific DNA structure in the partition complex or a protein component is unclear. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate foreign chromosomes. Using chimeric proteins and chemical cross-linking, we find that ParB directly binds the Smc subunit. We map an interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex, presumably to initiate DNA loop extrusion. The bacterial DNA-binding protein ParB interacts with the condensin-like Smc-ScpAB Genetic mapping and structure predictions reveal an Smc joint-ParB binding interface Mutating the binding interface hampers Smc recruitment but not other ParB functions ParB and Smc-ScpAB form a transplantable unit for chromosome segregation in bacteria
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Affiliation(s)
- Florian P Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Anchimiuk
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Marie-Laure Diebold-Durand
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland.
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34
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Guo L, Zhao Y, Zhang Q, Feng Y, Bi L, Zhang X, Wang T, Liu C, Ma H, Sun B. Stochastically multimerized ParB orchestrates DNA assembly as unveiled by single-molecule analysis. Nucleic Acids Res 2022; 50:9294-9305. [PMID: 35904809 PMCID: PMC9458438 DOI: 10.1093/nar/gkac651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022] Open
Abstract
The tripartite ParABS system mediates chromosome segregation in a wide range of bacteria. Dimeric ParB was proposed to nucleate on parS sites and spread to neighboring DNA. However, how properly distributed ParB dimers further compact chromosomal DNA into a higher-order nucleoprotein complex for partitioning remains poorly understood. Here, using a single-molecule approach, we show that tens of Bacillus subtilis ParB (Spo0J) proteins can stochastically multimerize on and stably bind to nonspecific DNA. The introduction of CTP promotes the formation and diffusion of the multimeric ParB along DNA, offering an opportunity for ParB proteins to further forgather and cluster. Intriguingly, ParB multimers can recognize parS motifs and are more inclined to remain immobile on them. Importantly, the ParB multimer features distinct capabilities of not only bridging two independent DNA molecules but also mediating their transportation, both of which are enhanced by the presence of either CTP or parS in the DNA. These findings shed new light on ParB dynamics in self-multimerization and DNA organization and help to better comprehend the assembly of the ParB-DNA partition complex.
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Affiliation(s)
- Lijuan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yilin Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qian Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Feng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Teng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hanhui Ma
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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35
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Chan HY, Jensen SO, LeBard RJ, Figgett WA, Lai E, Simpson AE, Brzoska AJ, Davies DS, Connolly AM, Cordwell SJ, Travis BA, Salinas R, Skurray RA, Firth N, Schumacher MA. Molecular Analysis of pSK1 par: A Novel Plasmid Partitioning System Encoded by Staphylococcal Multiresistance Plasmids. J Mol Biol 2022;:167770. [PMID: 35907571 DOI: 10.1016/j.jmb.2022.167770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/23/2022]
Abstract
The segregation of prokaryotic plasmids typically requires a centromere-like site and two proteins, a centromere-binding protein (CBP) and an NTPase. By contrast, a single 245 residue Par protein mediates partition of the prototypical staphylococcal multiresistance plasmid pSK1 in the absence of an identifiable NTPase component. To gain insight into centromere binding by pSK1 Par and its segregation function we performed structural, biochemical and in vivo studies. Here we show that pSK1 Par binds a centromere consisting of seven repeat elements. We demonstrate this Par-centromere interaction also mediates Par autoregulation. To elucidate the Par centromere binding mechanism, we obtained a structure of the Par N-terminal DNA-binding domain bound to centromere DNA to 2.25 Å. The pSK1 Par structure, which harbors a winged-helix-turn-helix (wHTH), is distinct from other plasmid CBP structures but shows homology to the B. subtilis chromosome segregation protein, RacA. Biochemical studies suggest the region C-terminal to the Par wHTH forms coiled coils and mediates oligomerization. Fluorescence microscopy analyses show that pSK1 Par enhances the separation of plasmids from clusters, driving effective segregation upon cell division. Combined the data provide insight into the molecular properties of a single protein partition system.
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36
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Shodhan A, Xaver M, Wheeler D, Lichten M. Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae. Genetics 2022; 222:6649696. [PMID: 35876814 PMCID: PMC9434160 DOI: 10.1093/genetics/iyac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
The DNA double strand breaks (DSBs) that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in Saccharomyces cerevisiae contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red1 are important for DSB formation; DSB levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with DSB levels. How axis protein levels influence DSB formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased DSBs and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in DSBs did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote DSB formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, crossovers that formed at an insert locus were only modestly reduced in the absence of MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local DSB levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.
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Affiliation(s)
- Anura Shodhan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Martin Xaver
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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Pióro M, Matusiak I, Gawek A, Łebkowski T, Jaroszek P, Bergé M, Böhm K, Armitage J, Viollier PH, Bramkamp M, Jakimowicz D. Genus-Specific Interactions of Bacterial Chromosome Segregation Machinery Are Critical for Their Function. Front Microbiol 2022; 13:928139. [PMID: 35875543 PMCID: PMC9298525 DOI: 10.3389/fmicb.2022.928139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Most bacteria use the ParABS system to segregate their newly replicated chromosomes. The two protein components of this system from various bacterial species share their biochemical properties: ParB is a CTPase that binds specific centromere-like parS sequences to assemble a nucleoprotein complex, while the ParA ATPase forms a dimer that binds DNA non-specifically and interacts with ParB complexes. The ParA-ParB interaction incites the movement of ParB complexes toward the opposite cell poles. However, apart from their function in chromosome segregation, both ParAB may engage in genus-specific interactions with other protein partners. One such example is the polar-growth controlling protein DivIVA in Actinomycetota, which binds ParA in Mycobacteria while interacts with ParB in Corynebacteria. Here, we used heterologous hosts to investigate whether the interactions between DivIVA and ParA or ParB are maintained across phylogenic classes. Specifically, we examined interactions of proteins from four bacterial species, two belonging to the Gram positive Actinomycetota phylum and two belonging to the Gram-negative Pseudomonadota. We show that while the interactions between ParA and ParB are preserved for closely related orthologs, the interactions with polarly localised protein partners are not conferred by orthologous ParABs. Moreover, we demonstrate that heterologous ParA cannot substitute for endogenous ParA, despite their high sequence similarity. Therefore, we conclude that ParA orthologs are fine-tuned to interact with their partners, especially their interactions with polarly localised proteins are adjusted to particular bacterial species demands.
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Affiliation(s)
- Monika Pióro
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- *Correspondence: Monika Pióro,
| | - Izabela Matusiak
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Adam Gawek
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Tomasz Łebkowski
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Patrycja Jaroszek
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kati Böhm
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Judith Armitage
- Department of Biochemistry, University of Oxford, Oxford,United Kingdom
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Marc Bramkamp
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Dagmara Jakimowicz
- Faculty of Biotechnology, Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
- Dagmara Jakimowicz,
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Tišma M, Panoukidou M, Antar H, Soh YM, Barth R, Pradhan B, Barth A, van der Torre J, Michieletto D, Gruber S, Dekker C. ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment. Sci Adv 2022; 8:eabn3299. [PMID: 35767606 PMCID: PMC9242446 DOI: 10.1126/sciadv.abn3299] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in vitro single-molecule fluorescence imaging, we show that ParB from Bacillus subtilis can load onto DNA distantly of parS, as loaded ParB molecules themselves are found to be able to recruit additional ParB proteins from bulk. Notably, this recruitment can occur in cis but also in trans, where, at low tensions within the DNA, newly recruited ParB can bypass roadblocks as it gets loaded to spatially proximal but genomically distant DNA regions. The data are supported by molecular dynamics simulations, which show that cooperative ParB-ParB recruitment can enhance spreading. ParS-independent recruitment explains how ParB can cover substantial genomic distance during chromosome segregation, which is vital for the bacterial cell cycle.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Maria Panoukidou
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Young-Min Soh
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Roman Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Biswajit Pradhan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
- Corresponding author.
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Mishra D, Srinivasan R. Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins. Front Microbiol 2022; 13:856547. [PMID: 35694299 PMCID: PMC9178275 DOI: 10.3389/fmicb.2022.856547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/28/2022] [Indexed: 12/01/2022] Open
Abstract
Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
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40
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Possoz C, Yamaichi Y, Galli E, Ferat JL, Barre FX. Vibrio cholerae Chromosome Partitioning without Polar Anchoring by HubP. Genes (Basel) 2022; 13:genes13050877. [PMID: 35627261 PMCID: PMC9140986 DOI: 10.3390/genes13050877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Partition systems are widespread among bacterial chromosomes. They are composed of two effectors, ParA and ParB, and cis acting sites, parS, located close to the replication origin of the chromosome (oriC). ParABS participate in chromosome segregation, at least in part because they serve to properly position sister copies of oriC. A fourth element, located at cell poles, is also involved in some cases, such as HubP for the ParABS1 system of Vibrio cholerae chromosome 1 (ch1). The polar anchoring of oriC of ch1 (oriC1) is lost when HubP or ParABS1 are inactivated. Here, we report that in the absence of HubP, ParABS1 actively maintains oriC1 at mid-cell, leading to the subcellular separation of the two ch1 replication arms. We further show that parS1 sites ectopically inserted in chromosome 2 (ch2) stabilize the inheritance of this replicon in the absence of its endogenous partition system, even without HubP. We also observe the positioning interference between oriC1 and oriC of ch2 regions when their positionings are both driven by ParABS1. Altogether, these data indicate that ParABS1 remains functional in the absence of HubP, which raises questions about the role of the polar anchoring of oriC1 in the cell cycle.
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Czarnecki J, Chapkauskaitse E, Bos J, Sentkowska D, Wawrzyniak P, Wyszyńska A, Szuplewska M, Bartosik D. Differential Localization and Functional Specialization of parS Centromere-Like Sites in repABC Replicons of Alphaproteobacteria. Appl Environ Microbiol 2022;:e0020722. [PMID: 35389251 DOI: 10.1128/aem.00207-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Partitioning systems ensure the stable inheritance of bacterial low-copy-number replicons, such as chromosomes, chromids, and megaplasmids. These loci consist of two genes encoding partition proteins A and B, and at least one parS centromere-like sequence. In chromids and megaplasmids, partitioning systems are often located in the vicinity of replication systems. An extreme example of this co-localization are alphaproteobacterial repABC replicons, where the partition (repAB) and replication (repC) genes form a single operon, with parS sequences usually positioned in close proximity to these genes. In this study, we characterized a more complex repABC system found in Paracoccus aminophilus (Rhodobacterales) megaplasmid pAMI4 (438 kb). Besides the repABC operon with a single parS site, this replicon has a 2-kb non-coding locus positioned 11.5 kb downstream of repC, which contains three additional parS repeats (3parS). We demonstrated that 3parS is bound by partition protein B in vitro and is essential for proper pAMI4 partitioning in vivo. In search of similar loci, we conducted a comparative analysis of parS distribution in other repABC replicons. This revealed different patterns of parS localization in Rhodobacterales and Rhizobiales. However, in both these taxonomic orders, parS sites are almost always located inside or close to the repABC operon. No other 3parS-like loci were found in the closest relatives of pAMI4. Another evolutionarily-independent example of such a locus was identified as a conserved feature in chromosome 2 of Allorhizobium vitis and related replicons. IMPORTANCE The repABC replication/partitioning loci are widespread in extrachromosomal replicons of Alphaproteobacteria. They are evolutionarily diverse, subject to multi-layer self-regulation, and are responsible for the maintenance of different types of replicons, such as plasmids (e.g., Agrobacterium pTi and pRi tumorigenic and rhizogenic plasmids), megaplasmids (e.g., Sinorhizobium pSymA and pSymB) and essential chromids (e.g., secondary chromosomes of Agrobacterium, Brucella and Rhodobacter). In this study, we functionally analyzed an atypical partition-related component of repABC systems, the 3parS locus, found in the P. aminophilus megaplasmid pAMI4. We also identified parS centromere-like site distribution patterns in different groups of repABC replicons and found other unrelated 3parS-like loci, which had been overlooked. Our findings raise questions concerning the biological reasons for differential parS distribution, which may reflect variations in repABC operon regulation as well as different replication and partition modes of replicons belonging to the repABC family.
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42
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Giacomelli G, Feddersen H, Peng F, Martins GB, Grafemeyer M, Meyer F, Mayer B, Graumann PL, Bramkamp M. Subcellular Dynamics of a Conserved Bacterial Polar Scaffold Protein. Genes (Basel) 2022; 13:278. [PMID: 35205323 PMCID: PMC8872289 DOI: 10.3390/genes13020278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/05/2023] Open
Abstract
In order to survive, bacterial cells rely on precise spatiotemporal organization and coordination of essential processes such as cell growth, chromosome segregation, and cell division. Given the general lack of organelles, most bacteria are forced to depend on alternative localization mechanisms, such as, for example, geometrical cues. DivIVA proteins are widely distributed in mainly Gram-positive bacteria and were shown to bind the membrane, typically in regions of strong negative curvature, such as the cell poles and division septa. Here, they have been shown to be involved in a multitude of processes: from apical cell growth and chromosome segregation in actinobacteria to sporulation and inhibition of division re-initiation in firmicutes. Structural analyses revealed that DivIVA proteins can form oligomeric assemblies that constitute a scaffold for recruitment of other proteins. However, it remained unclear whether interaction with partner proteins influences DivIVA dynamics. Using structured illumination microscopy (SIM), single-particle tracking (SPT) microscopy, and fluorescent recovery after photobleaching (FRAP) experiments, we show that DivIVA from Corynebacterium glutamicum is mobilized by its binding partner ParB. In contrast, we show that the interaction between Bacillus subtilis DivIVA and its partner protein MinJ reduces DivIVA mobility. Furthermore, we show that the loss of the rod-shape leads to an increase in DivIVA dynamics in both organisms. Taken together, our study reveals the modulation of the polar scaffold protein by protein interactors and cell morphology. We reason that this leads to a very simple, yet robust way for actinobacteria to maintain polar growth and their rod-shape. In B. subtilis, however, the DivIVA protein is tailored towards a more dynamic function that allows quick relocalization from poles to septa upon division.
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43
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Babl L, Giacomelli G, Ramm B, Gelmroth AK, Bramkamp M, Schwille P. CTP-controlled liquid-liquid phase separation of ParB. J Mol Biol 2022; 434:167401. [PMID: 34902429 DOI: 10.1016/j.jmb.2021.167401] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022]
Abstract
The ParABS system is supposed to be responsible for plasmid partitioning and chromosome segregation in bacteria. ParABS ensures a high degree of fidelity in inheritance by dividing the genetic material equally between daughter cells during cell division. However, the molecular mechanisms underlying the assembly of the partition complex, representing the core of the ParABS system, are still far from being understood. Here we demonstrate that the partition complex is formed via liquid-liquid phase separation. Assembly of the partition complex is initiated by the formation of oligomeric ParB species, which in turn are regulated by CTP-binding. Phase diagrams and in vivo analysis show how the partition complex can further be spatially regulated by parS. By investigating the phylogenetic variation in phase separation and its regulation by CTP, we find a high degree of evolutionary conservation among distantly related prokaryotes. These results advance the understanding of partition complex formation and regulation in general, by confirming and extending recently proposed models.
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Affiliation(s)
- Leon Babl
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Giacomo Giacomelli
- Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Beatrice Ramm
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany
| | - Ann-Kathrin Gelmroth
- Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Marc Bramkamp
- Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Petra Schwille
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Planegg, Germany.
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Dugar G, Hofmann A, Heermann DW, Hamoen LW. A chromosomal loop anchor mediates bacterial genome organization. Nat Genet 2022; 54:194-201. [PMID: 35075232 DOI: 10.1038/s41588-021-00988-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/19/2021] [Indexed: 12/22/2022]
Abstract
Nucleoprotein complexes play an integral role in genome organization of both eukaryotes and prokaryotes. Apart from their role in locally structuring and compacting DNA, several complexes are known to influence global organization by mediating long-range anchored chromosomal loop formation leading to spatial segregation of large sections of DNA. Such megabase-range interactions are ubiquitous in eukaryotes, but have not been demonstrated in prokaryotes. Here, using a genome-wide sedimentation-based approach, we found that a transcription factor, Rok, forms large nucleoprotein complexes in the bacterium Bacillus subtilis. Using chromosome conformation capture and live-imaging of DNA loci, we show that these complexes robustly interact with each other over large distances. Importantly, these Rok-dependent long-range interactions lead to anchored chromosomal loop formation, thereby spatially isolating large sections of DNA, as previously observed for insulator proteins in eukaryotes.
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Affiliation(s)
- Gaurav Dugar
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Andreas Hofmann
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Dieter W Heermann
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Leendert W Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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45
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Antar H, Soh YM, Zamuner S, Bock FP, Anchimiuk A, Rios PDL, Gruber S. Relief of ParB autoinhibition by parS DNA catalysis and recycling of ParB by CTP hydrolysis promote bacterial centromere assembly. Sci Adv 2021; 7:eabj2854. [PMID: 34613769 PMCID: PMC8494293 DOI: 10.1126/sciadv.abj2854] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB acts as adaptor protein between the 16–base pair centromeric parS DNA sequences and the DNA segregation proteins ParA and Smc (structural maintenance of chromosomes). Upon cytidine triphosphate (CTP) and parS DNA binding, ParB dimers form DNA clamps that spread onto parS-flanking DNA by sliding, thus assembling the so-called partition complex. We show here that CTP hydrolysis is essential for efficient chromosome segregation by ParABS but largely dispensable for Smc recruitment. Our results suggest that CTP hydrolysis contributes to partition complex assembly via two mechanisms. It promotes ParB unloading from DNA to limit the extent of ParB spreading, and it recycles off-target ParB clamps to allow for parS retargeting, together superconcentrating ParB near parS. We also propose a model for clamp closure involving a steric clash when binding ParB protomers to opposing parS half sites.
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Affiliation(s)
- Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Young-Min Soh
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Stefano Zamuner
- Laboratory of Statistical Biophysics, Institute of Physics, School of Basic Sciences and Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Florian P. Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Anchimiuk
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
| | - Paolo De Los Rios
- Laboratory of Statistical Biophysics, Institute of Physics, School of Basic Sciences and Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne, 1015 Lausanne, Switzerland
- Corresponding author.
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Osorio-Valeriano M, Altegoer F, Das CK, Steinchen W, Panis G, Connolley L, Giacomelli G, Feddersen H, Corrales-Guerrero L, Giammarinaro PI, Hanßmann J, Bramkamp M, Viollier PH, Murray S, Schäfer LV, Bange G, Thanbichler M. The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes. Mol Cell 2021; 81:3992-4007.e10. [PMID: 34562373 DOI: 10.1016/j.molcel.2021.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 01/29/2023]
Abstract
ParB-like CTPases mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromere of target DNA molecules and spread laterally to form large nucleoprotein complexes serving as docking points for the DNA segregation machinery. Here, we solve crystal structures of ParB in the pre- and post-hydrolysis state and illuminate the catalytic mechanism of nucleotide hydrolysis. Moreover, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. The study of CTPase-deficient ParB variants reveals that CTP hydrolysis serves to limit the sliding time of ParB clamps and thus drives the establishment of a well-defined ParB diffusion gradient across the centromere whose dynamics are critical for DNA segregation. These findings clarify the role of the ParB CTPase cycle in partition complex assembly and function and thus advance our understanding of this prototypic CTP-dependent molecular switch.
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Affiliation(s)
- Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Florian Altegoer
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Connolley
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Giacomo Giacomelli
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Helge Feddersen
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | | | - Pietro I Giammarinaro
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Juri Hanßmann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, 24118 Kiel, Germany
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Seán Murray
- Department of Systems & Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gert Bange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology, 35043 Marburg, Germany.
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Hu L, Rech J, Bouet JY, Liu J. Spatial control over near-critical-point operation ensures fidelity of ParABS-mediated DNA partition. Biophys J 2021; 120:3911-3924. [PMID: 34418367 PMCID: PMC8511131 DOI: 10.1016/j.bpj.2021.08.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/26/2021] [Accepted: 08/13/2021] [Indexed: 01/20/2023] Open
Abstract
In bacteria, most low-copy-number plasmid and chromosomally encoded partition systems belong to the tripartite ParABS partition machinery. Despite the importance in genetic inheritance, the mechanisms of ParABS-mediated genome partition are not well understood. Combining theory and experiment, we provided evidence that the ParABS system-DNA partitioning in vivo via the ParA-gradient-based Brownian ratcheting-operates near a transition point in parameter space (i.e., a critical point), across which the system displays qualitatively different motile behaviors. This near-critical-point operation adapts the segregation distance of replicated plasmids to the half length of the elongating nucleoid, ensuring both cell halves to inherit one copy of the plasmids. Further, we demonstrated that the plasmid localizes the cytoplasmic ParA to buffer the partition fidelity against the large cell-to-cell fluctuations in ParA level. The spatial control over the near-critical-point operation not only ensures both sensitive adaptation and robust execution of partitioning but also sheds light on the fundamental question in cell biology: how do cells faithfully measure cellular-scale distance by only using molecular-scale interactions?
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Affiliation(s)
- Longhua Hu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jérôme Rech
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse, France.
| | - Jian Liu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Liu K, Hu XR, Zhao LX, Wang Y, Deng Z, Tao M. Enhancing Ristomycin A Production by Overexpression of ParB-Like StrR Family Regulators Controlling the Biosynthesis Genes. Appl Environ Microbiol 2021; 87:e0106621. [PMID: 34505824 DOI: 10.1128/AEM.01066-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Amycolatopsis sp. strain TNS106 harbors a ristomycin-biosynthetic gene cluster (asr) in its genome and produces ristomycin A. Deletion of the sole cluster-situated StrR family regulatory gene, asrR, abolished ristomycin A production and the transcription of the asr genes orf5 to orf39. The ristomycin A fermentation titer in Amycolatopsis sp. strain TNS106 was dramatically improved by overexpression of asrR and a heterologous StrR family regulatory gene, bbr, from the balhimycin-biosynthetic gene cluster (BGC) utilizing strong promoters and multiple gene copies. Ristomycin A production was improved by approximately 60-fold, resulting in a fermentation titer of 4.01 g/liter in flask culture, in one of the engineered strains. Overexpression of AsrR and Bbr upregulated transcription of tested asr biosynthetic genes, indicating that these asr genes were positively regulated by AsrR and Bbr. However, only the promoter region of the asrR operon and the intergenic region upstream of orf12 were bound by AsrR and Bbr in gel retardation assays, suggesting that AsrR and Bbr directly regulated the asrR operon and probably orf12 to orf14 but no other asr biosynthetic genes. Further assays with synthetic short probes showed that AsrR and Bbr specifically bound not only probes containing the canonical inverted repeats but also a probe with only one 7-bp element of the inverted repeats in its native context. AsrR and Bbr have an N-terminal ParB-like domain and a central winged helix-turn-helix DNA-binding domain. Site-directed mutations indicated that the N-terminal ParB-like domain was involved in activation of ristomycin A biosynthesis and did not affect the DNA-binding activity of AsrR and Bbr. IMPORTANCE This study showed that overexpression of either a native StrR family regulator (AsrR) or a heterologous StrR family regulator (Bbr) dramatically improved ristomycin A production by increasing the transcription of biosynthetic genes directly or indirectly. The conserved ParB-like domain of AsrR and Bbr was demonstrated to be involved in the regulation of asr BGC expression. These findings provide new insights into the mechanism of StrR family regulators in the regulation of glycopeptide antibiotic biosynthesis. Furthermore, the regulator overexpression plasmids constructed in this study could serve as valuable tools for strain improvement and genome mining for new glycopeptide antibiotics. In addition, ristomycin A is a type III glycopeptide antibiotic clinically used as a diagnostic reagent due to its side effects. The overproduction strains engineered in this study are ideal materials for industrial production of ristomycin A.
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Jalal ASB, Tran NT, Wu LJ, Ramakrishnan K, Rejzek M, Gobbato G, Stevenson CEM, Lawson DM, Errington J, Le TBK. CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc. Mol Cell 2021; 81:3623-3636.e6. [PMID: 34270916 DOI: 10.1101/2021.02.11.430593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 05/25/2023]
Abstract
ATP- and GTP-dependent molecular switches are extensively used to control functions of proteins in a wide range of biological processes. However, CTP switches are rarely reported. Here, we report that a nucleoid occlusion protein Noc is a CTPase enzyme whose membrane-binding activity is directly regulated by a CTP switch. In Bacillus subtilis, Noc nucleates on 16 bp NBS sites before associating with neighboring non-specific DNA to form large membrane-associated nucleoprotein complexes to physically occlude assembly of the cell division machinery. By in vitro reconstitution, we show that (1) CTP is required for Noc to form the NBS-dependent nucleoprotein complex, and (2) CTP binding, but not hydrolysis, switches Noc to a membrane-active state. Overall, we suggest that CTP couples membrane-binding activity of Noc to nucleoprotein complex formation to ensure productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity.
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | | | - Martin Rejzek
- Chemistry Platform, John Innes Centre, Norwich, NR4 7UH, UK
| | - Giulia Gobbato
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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50
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Szafran MJ, Małecki T, Strzałka A, Pawlikiewicz K, Duława J, Zarek A, Kois-Ostrowska A, Findlay KC, Le TBK, Jakimowicz D. Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development. Nat Commun 2021; 12:5222. [PMID: 34471115 DOI: 10.1038/s41467-021-25461-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria of the genus Streptomyces have a linear chromosome, with a core region and two ‘arms’. During their complex life cycle, these bacteria develop multi-genomic hyphae that differentiate into chains of exospores that carry a single copy of the genome. Sporulation-associated cell division requires chromosome segregation and compaction. Here, we show that the arms of Streptomyces venezuelae chromosomes are spatially separated at entry to sporulation, but during sporogenic cell division they are closely aligned with the core region. Arm proximity is imposed by segregation protein ParB and condensin SMC. Moreover, the chromosomal terminal regions are organized into distinct domains by the Streptomyces-specific HU-family protein HupS. Thus, as seen in eukaryotes, there is substantial chromosomal remodelling during the Streptomyces life cycle, with the chromosome undergoing rearrangements from an ‘open’ to a ‘closed’ conformation. Streptomyces bacteria have a linear chromosome and a complex life cycle, including development of multi-genomic hyphae that differentiate into mono-genomic exospores. Here, Szafran et al. show that the chromosome of Streptomyces venezuelae undergoes substantial remodelling during sporulation, from an ‘open’ to a ‘closed’ conformation.
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