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Gras K, Fange D, Elf J. The Escherichia coli chromosome moves to the replisome. Nat Commun 2024; 15:6018. [PMID: 39019870 PMCID: PMC11255300 DOI: 10.1038/s41467-024-50047-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 06/28/2024] [Indexed: 07/19/2024] Open
Abstract
In Escherichia coli, it is debated whether the two replisomes move independently along the two chromosome arms during replication or if they remain spatially confined. Here, we use high-throughput fluorescence microscopy to simultaneously determine the location and short-time-scale (1 s) movement of the replisome and a chromosomal locus throughout the cell cycle. The assay is performed for several loci. We find that (i) the two replisomes are confined to a region of ~250 nm and ~120 nm along the cell's long and short axis, respectively, (ii) the chromosomal loci move to and through this region sequentially based on their distance from the origin of replication, and (iii) when a locus is being replicated, its short time-scale movement slows down. This behavior is the same at different growth rates. In conclusion, our data supports a model with DNA moving towards spatially confined replisomes at replication.
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Affiliation(s)
- Konrad Gras
- Dept. of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Fange
- Dept. of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Johan Elf
- Dept. of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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2
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Zhang C, Joseph AM, Casini L, Collier J, Badrinarayanan A, Manley S. Chromosome organization shapes replisome dynamics in Caulobacter crescentus. Nat Commun 2024; 15:3460. [PMID: 38658616 PMCID: PMC11043382 DOI: 10.1038/s41467-024-47849-6] [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: 08/28/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial species, driving the hypothesis that a physical linker may tether them together. However, replisome splitting has also been reported in many of the same species, leaving the principles behind replisome organization a long-standing puzzle. Here, by tracking the replisome β-clamp subunit in live Caulobacter crescentus, we find that rapid DNA segregation can give rise to a second focus which resembles a replisome, but does not replicate DNA. Sister replisomes can remain colocalized, or split apart to travel along DNA separately upon disruption of chromosome inter-arm alignment. Furthermore, chromosome arm-specific replication-transcription conflicts differentially modify replication speed on the two arms, facilitate the decoupling of the two replisomes. With these observations, we conclude that the dynamic chromosome organization flexibly shapes the organization of sister replisomes, and we outline principles which can help to reconcile previously conflicting models of replisome architecture.
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Affiliation(s)
- Chen Zhang
- Laboratory of Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Asha Mary Joseph
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Laurent Casini
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Justine Collier
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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3
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Yuan T, Yan H, Bailey MLP, Williams JF, Surovtsev I, King MC, Mochrie SGJ. Effect of loops on the mean-square displacement of Rouse-model chromatin. Phys Rev E 2024; 109:044502. [PMID: 38755928 DOI: 10.1103/physreve.109.044502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.
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Affiliation(s)
- Tianyu Yuan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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4
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Mitra D, Pande S, Chatterji A. Polymer architecture orchestrates the segregation and spatial organization of replicating E. coli chromosomes in slow growth. SOFT MATTER 2022; 18:5615-5631. [PMID: 35861071 DOI: 10.1039/d2sm00734g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The mechanism of chromosome segregation and organization in the bacterial cell cycle of E. coli is one of the least understood aspects in its life cycle. The E. coli chromosome is often modelled as a bead spring ring polymer. We introduce cross-links in the DNA-ring polymer, resulting in the formation of loops within each replicating bacterial chromosome. We use simulations to show that the chosen polymer-topology ensures its self-organization along the cell long-axis, such that various chromosomal loci get spatially localized as seen in vivo. The localization of loci arises due to entropic repulsion between polymer loops within each daughter DNA confined in a cylinder. The cellular addresses of the loci in our model are in fair agreement with those seen in experiments as given in J. A. Cass et al., Biophys. J., 2016, 110, 2597-2609. We also show that the adoption of such modified polymer architectures by the daughter DNAs leads to an enhanced propensity of their spatial segregation. Secondly, we match other experimentally reported results, including observation of the cohesion time and the ter-transition. Additionally, the contact map generated from our simulations reproduces the macro-domain like organization as seen in the experimentally obtained Hi-C map. Lastly, we have also proposed a plausible reconciliation of the 'Train Track' and the 'Replication Factory' models which provide conflicting descriptions of the spatial organization of the replication forks. Thus, we reconcile observations from complementary experimental techniques probing bacterial chromosome organization.
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Anatomy of a twin DNA replication factory. Biochem Soc Trans 2020; 48:2769-2778. [PMID: 33300972 PMCID: PMC7752080 DOI: 10.1042/bst20200640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
The replication of DNA in chromosomes is initiated at sequences called origins at which two replisome machines are assembled at replication forks that move in opposite directions. Interestingly, in vivo studies observe that the two replication forks remain fastened together, often referred to as a replication factory. Replication factories containing two replisomes are well documented in cellular studies of bacteria (Escherichia coli and Bacillus subtilis) and the eukaryote, Saccharomyces cerevisiae. This basic twin replisome factory architecture may also be preserved in higher eukaryotes. Despite many years of documenting the existence of replication factories, the molecular details of how the two replisome machines are tethered together has been completely unknown in any organism. Recent structural studies shed new light on the architecture of a eukaryote replisome factory, which brings with it a new twist on how a replication factory may function.
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van Raaphorst R, Kjos M, Veening J. BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data. Mol Microbiol 2020; 113:297-308. [PMID: 31693257 PMCID: PMC7027861 DOI: 10.1111/mmi.14417] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2019] [Indexed: 12/13/2022]
Abstract
High-throughput analyses of single-cell microscopy data are a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP complies with standard practice in R which enables the use of advanced statistical analysis tools, and its graphic output is compatible with ggplot2, enabling adjustable plot graphics in every operating system. User feedback will be used to create a fully automated Graphical User Interface version of BactMAP in the future. Using BactMAP, we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z-ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap.
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Affiliation(s)
- Renske van Raaphorst
- Department of Fundamental MicrobiologyFaculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- Molecular Genetics GroupGroningen Biomolecular Sciences and Biotechnology InstituteCentre for Synthetic BiologyUniversity of GroningenGroningenThe Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Jan‐Willem Veening
- Department of Fundamental MicrobiologyFaculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- Molecular Genetics GroupGroningen Biomolecular Sciences and Biotechnology InstituteCentre for Synthetic BiologyUniversity of GroningenGroningenThe Netherlands
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7
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Kisner JR, Kuwada NJ. Nucleoid-mediated positioning and transport in bacteria. Curr Genet 2019; 66:279-291. [PMID: 31691024 DOI: 10.1007/s00294-019-01041-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022]
Abstract
Precise management of the spatiotemporal position of subcellular components is critical to a number of essential processes in the bacterial cell. The bacterial nucleoid is a highly structured yet dynamic object that undergoes significant reorganization during the relatively short cell cycle, e.g. during gene expression, chromosome replication, and segregation. Although the nucleoid takes up a large fraction of the volume of the cell, the mobility of macromolecules within these dense regions is relatively high and recent results suggest that the nucleoid plays an integral role of dynamic localization in a host of seemingly disparate cellular processes. Here, we review a number of recent reports of nucleoid-mediated positioning and transport in the model bacteria Escherichia coli. These results viewed as a whole suggest that the dynamic, cellular-scale structure of the nucleoid may be a key driver of positioning and transport within the cell. This model of a global, default positioning and transport system may help resolve many unanswered questions about the mechanisms of partitioning and segregation in bacteria.
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Affiliation(s)
- Jessica R Kisner
- Department of Physics, Central Washington University, Ellensburg, WA, 98926, USA
| | - Nathan J Kuwada
- Department of Physics, Central Washington University, Ellensburg, WA, 98926, USA.
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Li Y, Chen Z, Matthews LA, Simmons LA, Biteen JS. Dynamic Exchange of Two Essential DNA Polymerases during Replication and after Fork Arrest. Biophys J 2019; 116:684-693. [PMID: 30686488 DOI: 10.1016/j.bpj.2019.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/23/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023] Open
Abstract
The replisome is a multiprotein machine responsible for the faithful replication of chromosomal and plasmid DNA. Using single-molecule super-resolution imaging, we characterized the dynamics of three replisomal proteins in live Bacillus subtilis cells: the two replicative DNA polymerases, PolC and DnaE, and a processivity clamp loader subunit, DnaX. We quantified the protein mobility and dwell times during normal replication and following replication fork stress using damage-independent and damage-dependent conditions. With these results, we report the dynamic and cooperative process of DNA replication based on changes in the measured diffusion coefficients and dwell times. These experiments show that the replication proteins are all highly dynamic and that the exchange rate depends on whether DNA synthesis is active or arrested. Our results also suggest coupling between PolC and DnaX in the DNA replication process and indicate that DnaX provides an important role in synthesis during repair. Furthermore, our results suggest that DnaE provides a limited contribution to chromosomal replication and repair in vivo.
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Affiliation(s)
- Yilai Li
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Lindsay A Matthews
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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