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Scholl D, Boyd T, Latham AP, Salazar A, Khan A, Boeynaems S, Holehouse AS, Lander GC, Sali A, Park D, Deniz AA, Lasker K. Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.27.630454. [PMID: 39763716 PMCID: PMC11703246 DOI: 10.1101/2024.12.27.630454] [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: 01/11/2025]
Abstract
Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ) as a model system, revealing how its material properties and cellular function depend on its ultrastructure. We revealed PopZ's hierarchical assembly into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques, and molecular dynamics simulations. The helical domain drives filamentation and condensation, while the disordered domain inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client binding sites in the dense phase. These findings establish a multiscale framework that links molecular interactions and condensate ultrastructure to macroscopic material properties that drive cellular function.
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Affiliation(s)
- Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tumara Boyd
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrew P. Latham
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexandra Salazar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Asma Khan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Center for Infectious Disease Imaging, National Institutes of Health, Clinical Center, 10 Center Drive, Bethesda, MD 20892, USA
| | - Steven Boeynaems
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
- Center for Alzheimer’s and Neurodegenerative Diseases (CAND), Texas Children’s Hospital, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center (DLDCCC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrej Sali
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Donghyun Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Keren Lasker
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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Letzkus M, Trela C, Mera PE. Three factors ParA, TipN, and DnaA-mediated chromosome replication initiation are contributors of centromere segregation in Caulobacter crescentus. Mol Biol Cell 2024; 35:ar68. [PMID: 38568781 PMCID: PMC11151105 DOI: 10.1091/mbc.e23-12-0503] [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: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The ability of bacteria to maintain chromosomal integrity throughout their life cycle is crucial for survival. In Caulobacter crescentus, the polar factor TipN has been proposed to be involved with the partitioning system ParABS. Cells with tipN knocked out display subtle segregation defects of the centromere-like region parS. We hypothesized that TipN's role with parS segregation is obscured by other forces that are ParABS-independent. To test our hypothesis, we removed one of those forces - chromosome replication - and analyzed the role of TipN with ParA. We first confirm that ParA retains its ability to transport the centromeric region parS from the stalked pole to the opposite pole in the absence of chromosome replication. Our data revealed that in the absence of chromosome replication, TipN becomes essential for ParA's ability to transport parS. Furthermore, we identify a potential connection between the replication initiator DnaA and TipN. Although TipN is not essential for viability, tipN knockout cells lose viability when the regulation of DnaA levels is altered. Our data suggest that the DnaA-dependent susceptibility of tipN knockout cells is connected to parS segregation. Collectively, this work provides insights into the complex regulation involved in the coordination of chromosome replication and segregation in bacteria.
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Affiliation(s)
- Morgan Letzkus
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Corey Trela
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Paola E. Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Letzkus M, Trela C, Mera PE. TipN's involvement with centromere segregation in Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572679. [PMID: 38187783 PMCID: PMC10769339 DOI: 10.1101/2023.12.20.572679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bacteria's ability to maintain chromosomal integrity throughout their life cycle is crucial for their survival. In Caulobacter crescentus, the polar factor TipN has been proposed to be involved with the partitioning system ParABS. However, cells with tipN knocked out display subtle parS segregation defects. We hypothesized that TipN's role with parS segregation is obscured by other forces that are ParABS-independent. To test our hypothesis, we removed one of those forces - chromosome replication - and analyzed the role of TipN with ParA. We first demonstrate that ParA retains its ability to transport the centromeric region parS from the stalked pole to the opposite pole in the absence of chromosome replication. Our data revealed that in the absence of chromosome replication, TipN becomes essential for ParA's ability to transport parS. Furthermore, we identify a potential connection between the replication initiator DnaA and TipN. Although TipN is not essential for viability, tipN knockout cells lose viability when the regulation of DnaA levels is altered. Our data suggest that the DnaA-dependent susceptibility of tipN knockout cells is connected to parS segregation. Collectively, this work provides insights into the complex regulation involved in the coordination of chromosome replication and segregation in bacteria.
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Affiliation(s)
- Morgan Letzkus
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Corey Trela
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paola E. Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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