1
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Zhao Y, Guo L, Hu J, Ren Z, Li Y, Hu M, Zhang X, Bi L, Li D, Ma H, Liu C, Sun B. Phase-separated ParB enforces diverse DNA compaction modes and stabilizes the parS-centered partition complex. Nucleic Acids Res 2024; 52:8385-8398. [PMID: 38908027 PMCID: PMC11317135 DOI: 10.1093/nar/gkae533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/20/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024] Open
Abstract
The tripartite ParABS system mediates chromosome segregation in the majority of bacterial species. Typically, DNA-bound ParB proteins around the parS sites condense the chromosomal DNA into a higher-order multimeric nucleoprotein complex for the ParA-driven partition. Despite extensive studies, the molecular mechanism underlying the dynamic assembly of the partition complex remains unclear. Herein, we demonstrate that Bacillus subtilis ParB (Spo0J), through the multimerization of its N-terminal domain, forms phase-separated condensates along a single DNA molecule, leading to the concurrent organization of DNA into a compact structure. Specifically, in addition to the co-condensation of ParB dimers with DNA, the engagement of well-established ParB condensates with DNA allows for the compression of adjacent DNA and the looping of distant DNA. Notably, the presence of CTP promotes the formation of condensates by a low amount of ParB at parS sites, triggering two-step DNA condensation. Remarkably, parS-centered ParB-DNA co-condensate constitutes a robust nucleoprotein architecture capable of withstanding disruptive forces of tens of piconewton. Overall, our findings unveil diverse modes of DNA compaction enabled by phase-separated ParB and offer new insights into the dynamic assembly and maintenance of the bacterial partition complex.
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Affiliation(s)
- Yilin Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lijuan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiyun Ren
- 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
| | - Yanan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Meng Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hanhui Ma
- 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
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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2
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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] [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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3
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Park J, Kim JJ, Ryu JK. Mechanism of phase condensation for chromosome architecture and function. Exp Mol Med 2024; 56:809-819. [PMID: 38658703 PMCID: PMC11059216 DOI: 10.1038/s12276-024-01226-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/26/2024] Open
Abstract
Chromosomal phase separation is involved in a broad spectrum of chromosome organization and functional processes. Nonetheless, the intricacy of this process has left its molecular mechanism unclear. Here, we introduce the principles governing phase separation and its connections to physiological roles in this context. Our primary focus is contrasting two phase separation mechanisms: self-association-induced phase separation (SIPS) and bridging-induced phase separation (BIPS). We provide a comprehensive discussion of the distinct features characterizing these mechanisms and offer illustrative examples that suggest their broad applicability. With a detailed understanding of these mechanisms, we explore their associations with nucleosomes and chromosomal biological functions. This comprehensive review contributes to the exploration of uncharted territory in the intricate interplay between chromosome architecture and function.
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Affiliation(s)
- Jeongveen Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Jeong-Jun Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Je-Kyung Ryu
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea.
- Institute of Applied Physics of Seoul National University, Seoul, 08826, South Korea.
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, 08826, South Korea.
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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] [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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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] [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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6
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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] [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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7
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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 REPORTS 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] [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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8
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Merino Urteaga R, Ha T. Mind your tag in single-molecule measurements. CELL REPORTS METHODS 2023; 3:100623. [PMID: 37883922 PMCID: PMC10626269 DOI: 10.1016/j.crmeth.2023.100623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
In this issue of Cell Reports Methods, Molina and colleagues use in vitro single-molecule DNA flow-stretching to demonstrate the severe effects of appending a short lysine-cysteine-lysine (KCK) tag on the Bacillus subtilis ParB protein. This assay could be further utilized to evaluate the impact of other tags on DNA-binding proteins.
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Affiliation(s)
- Raquel Merino Urteaga
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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9
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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] [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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10
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Liu D, Pan L, Zhai H, Qiu HJ, Sun Y. Virus tracking technologies and their applications in viral life cycle: research advances and future perspectives. Front Immunol 2023; 14:1204730. [PMID: 37334362 PMCID: PMC10272434 DOI: 10.3389/fimmu.2023.1204730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Viruses are simple yet highly pathogenic microorganisms that parasitize within cells and pose serious threats to the health, economic development, and social stability of both humans and animals. Therefore, it is crucial to understand the dynamic mechanism of virus infection in hosts. One effective way to achieve this is through virus tracking technology, which utilizes fluorescence imaging to track the life processes of virus particles in living cells in real-time, providing a comprehensively and detailed spatiotemporal dynamic process and mechanism of virus infection. This paper provides a broad overview of virus tracking technology, including the selection of fluorescent labels and virus labeling components, the development of imaging microscopes, and its applications in various virus studies. Additionally, we discuss the possibilities and challenges of its future development, offering theoretical guidance and technical support for effective prevention and control of the viral disease outbreaks and epidemics.
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Affiliation(s)
| | | | | | - Hua-Ji Qiu
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
| | - Yuan Sun
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
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11
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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12
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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13
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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] [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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14
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Diverse Partners of the Partitioning ParB Protein in Pseudomonas aeruginosa. Microbiol Spectr 2023; 11:e0428922. [PMID: 36622167 PMCID: PMC9927451 DOI: 10.1128/spectrum.04289-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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15
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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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16
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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] [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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17
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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] [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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18
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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] [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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19
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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] [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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20
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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] [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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21
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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. SCIENCE ADVANCES 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] [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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22
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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] [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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23
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Abstract
Nucleoid-associated proteins (NAPs) help structure bacterial genomes and function in an array of DNA transactions, including transcription, recombination, and repair. In most bacteria, NAPs are nonessential in part due to functional redundancy. In contrast, in Bacillus subtilis the HU homolog HBsu is essential for cell viability. HBsu helps compact the B. subtilis chromosome and participates in homologous recombination and DNA repair. However, none of these activities explain HBsu's essentiality. Here, using two complementary conditional HBsu alleles, we investigated the terminal phenotype of the mutants. Our analysis revealed that cells without functional HBsu fail to initiate DNA replication. Importantly, when the chromosomal replication origin (oriC) was replaced with a plasmid origin (oriN) whose replication does not require the initiator DnaA, cells without HBsu initiated DNA replication normally. However, HBsu was still essential in this oriN-containing strain. We conclude that HBsu plays an essential role in the initiation of DNA replication, likely acting to promote origin melting by DnaA, but also has a second essential function that remains to be discovered. IMPORTANCE While it is common for a bacterial species to express multiple nucleoid-associated proteins (NAPs), NAPs are seldomly essential for cell survival. In B. subtilis, HBsu is a NAP essential for cell viability. Here, using conditional alleles to rapidly remove or inactivate HBsu, we show that the absence of HBsu abolishes the initiation of DNA replication in vivo. Understanding HBsu's function can provide new insights into the regulation of DNA replication initiation in bacteria.
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24
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Abstract
Many pathogens or symbionts of animals and plants contain multiple replicons, a configuration called a multipartite genome. Multipartite genomes enable those species to replicate their genomes faster and better adapt to new niches. Despite their prevalence, the mechanisms by which multipartite genomes are stably maintained are poorly understood. Agrobacterium tumefaciens is a plant pathogen that contains four replicons: a circular chromosome (Ch1), a linear chromosome (Ch2), and two large plasmids. Recent work indicates that their replication origins are clustered at the cell poles in a manner that depends on their ParB family centromeric proteins: ParB1 for Ch1 and individual RepB paralogs for Ch2 and the plasmids. However, understanding of these interactions and how they contribute to genome maintenance is limited. By combining genome-wide chromosome conformation capture (Hi-C) assays, chromatin-immunoprecipitation sequencing (ChIP-seq), and live cell fluorescence microscopy, we provide evidence here that centromeric clustering is mediated by interactions between these centromeric proteins. We further show that the disruption of centromere clustering results in the loss of replicons. Our data establish the role of centromeric clustering in multipartite genome stability. IMPORTANCE About 10% of sequenced bacteria have multiple replicons, also known as multipartite genomes. How these multipartite genomes are maintained is still poorly understood. Here, we use Agrobacterium tumefaciens as a model and show that the replication origins of the four replicons are clustered through direct interactions between the centromeric proteins; disruption of origin clustering leads to the loss of replicons. Thus, our study provided evidence that centromeric clustering is important for maintaining multipartite genomes.
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25
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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: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [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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26
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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: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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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27
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Montero Llopis P, Stephansky R, Wang X. High-Throughput Imaging of Bacillus subtilis. Methods Mol Biol 2022; 2476:277-292. [PMID: 35635710 DOI: 10.1007/978-1-0716-2221-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacillus subtilis is a widely used model bacterium to study cellular processes and development. The availability of an arrayed mutant library gave us the opportunity to cytologically analyze every mutant and screen for new genes involved in cell shape determination, cell division, and chromosome segregation. Here we describe a high-throughput method to image arrayed B. subtilis mutant libraries using wide-field fluorescence microscopy. We provide a detailed description of growing the arrayed strain collection, preparing slides containing agarose pedestals, setting up the microscopy procedure, acquiring images, and analyzing the images.
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Affiliation(s)
| | | | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN, USA.
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28
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Yen CY, Lin MG, Chen BW, Ng IW, Read N, Kabli AF, Wu CT, Shen YY, Chen CH, Barillà D, Sun YJ, Hsiao CD. Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly. Nucleic Acids Res 2021; 49:13150-13164. [PMID: 34850144 PMCID: PMC8682754 DOI: 10.1093/nar/gkab1155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Genome segregation is a vital process in all organisms. Chromosome partitioning remains obscure in Archaea, the third domain of life. Here, we investigated the SegAB system from Sulfolobus solfataricus. SegA is a ParA Walker-type ATPase and SegB is a site-specific DNA-binding protein. We determined the structures of both proteins and those of SegA–DNA and SegB–DNA complexes. The SegA structure revealed an atypical, novel non-sandwich dimer that binds DNA either in the presence or in the absence of ATP. The SegB structure disclosed a ribbon–helix–helix motif through which the protein binds DNA site specifically. The association of multiple interacting SegB dimers with the DNA results in a higher order chromatin-like structure. The unstructured SegB N-terminus plays an essential catalytic role in stimulating SegA ATPase activity and an architectural regulatory role in segrosome (SegA–SegB–DNA) formation. Electron microscopy results also provide a compact ring-like segrosome structure related to chromosome organization. These findings contribute a novel mechanistic perspective on archaeal chromosome segregation.
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Affiliation(s)
- Cheng-Yi Yen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Guan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Bo-Wei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Irene W Ng
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Nicholas Read
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Azhar F Kabli
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Che-Ting Wu
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yo-You Shen
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chen-Hao Chen
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Daniela Barillà
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Yuh-Ju Sun
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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29
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Gao Z, Zhang W, Chang R, Zhang S, Yang G, Zhao G. Liquid-Liquid Phase Separation: Unraveling the Enigma of Biomolecular Condensates in Microbial Cells. Front Microbiol 2021; 12:751880. [PMID: 34759902 PMCID: PMC8573418 DOI: 10.3389/fmicb.2021.751880] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
Numerous examples of microbial phase-separated biomolecular condensates have now been identified following advances in fluorescence imaging and single molecule microscopy technologies. The structure, function, and potential applications of these microbial condensates are currently receiving a great deal of attention. By neatly compartmentalizing proteins and their interactors in membrane-less organizations while maintaining free communication between these macromolecules and the external environment, microbial cells are able to achieve enhanced metabolic efficiency. Typically, these condensates also possess the ability to rapidly adapt to internal and external changes. The biological functions of several phase-separated condensates in small bacterial cells show evolutionary convergence with the biological functions of their eukaryotic paralogs. Artificial microbial membrane-less organelles are being constructed with application prospects in biocatalysis, biosynthesis, and biomedicine. In this review, we provide an overview of currently known biomolecular condensates driven by liquid-liquid phase separation (LLPS) in microbial cells, and we elaborate on their biogenesis mechanisms and biological functions. Additionally, we highlight the major challenges and future research prospects in studying microbial LLPS.
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Affiliation(s)
| | | | | | | | - Guiwen Yang
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guoyan Zhao
- College of Life Science, Shandong Normal University, Jinan, China
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30
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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. SCIENCE ADVANCES 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] [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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31
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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: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [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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32
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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] [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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33
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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] [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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34
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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] [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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35
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Jalal AS, Tran NT, Stevenson CE, Chimthanawala A, Badrinarayanan A, Lawson DM, Le TB. A CTP-dependent gating mechanism enables ParB spreading on DNA. eLife 2021; 10:69676. [PMID: 34397383 DOI: 10.1101/816959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/03/2021] [Indexed: 05/25/2023] Open
Abstract
Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA (Jalal et al., 2020). Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products are likely associated with reopening of the gates to release DNA and recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling.
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Affiliation(s)
- Adam Sb Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Clare Em Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Afroze Chimthanawala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- SASTRA University, Thanjavur, Tamil Nadu, India
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Tung Bk Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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36
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Jalal AS, Tran NT, Stevenson CE, Chimthanawala A, Badrinarayanan A, Lawson DM, Le TB. A CTP-dependent gating mechanism enables ParB spreading on DNA. eLife 2021; 10:69676. [PMID: 34397383 PMCID: PMC8367383 DOI: 10.7554/elife.69676] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022] Open
Abstract
Proper chromosome segregation is essential in all living organisms. The ParA-ParB-parS system is widely employed for chromosome segregation in bacteria. Previously, we showed that Caulobacter crescentus ParB requires cytidine triphosphate to escape the nucleation site parS and spread by sliding to the neighboring DNA (Jalal et al., 2020). Here, we provide the structural basis for this transition from nucleation to spreading by solving co-crystal structures of a C-terminal domain truncated C. crescentus ParB with parS and with a CTP analog. Nucleating ParB is an open clamp, in which parS is captured at the DNA-binding domain (the DNA-gate). Upon binding CTP, the N-terminal domain (NTD) self-dimerizes to close the NTD-gate of the clamp. The DNA-gate also closes, thus driving parS into a compartment between the DNA-gate and the C-terminal domain. CTP hydrolysis and/or the release of hydrolytic products are likely associated with reopening of the gates to release DNA and recycle ParB. Overall, we suggest a CTP-operated gating mechanism that regulates ParB nucleation, spreading, and recycling.
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Affiliation(s)
- Adam Sb Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Clare Em Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Afroze Chimthanawala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.,SASTRA University, Thanjavur, Tamil Nadu, India
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Tung Bk Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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37
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Merino-Salomón A, Babl L, Schwille P. Self-organized protein patterns: The MinCDE and ParABS systems. Curr Opin Cell Biol 2021; 72:106-115. [PMID: 34399108 DOI: 10.1016/j.ceb.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/04/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Self-organized protein patterns are of tremendous importance for biological decision-making processes. Protein patterns have been shown to identify the site of future cell division, establish cell polarity, and organize faithful DNA segregation. Intriguingly, several key concepts of pattern formation and regulation apply to a variety of different protein systems. Herein, we explore recent advances in the understanding of two prokaryotic pattern-forming systems: the MinCDE system, positioning the FtsZ ring precisely at the midcell, and the ParABS system, distributing newly synthesized DNA along with the cell. Despite differences in biological functionality, these two systems have remarkably similar molecular components, mechanisms, and strategies to achieve biological robustness.
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Affiliation(s)
- Adrián Merino-Salomón
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Leon Babl
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Petra Schwille
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany.
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38
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Anchimiuk A, Lioy VS, Bock FP, Minnen A, Boccard F, Gruber S. A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis. eLife 2021; 10:65467. [PMID: 34346312 PMCID: PMC8357415 DOI: 10.7554/elife.65467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
SMC complexes are widely conserved ATP-powered DNA-loop-extrusion motors indispensable for organizing and faithfully segregating chromosomes. How SMC complexes translocate along DNA for loop extrusion and what happens when two complexes meet on the same DNA molecule is largely unknown. Revealing the origins and the consequences of SMC encounters is crucial for understanding the folding process not only of bacterial, but also of eukaryotic chromosomes. Here, we uncover several factors that influence bacterial chromosome organization by modulating the probability of such clashes. These factors include the number, the strength, and the distribution of Smc loading sites, the residency time on the chromosome, the translocation rate, and the cellular abundance of Smc complexes. By studying various mutants, we show that these parameters are fine-tuned to reduce the frequency of encounters between Smc complexes, presumably as a risk mitigation strategy. Mild perturbations hamper chromosome organization by causing Smc collisions, implying that the cellular capacity to resolve them is limited. Altogether, we identify mechanisms that help to avoid Smc collisions and their resolution by Smc traversal or other potentially risky molecular transactions.
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Affiliation(s)
- Anna Anchimiuk
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Florian Patrick Bock
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anita Minnen
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Frederic Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stephan Gruber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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39
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Taylor JA, Seol Y, Budhathoki J, Neuman KC, Mizuuchi K. CTP and parS coordinate ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning. eLife 2021; 10:65651. [PMID: 34286695 PMCID: PMC8357417 DOI: 10.7554/elife.65651] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS-binding ParB-CTPase, and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. F-plasmid partition complexes containing ParBF and parSF move by generating and following a local concentration gradient of nucleoid-bound ParAF. However, the process through which ParBF activates ParAF-ATPase has not been defined. We studied CTP- and parSF-modulated ParAF-ParBF complex assembly, in which DNA-bound ParAF-ATP dimers are activated for ATP hydrolysis by interacting with two ParBF N-terminal domains. CTP or parSF enhances the ATPase rate without significantly accelerating ParAF-ParBF complex assembly. Together, parSF and CTP accelerate ParAF-ParBF assembly without further significant increase in ATPase rate. Magnetic-tweezers experiments showed that CTP promotes multiple ParBF loading onto parSF-containing DNA, generating condensed partition complex-like assemblies. We propose that ParBF in the partition complex adopts a conformation that enhances ParBF-ParBF and ParAF-ParBF interactions promoting efficient partitioning.
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Affiliation(s)
- James A Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Yeonee Seol
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jagat Budhathoki
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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40
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Taylor JA, Seol Y, Budhathoki J, Neuman KC, Mizuuchi K. CTP and parS coordinate ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning. eLife 2021; 10:65651. [PMID: 34286695 DOI: 10.1101/2021.01.24.427996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/20/2021] [Indexed: 05/25/2023] Open
Abstract
ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS-binding ParB-CTPase, and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. F-plasmid partition complexes containing ParBF and parSF move by generating and following a local concentration gradient of nucleoid-bound ParAF. However, the process through which ParBF activates ParAF-ATPase has not been defined. We studied CTP- and parSF-modulated ParAF-ParBF complex assembly, in which DNA-bound ParAF-ATP dimers are activated for ATP hydrolysis by interacting with two ParBF N-terminal domains. CTP or parSF enhances the ATPase rate without significantly accelerating ParAF-ParBF complex assembly. Together, parSF and CTP accelerate ParAF-ParBF assembly without further significant increase in ATPase rate. Magnetic-tweezers experiments showed that CTP promotes multiple ParBF loading onto parSF-containing DNA, generating condensed partition complex-like assemblies. We propose that ParBF in the partition complex adopts a conformation that enhances ParBF-ParBF and ParAF-ParBF interactions promoting efficient partitioning.
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Affiliation(s)
- James A Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Yeonee Seol
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jagat Budhathoki
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Keir C Neuman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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41
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Balaguer FDA, Aicart-Ramos C, Fisher GL, de Bragança S, Martin-Cuevas EM, Pastrana CL, Dillingham MS, Moreno-Herrero F. CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS. eLife 2021; 10:67554. [PMID: 34250901 PMCID: PMC8299390 DOI: 10.7554/elife.67554] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022] Open
Abstract
Faithful segregation of bacterial chromosomes relies on the ParABS partitioning system and the SMC complex. In this work, we used single-molecule techniques to investigate the role of cytidine triphosphate (CTP) binding and hydrolysis in the critical interaction between centromere-like parS DNA sequences and the ParB CTPase. Using a combined optical tweezers confocal microscope, we observe the specific interaction of ParB with parS directly. Binding around parS is enhanced by the presence of CTP or the non-hydrolysable analogue CTPγS. However, ParB proteins are also detected at a lower density in distal non-specific DNA. This requires the presence of a parS loading site and is prevented by protein roadblocks, consistent with one-dimensional diffusion by a sliding clamp. ParB diffusion on non-specific DNA is corroborated by direct visualization and quantification of movement of individual quantum dot labelled ParB. Magnetic tweezers experiments show that the spreading activity, which has an absolute requirement for CTP binding but not hydrolysis, results in the condensation of parS-containing DNA molecules at low nanomolar protein concentrations.
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Affiliation(s)
- Francisco de Asis Balaguer
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gemma Lm Fisher
- DNA:Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, United Kingdom
| | - Sara de Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eva M Martin-Cuevas
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mark Simon Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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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 PMCID: PMC8429893 DOI: 10.1016/j.molcel.2021.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
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. CTP is required for Noc to form a higher-order nucleoprotein complex on DNA CTP binding switches DNA-entrapped Noc to a membrane-active state CTP hydrolysis likely reverses the association between Noc-DNA and the membrane The membrane-targeting helix adopts an autoinhibitory conformation in apo-Noc
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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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43
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VirB, a key transcriptional regulator of virulence plasmid genes in Shigella flexneri, forms DNA-binding site dependent foci in the bacterial cytoplasm. J Bacteriol 2021; 203:JB.00627-20. [PMID: 33722845 PMCID: PMC8117518 DOI: 10.1128/jb.00627-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
VirB is a key regulator of genes located on the large virulence plasmid (pINV) in the bacterial pathogen Shigella flexneri VirB is unusual; it is not related to other transcriptional regulators, instead, it belongs to a family of proteins that primarily function in plasmid and chromosome partitioning; exemplified by ParB. Despite this, VirB does not function to segregate DNA, but rather counters transcriptional silencing mediated by the nucleoid structuring protein, H-NS. Since ParB localizes subcellularly as discrete foci in the bacterial cytoplasm, we chose to investigate the subcellular localization of VirB to gain novel insight into how VirB functions as a transcriptional anti-silencer. To do this, a GFP-VirB fusion that retains the regulatory activity of VirB and yet, does not undergo significant protein degradation in S. flexneri, was used. Surprisingly, discrete fluorescent foci were observed in live wild-type S. flexneri cells and an isogenic virB mutant using fluorescence microscopy. In contrast, foci were rarely observed (<10%) in pINV-cured cells or in cells expressing a GFP-VirB fusion carrying amino acid substitutions in the VirB DNA binding domain. Finally, the 25 bp VirB-binding site was demonstrated to be sufficient and necessary for GFP-VirB focus formation using a set of small surrogate plasmids. Combined, these data demonstrate that the VirB:DNA interactions required for the transcriptional anti-silencing activity of VirB on pINV are a prerequisite for the subcellular localization of VirB in the bacterial cytoplasm. The significance of these findings, in light of the anti-silencing activity of VirB, is discussed.ImportanceThis study reveals the subcellular localization of VirB, a key transcriptional regulator of virulence genes found on the large virulence plasmid (pINV) in Shigella. Fluorescent signals generated by an active GFP-VirB fusion form 2, 3, or 4 discrete foci in the bacterial cytoplasm, predominantly at the quarter cell position. These signals are completely dependent upon VirB interacting with its DNA binding site found either on the virulence plasmid or an engineered surrogate. Our findings: 1) provide novel insight into VirB:pINV interactions, 2) suggest that VirB may have utility as a DNA marker, and 3) raise questions about how and why this anti-silencing protein that controls virulence gene expression on pINV of Shigella spp. forms discrete foci/hubs within the bacterial cytoplasm.
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Azaldegui CA, Vecchiarelli AG, Biteen JS. The emergence of phase separation as an organizing principle in bacteria. Biophys J 2021; 120:1123-1138. [PMID: 33186556 PMCID: PMC8059088 DOI: 10.1016/j.bpj.2020.09.023] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Recent investigations in bacteria suggest that membraneless organelles play a crucial role in the subcellular organization of bacterial cells. However, the biochemical functions and assembly mechanisms of these compartments have not yet been completely characterized. This article assesses the current methodologies used in the study of membraneless organelles in bacteria, highlights the limitations in determining the phase of complexes in cells that are typically an order of magnitude smaller than a eukaryotic cell, and identifies gaps in our current knowledge about the functional role of membraneless organelles in bacteria. Liquid-liquid phase separation (LLPS) is one proposed mechanism for membraneless organelle assembly. Overall, we outline the framework to evaluate LLPS in vivo in bacteria, we describe the bacterial systems with proposed LLPS activity, and we comment on the general role LLPS plays in bacteria and how it may regulate cellular function. Lastly, we provide an outlook for super-resolution microscopy and single-molecule tracking as tools to assess condensates in bacteria.
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Affiliation(s)
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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45
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Messelink JJB, van Teeseling MCF, Janssen J, Thanbichler M, Broedersz CP. Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales. Nat Commun 2021; 12:1963. [PMID: 33785756 PMCID: PMC8010069 DOI: 10.1038/s41467-021-22189-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 02/15/2021] [Indexed: 02/01/2023] Open
Abstract
The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.
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Affiliation(s)
- Joris J B Messelink
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig Maximilian University Munich, Munich, Germany
| | - Muriel C F van Teeseling
- Department of Biology, University of Marburg, Marburg, Germany
- Prokaryotic Cell Biology Group, Department of Microbial Interactions, Institute for Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Jacqueline Janssen
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig Maximilian University Munich, Munich, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Chase P Broedersz
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig Maximilian University Munich, Munich, Germany.
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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Szafran MJ, Jakimowicz D, Elliot MA. Compaction and control-the role of chromosome-organizing proteins in Streptomyces. FEMS Microbiol Rev 2021; 44:725-739. [PMID: 32658291 DOI: 10.1093/femsre/fuaa028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Chromosomes are dynamic entities, whose organization and structure depend on the concerted activity of DNA-binding proteins and DNA-processing enzymes. In bacteria, chromosome replication, segregation, compaction and transcription are all occurring simultaneously, and to ensure that these processes are appropriately coordinated, all bacteria employ a mix of well-conserved and species-specific proteins. Unusually, Streptomyces bacteria have large, linear chromosomes and life cycle stages that include multigenomic filamentous hyphae and unigenomic spores. Moreover, their prolific secondary metabolism yields a wealth of bioactive natural products. These different life cycle stages are associated with profound changes in nucleoid structure and chromosome compaction, and require distinct repertoires of architectural-and regulatory-proteins. To date, chromosome organization is best understood during Streptomyces sporulation, when chromosome segregation and condensation are most evident, and these processes are coordinated with synchronous rounds of cell division. Advances are, however, now being made in understanding how chromosome organization is achieved in multigenomic hyphal compartments, in defining the functional and regulatory interplay between different architectural elements, and in appreciating the transcriptional control exerted by these 'structural' proteins.
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Affiliation(s)
- Marcin J Szafran
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Dagmara Jakimowicz
- Laboratory of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Marie A Elliot
- Department of Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
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Scoca V, Di Nunzio F. The HIV-1 Capsid: From Structural Component to Key Factor for Host Nuclear Invasion. Viruses 2021; 13:273. [PMID: 33578999 PMCID: PMC7916756 DOI: 10.3390/v13020273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of HIV-1, the viral capsid has been recognized to have an important role as a structural protein that holds the viral genome, together with viral proteins essential for viral life cycle, such as the reverse transcriptase (RT) and the integrase (IN). The reverse transcription process takes place between the cytoplasm and the nucleus of the host cell, thus the Reverse Transcription Complexes (RTCs)/Pre-integration Complexes (PICs) are hosted in intact or partial cores. Early biochemical assays failed to identify the viral CA associated to the RTC/PIC, possibly due to the stringent detergent conditions used to fractionate the cells or to isolate the viral complexes. More recently, it has been observed that some host partners of capsid, such as Nup153 and CPSF6, can only bind multimeric CA proteins organized in hexamers. Those host factors are mainly located in the nuclear compartment, suggesting the entrance of the viral CA as multimeric structure inside the nucleus. Recent data show CA complexes within the nucleus having a different morphology from the cytoplasmic ones, clearly highlighting the remodeling of the viral cores during nuclear translocation. Thus, the multimeric CA complexes lead the viral genome into the host nuclear compartment, piloting the intranuclear journey of HIV-1 in order to successfully replicate. The aim of this review is to discuss and analyze the main discoveries to date that uncover the viral capsid as a key player in the reverse transcription and PIC maturation until the viral DNA integration into the host genome.
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Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology Pasteur Institute, 75015 Paris, France;
- BioSPC Doctoral School, Universitè de Paris, 75015 Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology Pasteur Institute, 75015 Paris, France;
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48
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Impact of Self-Association on the Architectural Properties of Bacterial Nucleoid Proteins. Biophys J 2020; 120:370-378. [PMID: 33340542 DOI: 10.1016/j.bpj.2020.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (∼80%), RNA (∼10%), and a number of different proteins (∼10%). These nucleoid proteins act as regulators of gene expression and influence the organization of the nucleoid by bridging, bending, or wrapping the DNA. These so-called architectural properties of nucleoid proteins are still poorly understood. For example, the reason why certain proteins compact the DNA coil in certain environments but make the DNA more rigid instead in other environments is the subject of ongoing debates. Here, we address the question of the impact of the self-association of nucleoid proteins on their architectural properties and try to determine whether differences in self-association are sufficient to induce large changes in the organization of the DNA coil. More specifically, we developed two coarse-grained models of proteins, which interact identically with the DNA but self-associate differently by forming either clusters or filaments in the absence of the DNA. We showed through Brownian dynamics simulations that self-association of the proteins dramatically increases their ability to shape the DNA coil. Moreover, we observed that cluster-forming proteins significantly compact the DNA coil (similar to the DNA-bridging mode of H-NS proteins), whereas filament-forming proteins significantly increase the stiffness of the DNA chain instead (similar to the DNA-stiffening mode of H-NS proteins). This work consequently suggests that the knowledge of the DNA-binding properties of the proteins is in itself not sufficient to understand their architectural properties. Rather, their self-association properties must also be investigated in detail because they might actually drive the formation of different DNA-protein complexes.
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Madariaga-Marcos J, Corti R, Hormeño S, Moreno-Herrero F. Characterizing microfluidic approaches for a fast and efficient reagent exchange in single-molecule studies. Sci Rep 2020; 10:18069. [PMID: 33093484 PMCID: PMC7581773 DOI: 10.1038/s41598-020-74523-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/21/2020] [Indexed: 11/09/2022] Open
Abstract
Single-molecule experiments usually take place in flow cells. This experimental approach is essential for experiments requiring a liquid environment, but is also useful to allow the exchange of reagents before or during measurements. This is crucial in experiments that need to be triggered by ligands or require a sequential addition of proteins. Home-fabricated flow cells using two glass coverslips and a gasket made of paraffin wax are a widespread approach. The volume of the flow cell can be controlled by modifying the dimensions of the channel while the reagents are introduced using a syringe pump. In this system, high flow rates disturb the biological system, whereas lower flow rates lead to the generation of a reagent gradient in the flow cell. For very precise measurements it is thus desirable to have a very fast exchange of reagents with minimal diffusion. We propose the implementation of multistream laminar microfluidic cells with two inlets and one outlet, which achieve a minimum fluid switching time of 0.25 s. We additionally define a phenomenological expression to predict the boundary switching time for a particular flow cell cross section. Finally, we study the potential applicability of the platform to study kinetics at the single molecule level.
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Affiliation(s)
- Julene Madariaga-Marcos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Roberta Corti
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Department of Materials Science, University of Milano-Bicocca, Milan, Italy
| | - Silvia Hormeño
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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50
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Cohesion of Sister Chromosome Termini during the Early Stages of Sporulation in Bacillus subtilis. J Bacteriol 2020; 202:JB.00296-20. [PMID: 32778559 PMCID: PMC7515245 DOI: 10.1128/jb.00296-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/31/2020] [Indexed: 11/28/2022] Open
Abstract
During sporulation of Bacillus subtilis, the cell cycle is reorganized to generate separated prespore and mother cell compartments, each containing a single fully replicated chromosome. The process begins with reorganization of the nucleoid to form an elongated structure, the axial filament, in which the two chromosome origins are attached to opposite cell poles, with the remainder of the DNA stretched between these sites. When the cell then divides asymmetrically, the division septum closes around the chromosome destined for the smaller prespore, trapping the origin-proximal third of the chromosome in the prespore. A translocation pore is assembled through which a DNA transporter, SpoIIIE/FtsK, transfers the bulk of the chromosome to complete the segregation process. Although the mechanisms involved in attaching origin regions to the cell poles are quite well understood, little is known about other aspects of axial filament morphology. We have studied the behavior of the terminus region of the chromosome during sporulation using time-lapse imaging of wild-type and mutant cells. The results suggest that the elongated structure involves cohesion of the terminus regions of the sister chromosomes and that this cohesion is resolved when the termini reach the asymmetric septum or translocation pore. Possible mechanisms and roles of cohesion and resolution are discussed.IMPORTANCE Endospore formation in Firmicutes bacteria provides one of the most highly resistant life forms on earth. During the early stages of endospore formation, the cell cycle is reorganized so that exactly two fully replicated chromosomes are generated, before the cell divides asymmetrically to generate the prespore and mother cell compartments that are critical for the developmental process. Decades ago, it was discovered that just prior to asymmetrical division the two chromosomes enter an unusual elongated configuration called the axial filament. This paper provides new insights into the nature of the axial filament structure and suggests that cohesion of the normally separated sister chromosome termini plays an important role in axial filament formation.
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