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:gkae533. [PMID: 38908027 DOI: 10.1093/nar/gkae533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Zhao H, Peramuna T, Ajmal S, Wendt KL, Petrushenko ZM, Premachandra K, Cichewicz RH, Rybenkov VV. Inhibitor of Chromosome Segregation in Pseudomonas aeruginosa from Fungal Extracts. ACS Chem Biol 2024; 19:1387-1396. [PMID: 38843873 PMCID: PMC11197941 DOI: 10.1021/acschembio.4c00264] [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: 04/15/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024]
Abstract
Chromosome segregation is an essential cellular process that has the potential to yield numerous targets for drug development. This pathway is presently underutilized partially due to the difficulties in the development of robust reporter assays suitable for high throughput screening. In bacteria, chromosome segregation is mediated by two partially redundant systems, condensins and ParABS. Based on the synthetic lethality of the two systems, we developed an assay suitable for screening and then screened a library of fungal extracts for potential inhibitors of the ParABS pathway, as judged by their enhanced activity on condensin-deficient cells. We found such activity in extracts of Humicola sp. Fractionation of the extract led to the discovery of four new analogues of sterigmatocystin, one of which, 4-hydroxy-sterigmatocystin (4HS), displayed antibacterial activity. 4HS induced the phenotype typical for parAB mutants including defects in chromosome segregation and cell division. Specifically, bacteria exposed to 4HS produced anucleate cells and were impaired in the assembly of the FtsZ ring. Moreover, 4HS binds to purified ParB in a ParS-modulated manner and inhibits its ParS-dependent CTPase activity. The data describe a small molecule inhibitor of ParB and expand the known spectrum of activities of sterigmatocystin to include bacterial chromosome segregation.
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Affiliation(s)
- Hang Zhao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Thilini Peramuna
- Natural
Products Discovery Group, Institute for Natural Products Applications
and Research Technologies, Department of Chemistry & Biochemistry,
Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Sidra Ajmal
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L. Wendt
- Natural
Products Discovery Group, Institute for Natural Products Applications
and Research Technologies, Department of Chemistry & Biochemistry,
Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zoya M. Petrushenko
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kaushika Premachandra
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
| | - Robert H. Cichewicz
- Natural
Products Discovery Group, Institute for Natural Products Applications
and Research Technologies, Department of Chemistry & Biochemistry,
Stephenson Life Science Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Valentin V. Rybenkov
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019, United States
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3
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Prevo B, Earnshaw WC. DNA packaging by molecular motors: from bacteriophage to human chromosomes. Nat Rev Genet 2024:10.1038/s41576-024-00740-y. [PMID: 38886215 DOI: 10.1038/s41576-024-00740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Dense packaging of genomic DNA is crucial for organismal survival, as DNA length always far exceeds the dimensions of the cells that contain it. Organisms, therefore, use sophisticated machineries to package their genomes. These systems range across kingdoms from a single ultra-powerful rotary motor that spools the DNA into a bacteriophage head, to hundreds of thousands of relatively weak molecular motors that coordinate the compaction of mitotic chromosomes in eukaryotic cells. Recent technological advances, such as DNA proximity-based sequencing approaches, polymer modelling and in vitro reconstitution of DNA loop extrusion, have shed light on the biological mechanisms driving DNA organization in different systems. Here, we discuss DNA packaging in bacteriophage, bacteria and eukaryotic cells, which, despite their extreme variation in size, structure and genomic content, all rely on the action of molecular motors to package their genomes.
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Affiliation(s)
- Bram Prevo
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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4
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Chang MH, Lavrentovich MO, Männik J. Differentiating the roles of proteins and polysomes in nucleoid size homeostasis in Escherichia coli. Biophys J 2024; 123:1435-1448. [PMID: 37974398 PMCID: PMC11163298 DOI: 10.1016/j.bpj.2023.11.010] [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: 05/16/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
A defining feature of the bacterial cytosolic interior is a distinct membrane-less organelle, the nucleoid, that contains the chromosomal DNA. Although increasing experimental evidence indicates that macromolecular crowding is the dominant mechanism for nucleoid formation, it has remained unclear which crowders control nucleoid volume. It is commonly assumed that polyribosomes play a dominant role, yet the volume fraction of soluble proteins in the cytosol is comparable with that of polyribosomes. Here, we develop a free energy-based model for the cytosolic interior of a bacterial cell to distinguish contributions arising from polyribosomes and cytosolic proteins in nucleoid volume control. The parameters of the model are determined from the existing experimental data. We show that, while the polysomes establish the existence of the nucleoid as a distinct phase, the proteins control the nucleoid volume in physiologically relevant conditions. Our model explains experimental findings in Escherichia coli that the nucleoid compaction curves in osmotic shock measurements do not depend on cell growth rate and that dissociation of polysomes in slow growth rates does not lead to significant nucleoid expansion, while the nucleoid phase disappears in fastest growth rates. Furthermore, the model predicts a cross-over in the exclusion of crowders by their linear dimensions from the nucleoid phase: below the cross-over of 30-50 nm, the concentration of crowders in the nucleoid phase decreases linearly as a function of the crowder diameter, while decreasing exponentially above the cross-over size. Our work points to the possibility that bacterial cells maintain nucleoid size and protein concentration homeostasis via feedback in which protein concentration controls nucleoid dimensions and the nucleoid dimensions control protein synthesis rate.
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Affiliation(s)
- Mu-Hung Chang
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee
| | - Maxim O Lavrentovich
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee; Department of Earth, Environment, and Physics, Worcester State University, Worcester, Massachusetts.
| | - Jaan Männik
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, Tennessee.
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5
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Harju J, van Teeseling MCF, Broedersz CP. Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation. Nat Commun 2024; 15:4618. [PMID: 38816445 PMCID: PMC11139863 DOI: 10.1038/s41467-024-49039-w] [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: 11/28/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Entropic forces have been argued to drive bacterial chromosome segregation during replication. In many bacterial species, however, specifically evolved mechanisms, such as loop-extruding SMC complexes and the ParABS origin segregation system, contribute to or are even required for chromosome segregation, suggesting that entropic forces alone may be insufficient. The interplay between and the relative contributions of these segregation mechanisms remain unclear. Here, we develop a biophysical model showing that purely entropic forces actually inhibit bacterial chromosome segregation until late replication stages. By contrast, our model reveals that loop-extruders loaded at the origins of replication, as observed in many bacterial species, alter the effective topology of the chromosome, thereby redirecting and enhancing entropic forces to enable accurate chromosome segregation during replication. We confirm our model predictions with polymer simulations: purely entropic forces do not allow for concurrent replication and segregation, whereas entropic forces steered by specifically loaded loop-extruders lead to robust, global chromosome segregation during replication. Finally, we show how loop-extruders can complement locally acting origin separation mechanisms, such as the ParABS system. Together, our results illustrate how changes in the geometry and topology of the polymer, induced by DNA-replication and loop-extrusion, impact the organization and segregation of bacterial chromosomes.
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Affiliation(s)
- Janni Harju
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Muriel C F van Teeseling
- Junior research group Prokaryotic Cell Biology, Department for Microbial Interactions, Institute of Microbiology, Friedrich-Schiller-Universität, Jena, Germany
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilian-University Munich, Munich, Germany.
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6
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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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7
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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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8
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Figueroa-Bossi N, Fernández-Fernández R, Kerboriou P, Bouloc P, Casadesús J, Sánchez-Romero MA, Bossi L. Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin. Nat Commun 2024; 15:2787. [PMID: 38555352 PMCID: PMC10981669 DOI: 10.1038/s41467-024-47114-w] [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: 10/09/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negatively-supercoiled plectoneme to "unroll" disrupting the H-NS bridges and releasing H-NS.
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Affiliation(s)
- Nara Figueroa-Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Rocío Fernández-Fernández
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Patricia Kerboriou
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Lionello Bossi
- Université Paris-Saclay, CEA, CNRS, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France.
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9
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Tišma M, Bock FP, Kerssemakers J, Antar H, Japaridze A, Gruber S, Dekker C. Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells. Nat Commun 2024; 15:2737. [PMID: 38548820 PMCID: PMC10979009 DOI: 10.1038/s41467-024-47094-x] [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: 02/16/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Bacterial chromosomes are folded into tightly regulated three-dimensional structures to ensure proper transcription, replication, and segregation of the genetic information. Direct visualization of chromosomal shape within bacterial cells is hampered by cell-wall confinement and the optical diffraction limit. Here, we combine cell-shape manipulation strategies, high-resolution fluorescence microscopy techniques, and genetic engineering to visualize the shape of unconfined bacterial chromosome in real-time in live Bacillus subtilis cells that are expanded in volume. We show that the chromosomes predominantly exhibit crescent shapes with a non-uniform DNA density that is increased near the origin of replication (oriC). Additionally, we localized ParB and BsSMC proteins - the key drivers of chromosomal organization - along the contour of the crescent chromosome, showing the highest density near oriC. Opening of the BsSMC ring complex disrupted the crescent chromosome shape and instead yielded a torus shape. These findings help to understand the threedimensional organization of the chromosome and the main protein complexes that underlie its structure.
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Affiliation(s)
- Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Florian Patrick Bock
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Jacob Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Hammam Antar
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - 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.
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10
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [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] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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11
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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12
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Tan BG, Gustafsson CM, Falkenberg M. Mechanisms and regulation of human mitochondrial transcription. Nat Rev Mol Cell Biol 2024; 25:119-132. [PMID: 37783784 DOI: 10.1038/s41580-023-00661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2023] [Indexed: 10/04/2023]
Abstract
The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.
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Affiliation(s)
- Benedict G Tan
- Institute for Mitochondrial Diseases and Ageing, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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13
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Junier I, Ghobadpour E, Espeli O, Everaers R. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Front Microbiol 2023; 14:1192831. [PMID: 37965550 PMCID: PMC10642903 DOI: 10.3389/fmicb.2023.1192831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023] Open
Abstract
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.
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Affiliation(s)
- Ivan Junier
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
| | - Elham Ghobadpour
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Ralf Everaers
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
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14
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Kawalek A, Bartosik AA, Jagura-Burdzy G. Robust ParB Binding to Half- parS Sites in Pseudomonas aeruginosa-A Mechanism for Retaining ParB on the Nucleoid? Int J Mol Sci 2023; 24:12517. [PMID: 37569892 PMCID: PMC10419367 DOI: 10.3390/ijms241512517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Chromosome segregation in Pseudomonas aeruginosa is assisted by the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB) and its target parS sequence(s). ParB forms a nucleoprotein complex around four parSs (parS1-parS4) that overlaps oriC and facilitates relocation of newly synthesized ori domains inside the cells by ParA. Remarkably, ParB of P. aeruginosa also binds to numerous heptanucleotides (half-parSs) scattered in the genome. Here, using chromatin immunoprecipitation-sequencing (ChIP-seq), we analyzed patterns of ParB genome occupancy in cells growing under conditions of coupling or uncoupling between replication and cell division processes. Interestingly, a dissipation of ParB-parS complexes and a shift of ParB to half-parSs were observed during the transition from the exponential to stationary phase of growth on rich medium, suggesting the role of half-parSs in retaining ParB on the nucleoid within non-dividing P. aeruginosa cells. The ChIP-seq analysis of strains expressing ParB variants unable to dislocate from parSs showed that the ParB spreading ability is not required for ParB binding to half-parSs. Finally, a P. aeruginosa strain with mutated 25 half-parSs of the highest affinity towards ParB was constructed and analyzed. It showed altered ParB coverage of the oriC region and moderate changes in gene expression. Overall, this study characterizes a novel aspect of conserved bacterial chromosome segregation machinery.
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Affiliation(s)
- Adam Kawalek
- Laboratory of DNA Segregation and Life Cycle of Proteobacteria, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Grazyna Jagura-Burdzy
- Laboratory of DNA Segregation and Life Cycle of Proteobacteria, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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15
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Ren Z, Takacs CN, Brandão HB, Jacobs-Wagner C, Wang X. Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi. PLoS Genet 2023; 19:e1010857. [PMID: 37494383 PMCID: PMC10406323 DOI: 10.1371/journal.pgen.1010857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/07/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Borrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that B. burgdorferi is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the B. burgdorferi genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome oriC region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome oriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
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Affiliation(s)
- Zhongqing Ren
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Constantin N. Takacs
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Hugo B. Brandão
- Illumina Inc., 5200 Illumina Way, San Diego, California, United States of America
| | - Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, California, United States of America
- Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford, California, United States of America
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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16
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Santin YG, Lamot T, van Raaphorst R, Kaljević J, Laloux G. Modulation of prey size reveals adaptability and robustness in the cell cycle of an intracellular predator. Curr Biol 2023:S0960-9822(23)00541-9. [PMID: 37207648 DOI: 10.1016/j.cub.2023.04.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/21/2023]
Abstract
Despite a remarkable diversity of lifestyles, bacterial replication has only been investigated in a few model species. In bacteria that do not rely on canonical binary division for proliferation, the coordination of major cellular processes is still largely mysterious. Moreover, the dynamics of bacterial growth and division remain unexplored within spatially confined niches where nutrients are limited. This includes the life cycle of the model endobiotic predatory bacterium Bdellovibrio bacteriovorus, which grows by filamentation within its prey and produces a variable number of daughter cells. Here, we examined the impact of the micro-compartment in which predators replicate (i.e., the prey bacterium) on their cell-cycle progression at the single-cell level. Using Escherichia coli with genetically encoded size differences, we show that the duration of the predator cell cycle scales with prey size. Consequently, prey size determines predator offspring numbers. We found that individual predators elongate exponentially, with a growth rate determined by the nutritional quality of the prey, irrespective of prey size. However, the size of newborn predator cells is remarkably stable across prey nutritional content and size variations. Tuning the predatory cell cycle by modulating prey dimensions also allowed us to reveal invariable temporal connections between key cellular processes. Altogether, our data imply adaptability and robustness shaping the enclosed cell-cycle progression of B. bacteriovorus, which might contribute to optimal exploitation of the finite resources and space in their prey. This study extends the characterization of cell cycle control strategies and growth patterns beyond canonical models and lifestyles.
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Affiliation(s)
- Yoann G Santin
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200 Brussels, Belgium
| | - Thomas Lamot
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200 Brussels, Belgium
| | | | - Jovana Kaljević
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200 Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200 Brussels, Belgium.
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17
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de Vasconcelos Junior AA, Tirado-Vélez JM, Martín-Galiano AJ, Megias D, Ferrándiz MJ, Hernández P, Amblar M, de la Campa AG. StaR Is a Positive Regulator of Topoisomerase I Activity Involved in Supercoiling Maintenance in Streptococcus pneumoniae. Int J Mol Sci 2023; 24:ijms24065973. [PMID: 36983048 PMCID: PMC10053502 DOI: 10.3390/ijms24065973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
The DNA topoisomerases gyrase and topoisomerase I as well as the nucleoid-associated protein HU maintain supercoiling levels in Streptococcus pneumoniae, a main human pathogen. Here, we characterized, for the first time, a topoisomerase I regulator protein (StaR). In the presence of sub-inhibitory novobiocin concentrations, which inhibit gyrase activity, higher doubling times were observed in a strain lacking staR, and in two strains in which StaR was over-expressed either under the control of the ZnSO4-inducible PZn promoter (strain ΔstaRPZnstaR) or of the maltose-inducible PMal promoter (strain ΔstaRpLS1ROMstaR). These results suggest that StaR has a direct role in novobiocin susceptibility and that the StaR level needs to be maintained within a narrow range. Treatment of ΔstaRPZnstaR with inhibitory novobiocin concentrations resulted in a change of the negative DNA supercoiling density (σ) in vivo, which was higher in the absence of StaR (σ = -0.049) than when StaR was overproduced (σ = -0.045). We have located this protein in the nucleoid by using super-resolution confocal microscopy. Through in vitro activity assays, we demonstrated that StaR stimulates TopoI relaxation activity, while it has no effect on gyrase activity. Interaction between TopoI and StaR was detected both in vitro and in vivo by co-immunoprecipitation. No alteration of the transcriptome was associated with StaR amount variation. The results suggest that StaR is a new streptococcal nucleoid-associated protein that activates topoisomerase I activity by direct protein-protein interaction.
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Affiliation(s)
| | - Jose M Tirado-Vélez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Antonio J Martín-Galiano
- Unidades Centrales Científico-Técnicas, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Diego Megias
- Unidad de Microscopía Confocal, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - María-José Ferrándiz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Pablo Hernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Mónica Amblar
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
| | - Adela G de la Campa
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28220 Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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18
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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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19
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The Spatial Organization of Bacterial Transcriptional Regulatory Networks. Microorganisms 2022; 10:microorganisms10122366. [PMID: 36557619 PMCID: PMC9787925 DOI: 10.3390/microorganisms10122366] [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] [Received: 10/27/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The transcriptional regulatory network (TRN) is the central pivot of a prokaryotic organism to receive, process and respond to internal and external environmental information. However, little is known about its spatial organization so far. In recent years, chromatin interaction data of bacteria such as Escherichia coli and Bacillus subtilis have been published, making it possible to study the spatial organization of bacterial transcriptional regulatory networks. By combining TRNs and chromatin interaction data of E. coli and B. subtilis, we explored the spatial organization characteristics of bacterial TRNs in many aspects such as regulation directions (positive and negative), central nodes (hubs, bottlenecks), hierarchical levels (top, middle, bottom) and network motifs (feed-forward loops and single input modules) of the TRNs and found that the bacterial TRNs have a variety of stable spatial organization features under different physiological conditions that may be closely related with biological functions. Our findings provided new insights into the connection between transcriptional regulation and the spatial organization of chromosome in bacteria and might serve as a factual foundation for trying spatial-distance-based gene circuit design in synthetic biology.
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20
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Mahaseth T, Kuzminov A. Catastrophic chromosome fragmentation probes the nucleoid structure and dynamics in Escherichia coli. Nucleic Acids Res 2022; 50:11013-11027. [PMID: 36243965 PMCID: PMC9638926 DOI: 10.1093/nar/gkac865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Escherichia coli cells treated with a combination of cyanide (CN) and hydrogen peroxide (HP) succumb to catastrophic chromosome fragmentation (CCF), detectable in pulsed-field gels as >100 double-strand breaks per genome equivalent. Here we show that CN + HP-induced double-strand breaks are independent of replication and occur uniformly over the chromosome,—therefore we used CCF to probe the nucleoid structure by measuring DNA release from precipitated nucleoids. CCF releases surprisingly little chromosomal DNA from the nucleoid suggesting that: (i) the nucleoid is a single DNA-protein complex with only limited stretches of protein-free DNA and (ii) CN + HP-induced breaks happen within these unsecured DNA stretches, rather than at DNA attachments to the central scaffold. Mutants lacking individual nucleoid-associated proteins (NAPs) release more DNA during CCF, consistent with NAPs anchoring chromosome to the central scaffold (Dps also reduces the number of double-strand breaks directly). Finally, significantly more broken DNA is released once ATP production is restored, with about two-thirds of this ATP-dependent DNA release being due to transcription, suggesting that transcription complexes act as pulleys to move DNA loops. In addition to NAPs, recombinational repair of double-strand breaks also inhibits DNA release by CCF, contributing to a dynamic and complex nucleoid structure.
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Affiliation(s)
- Tulip Mahaseth
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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21
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Liao Q, Ren Z, Wiesler EE, Fuqua C, Wang X. A dicentric bacterial chromosome requires XerC/D site-specific recombinases for resolution. Curr Biol 2022; 32:3609-3618.e7. [PMID: 35797999 PMCID: PMC9398967 DOI: 10.1016/j.cub.2022.06.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/24/2022] [Accepted: 06/15/2022] [Indexed: 12/18/2022]
Abstract
Unlike eukaryotes and archaea, which have multiple replication origins on their chromosomes, bacterial chromosomes usually contain a single replication origin.1 Here, we discovered a dicentric bacterial chromosome with two replication origins, which has resulted from the fusion of the circular and linear chromosomes in Agrobacterium tumefaciens. The fused chromosome is well tolerated, stably maintained, and retains similar subcellular organization and genome-wide DNA interactions found for the bipartite chromosomes. Strikingly, the two replication origins and their partitioning systems are both functional and necessary for cell survival. Finally, we discovered that the site-specific recombinases XerC and XerD2 are essential in cells harboring the fused chromosome but not in cells with bipartite chromosomes. Analysis of actively dividing cells suggests a model in which XerC/D are required to recombine the sister fusion chromosomes when the two centromeres on the same chromosome are segregated to opposite cell poles. Thus, faithful segregation of dicentric chromosomes in bacteria can occur because of site-specific recombination between the sister chromatids during chromosome partitioning. Our study provides a natural comparative platform to examine a bacterial chromosome with multiple origins and a possible explanation for the fundamental difference in bacterial genome architecture relative to eukaryotes and archaea.1.
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Affiliation(s)
- Qin Liao
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Emma E Wiesler
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3(rd) Street, Bloomington, IN 47405, USA.
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22
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Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli. Nat Commun 2022; 13:4524. [PMID: 35927234 PMCID: PMC9352719 DOI: 10.1038/s41467-022-32106-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 07/15/2022] [Indexed: 12/30/2022] Open
Abstract
Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is colocalized, genome-wide, with transcribing RNA polymerase (RNAP). Treatment with transcription elongation inhibitor rifampicin leads to EcTopoI relocation to promoter regions, where RNAP also accumulates. When a 14 kDa RNAP-binding EcTopoI C-terminal domain (CTD) is overexpressed, colocalization of EcTopoI and RNAP along the transcription units is reduced. Pull-down experiments directly show that the two enzymes interact in vivo. Using ChIP-Seq and Topo-Seq, we demonstrate that EcTopoI is enriched upstream (within up to 12-15 kb) of highly-active transcription units, indicating that EcTopoI relaxes negative supercoiling generated by transcription. Uncoupling of the RNAP:EcTopoI interaction by either overexpression of EcTopoI competitor (CTD or inactive EcTopoI Y319F mutant) or deletion of EcTopoI domains involved in the interaction is toxic for cells and leads to excessive negative plasmid supercoiling. Moreover, uncoupling of the RNAP:EcTopoI interaction leads to R-loops accumulation genome-wide, indicating that this interaction is required for prevention of R-loops formation. In E. coli, disruption of TopoI and RNAP interaction decreases cells viability and leads to hypernegative DNA supercoiling and R loops accumulation. TopoI and DNA gyrase bind around transcription units and TopoI recognizes cleavage sites by a specific motif and negative supercoiling.
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23
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Dash S, Palma CSD, Baptista ISC, Almeida BLB, Bahrudeen MNM, Chauhan V, Jagadeesan R, Ribeiro AS. Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Res 2022; 50:8512-8528. [PMID: 35920318 PMCID: PMC9410904 DOI: 10.1093/nar/gkac643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers' variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli's short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.
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Affiliation(s)
- Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Cristina S D Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Bilena L B Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Mohamed N M Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Rahul Jagadeesan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.,Center of Technology and Systems (CTS-Uninova), NOVA University of Lisbon 2829-516, Monte de Caparica, Portugal
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24
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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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25
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Wang Y, Shen W, Yin M, Huang W, Ye B, Li P, Shi S, Bai G, Guo X, Jin Y, Lin K, Zhang Y, Jiang Y, Wang J, Han Y, Zhao Z. Changes in Higher-Order Chromosomal Structure of Klebsiella pneumoniae Under Simulated Microgravity. Front Microbiol 2022; 13:879321. [PMID: 35711756 PMCID: PMC9197264 DOI: 10.3389/fmicb.2022.879321] [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: 02/19/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit significant phenotypic changes under simulated microgravity (SMG), including enhanced biofilm formation and cellulose synthesis, which may be evoked by changes in gene expression patterns. It is well known that prokaryotic cells genomic DNA can be hierarchically organized into different higher-order three-dimensional structures, which can highly influence gene expression. It is remain elusive whether phenotypic changes induced by SMG in the subpopulations of K. pneumoniae are driven by genome higher-order structural changes. Here, we investigated the above-mentioned issue using the wild-type (WT) K. pneumoniae (WT was used as a control strain and continuously cultivated for 2 weeks under standard culture conditions of normal gravity) and two previous identified subpopulations (M1 and M2) obtained after 2 weeks of continuous incubation in a SMG device. By the combination of genome-wide chromosome conformation capture (Hi-C), RNA-seq and whole-genome methylation (WGS) analyses, we found that the along with the global chromosome interactions change, the compacting extent of M1, M2 subpopulations were much looser under SMG and even with an increase in active, open chromosome regions. In addition, transcriptome data showed that most differentially expressed genes (DEGs) were upregulated, whereas a few DEGs were downregulated in M1 and M2. The functions of both types DEGs were mainly associated with membrane fractions. Additionally, WGS analysis revealed that methylation levels were lower in M1 and M2. Using combined analysis of multi-omics data, we discovered that most upregulated DEGs were significantly enriched in the boundary regions of the variable chromosomal interaction domains (CIDs), in which genes regulating biofilm formation were mainly located. These results suggest that K. pneumoniae may regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes in response to altered gravity.
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Affiliation(s)
- Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bingyu Ye
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Ge Bai
- Beijing Institute of Biotechnology, Beijing, China
| | - Xinjie Guo
- Beijing Institute of Biotechnology, Beijing, China
| | - Yifei Jin
- Beijing Institute of Biotechnology, Beijing, China
| | - Kailin Lin
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Junfeng Wang
- Second Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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26
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Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens. Proc Natl Acad Sci U S A 2022; 119:2115854119. [PMID: 35101983 PMCID: PMC8833148 DOI: 10.1073/pnas.2115854119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
How bacteria with multipartite genomes organize and segregate their DNA is poorly understood. Here, we investigate a prototypical multipartite genome in the plant pathogen Agrobacterium tumefaciens. We identify previously unappreciated interreplicon interactions: the four replicons cluster through interactions at their centromeres, and the two chromosomes, one circular and one linear, interact along their replication arms. Our data suggest that these interreplicon contacts play critical roles in the organization and maintenance of multipartite genomes. Bacterial species from diverse phyla contain multiple replicons, yet how these multipartite genomes are organized and segregated during the cell cycle remains poorly understood. Agrobacterium tumefaciens has a 2.8-Mb circular chromosome (Ch1), a 2.1-Mb linear chromosome (Ch2), and two large plasmids (pAt and pTi). We used this alpha proteobacterium as a model to investigate the global organization and temporal segregation of a multipartite genome. Using chromosome conformation capture assays, we demonstrate that both the circular and the linear chromosomes, but neither of the plasmids, have their left and right arms juxtaposed from their origins to their termini, generating interarm interactions that require the broadly conserved structural maintenance of chromosomes complex. Moreover, our study revealed two types of interreplicon interactions: “ori-ori clustering” in which the replication origins of all four replicons interact, and “Ch1-Ch2 alignment” in which the arms of Ch1 and Ch2 interact linearly along their lengths. We show that the centromeric proteins (ParB1 for Ch1 and RepBCh2 for Ch2) are required for both types of interreplicon contacts. Finally, using fluorescence microscopy, we validated the clustering of the origins and observed their frequent colocalization during segregation. Altogether, our findings provide a high-resolution view of the conformation of a multipartite genome. We hypothesize that intercentromeric contacts promote the organization and maintenance of diverse replicons.
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27
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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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28
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Dugar G, Hofmann A, Heermann DW, Hamoen LW. A chromosomal loop anchor mediates bacterial genome organization. Nat Genet 2022; 54:194-201. [PMID: 35075232 DOI: 10.1038/s41588-021-00988-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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29
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Geisel D, Lenz P. Machine learning classification of trajectories from molecular dynamics simulations of chromosome segregation. PLoS One 2022; 17:e0262177. [PMID: 35061790 PMCID: PMC8782305 DOI: 10.1371/journal.pone.0262177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022] Open
Abstract
In contrast to the well characterized mitotic machinery in eukaryotes it seems as if there is no universal mechanism organizing chromosome segregation in all bacteria. Apparently, some bacteria even use combinations of different segregation mechanisms such as protein machines or rely on physical forces. The identification of the relevant mechanisms is a difficult task. Here, we introduce a new machine learning approach to this problem. It is based on the analysis of trajectories of individual loci in the course of chromosomal segregation obtained by fluorescence microscopy. While machine learning approaches have already been applied successfully to trajectory classification in other areas, so far it has not been possible to use them to discriminate segregation mechanisms in bacteria. A main obstacle for this is the large number of trajectories required to train machine learning algorithms that we overcome here by using trajectories obtained from molecular dynamics simulations. We used these trajectories to train four different machine learning algorithms, two linear models and two tree-based classifiers, to discriminate segregation mechanisms and possible combinations of them. The classification was performed once using the complete trajectories as high-dimensional input vectors as well as on a set of features which were used to transform the trajectories into low-dimensional input vectors for the classifiers. Finally, we tested our classifiers on shorter trajectories with duration times comparable (or even shorter) than typical experimental trajectories and on trajectories measured with varying temporal resolutions. Our results demonstrate that machine learning algorithms are indeed capable of discriminating different segregation mechanisms in bacteria and to even resolve combinations of the mechanisms on rather short time scales.
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Affiliation(s)
- David Geisel
- Department of Physics, Philipps University Marburg, Marburg, Germany
| | - Peter Lenz
- Department of Physics, Philipps University Marburg, Marburg, Germany
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30
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Mancini L, Crozat E, Javer A, Lagomarsino MC, Cicuta P. Dynamics of Bacterial Chromosomes by Locus Tracking in Fluorescence Microscopy. Methods Mol Biol 2022; 2476:155-170. [PMID: 35635703 DOI: 10.1007/978-1-0716-2221-6_12] [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] [Indexed: 06/15/2023]
Abstract
In the last two decades, it has been shown that bacterial chromosomes have remarkable spatial organization at various scales, and they display well-defined movements during the cell cycle, for example to reliably segregate daughter chromosomes. More recently, various labs have begun investigating also the short time dynamics (displacements during time intervals of 0.1 s-100 s), which should be related to the molecular structure. Probing these dynamics is analogous to "microrheology" approaches that have been applied successfully to study mechanical response of complex fluids. These studies of chromosome fluctuation dynamics have revealed differences of fluctuation amplitude across the chromosome, and different characters of motion depending on the time window of interest. Different fluctuation amplitudes have also been observed for the same chromosomal loci under antibiotic treatments, with magnitudes that are correlated to changes in intracellular density and thus crowding. We describe how to carry out tracking experiments of single loci and how to analyze locus motility. We point out the importance of considering in the analysis the number of GFP molecules per fluorescent locus, as well as the nature of the protein they are fused to, and also how to measure intracellular density.
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Affiliation(s)
- Leonardo Mancini
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Estelle Crozat
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et de Génétique Moléculaires, Université de Toulouse, CNRS, UPS, Toulouse, France
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Avelino Javer
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
- Physics Department, University of Milan, and INFN, Milan, Italy
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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31
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Badrinarayanan A, Leake MC. Fluorescence Recovery After Photobleaching (FRAP) to Study Dynamics of the Structural Maintenance of Chromosome (SMC) Complex in Live Escherichia coli Bacteria. Methods Mol Biol 2022; 2476:31-41. [PMID: 35635695 DOI: 10.1007/978-1-0716-2221-6_4] [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
MukBEF, a structural maintenance of chromosome (SMC) complex, is an important molecular machine for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or "foci") composed of molecular assemblies in the cell, where it is thought to carry out most of its chromosome-associated activities. Here, we outline the technique of fluorescence recovery after photobleaching (FRAP) as a method to study the properties of YFP-tagged MukB in fluorescent foci. This method can provide important insight into the dynamics of MukB on DNA and be used to study its biochemical properties in vivo.
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Affiliation(s)
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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32
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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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33
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Zhu Y, Liu L, Mustafi M, Rank LA, Gellman SH, Weisshaar JC. Local rigidification and possible coacervation of the Escherichia coli DNA by cationic nylon-3 polymers. Biophys J 2021; 120:5243-5254. [PMID: 34757079 DOI: 10.1016/j.bpj.2021.10.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 12/17/2022] Open
Abstract
Synthetic, cationic random nylon-3 polymers (β-peptides) show promise as inexpensive antimicrobial agents less susceptible to proteolysis than normal peptides. We have used superresolution, single-cell, time-lapse fluorescence microscopy to compare the effects on live Escherichia coli cells of four such polymers and the natural antimicrobial peptides LL-37 and cecropin A. The longer, densely charged monomethyl-cyclohexyl (MM-CH) copolymer and MM homopolymer rapidly traverse the outer membrane and the cytoplasmic membrane. Over the next ∼5 min, they locally rigidify the chromosomal DNA and slow the diffusive motion of ribosomal species to a degree comparable to LL-37. The shorter dimethyl-dimethylcyclopentyl (DM-DMCP) and dimethyl-dimethylcyclohexyl (DM-DMCH) copolymers, and cecropin A are significantly less effective at rigidifying DNA. Diffusion of the DNA-binding protein HU and of ribosomal species is hindered as well. The results suggest that charge density and contour length are important parameters governing these antimicrobial effects. The data corroborate a model in which agents having sufficient cationic charge distributed across molecular contour lengths comparable to local DNA-DNA interstrand spacings (∼6 nm) form a dense network of multivalent, electrostatic "pseudo-cross-links" that cause the local rigidification. In addition, at times longer than ∼30 min, we observe that the MM-CH copolymer and the MM homopolymer (but not the other four agents) cause gradual coalescence of the two nucleoid lobes into a single dense lobe localized at one end of the cell. We speculate that this process involves coacervation of the DNA by the cationic polymer, and may be related to the liquid droplet coacervates observed in eukaryotic cells.
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Affiliation(s)
- Yanyu Zhu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Lei Liu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Mainak Mustafi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Leslie A Rank
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin.
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34
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Dame RT. Special Issue: Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution. Microorganisms 2021; 9:microorganisms9112406. [PMID: 34835530 PMCID: PMC8619304 DOI: 10.3390/microorganisms9112406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
A typical bacterial cell is micron-sized and contains a genome several million base pairs in length [...].
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Affiliation(s)
- Remus T. Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Centre for Microbial Cell Biology, Leiden University, 2333 CC Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, 2333 CC Leiden, The Netherlands
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35
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Rusková R, Račko D. Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures. Polymers (Basel) 2021; 13:3726. [PMID: 34771282 PMCID: PMC8588256 DOI: 10.3390/polym13213726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 01/03/2023] Open
Abstract
By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions.
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Affiliation(s)
- Renáta Rusková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 3, 84541 Bratislava, Slovakia;
- Department of Plastics, Rubber and Fibres (IPM FCFT), Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia
| | - Dušan Račko
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 3, 84541 Bratislava, Slovakia;
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36
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Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development. Nat Commun 2021; 12:5222. [PMID: 34471115 PMCID: PMC8410768 DOI: 10.1038/s41467-021-25461-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria of the genus Streptomyces have a linear chromosome, with a core region and two ‘arms’. During their complex life cycle, these bacteria develop multi-genomic hyphae that differentiate into chains of exospores that carry a single copy of the genome. Sporulation-associated cell division requires chromosome segregation and compaction. Here, we show that the arms of Streptomyces venezuelae chromosomes are spatially separated at entry to sporulation, but during sporogenic cell division they are closely aligned with the core region. Arm proximity is imposed by segregation protein ParB and condensin SMC. Moreover, the chromosomal terminal regions are organized into distinct domains by the Streptomyces-specific HU-family protein HupS. Thus, as seen in eukaryotes, there is substantial chromosomal remodelling during the Streptomyces life cycle, with the chromosome undergoing rearrangements from an ‘open’ to a ‘closed’ conformation. Streptomyces bacteria have a linear chromosome and a complex life cycle, including development of multi-genomic hyphae that differentiate into mono-genomic exospores. Here, Szafran et al. show that the chromosome of Streptomyces venezuelae undergoes substantial remodelling during sporulation, from an ‘open’ to a ‘closed’ conformation.
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37
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The Division Defect of a Bacillus subtilis minD noc Double Mutant Can Be Suppressed by Spx-Dependent and Spx-Independent Mechanisms. J Bacteriol 2021; 203:e0024921. [PMID: 34181483 DOI: 10.1128/jb.00249-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
During growth, bacteria increase in size and divide. Division is initiated by the formation of the Z-ring, a ring-like cytoskeletal structure formed by treadmilling protofilaments of the tubulin homolog FtsZ. FtsZ localization is thought to be controlled by the Min and Noc systems, and here we explore why cell division fails at high temperature when the Min and Noc systems are simultaneously mutated. Microfluidic analysis of a minD noc double mutant indicated that FtsZ formed proto-Z-rings at periodic interchromosome locations but that the rings failed to mature and become functional. Extragenic suppressor analysis indicated that a variety of mutations restored high temperature growth to the minD noc double mutant, and while many were likely pleiotropic, others implicated the proteolysis of the transcription factor Spx. Further analysis indicated that a Spx-dependent pathway activated the expression of ZapA, a protein that primarily compensates for the absence of Noc. In addition, an Spx-independent pathway reduced the length of the cytokinetic period, perhaps by increasing divisome activity. Finally, we provide evidence of an as-yet-unidentified protein that is activated by Spx and governs the frequency of polar division and minicell formation. IMPORTANCE Bacteria must properly position the location of the cell division machinery in order to grow, divide, and ensure each daughter cell receives one copy of the chromosome. In Bacillus subtilis, cell division site selection depends on the Min and Noc systems, and while neither is individually essential, cells fail to grow at high temperature when both are mutated. Here, we show that cell division fails in the absence of Min and Noc, due not to a defect in FtsZ localization but rather to a failure in the maturation of the cell division machinery. Suppressor mutations that restored growth were selected, and while some activated the expression of ZapA via the Spx stress response pathway, others appeared to directly enhance divisome activity.
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38
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Abstract
Circular chromosomes in rod-shaped bacteria exist inside a cell in two distinct configurations, “transverse” and “longitudinal,” relative to the long cell axis, with chromosomal loci occupying specific cellular locations in both cases. Bacteria with longitudinal chromosome organization (e.g., Caulobacter crescentus) typically tether their origins of replication to the cell membrane and do not undergo overlapping rounds of replication. In contrast, bacteria with transverse organization (e.g., Escherichia coli) orient their chromosomes by an unknown mechanism and have lifestyles compatible with overlapping rounds of replication. Here, we address the relative roles of two major players in chromosome organization–segregation and propose a model of how E. coli maintains chromosome conformation and orientation inside cells and how this organization is propagated over generations. Structural maintenance of chromosomes (SMC) complexes contribute to chromosome organization in all domains of life. In Escherichia coli, MukBEF, the functional SMC homolog, promotes spatiotemporal chromosome organization and faithful chromosome segregation. Here, we address the relative contributions of MukBEF and the replication terminus (ter) binding protein, MatP, to chromosome organization–segregation. We show that MukBEF, but not MatP, is required for the normal localization of the origin of replication to midcell and for the establishment of translational symmetry between newly replicated sister chromosomes. Overall, chromosome orientation is normally maintained through division from one generation to the next. Analysis of loci flanking the replication termination region (ter), which demark the ends of the linearly organized portion of the nucleoid, demonstrates that MatP is required for maintenance of chromosome orientation. We show that DNA-bound β2-processivity clamps, which mark the lagging strands at DNA replication forks, localize to the cell center, independent of replisome location but dependent on MukBEF action, and consistent with translational symmetry of sister chromosomes. Finally, we directly show that the older (“immortal”) template DNA strand, propagated from previous generations, is preferentially inherited by the cell forming at the old pole, dependent on MukBEF and MatP. The work further implicates MukBEF and MatP as central players in chromosome organization, segregation, and nonrandom inheritance of genetic material and suggests a general framework for understanding how chromosome conformation and dynamics shape subcellular organization.
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Feric M, Misteli T. Phase separation in genome organization across evolution. Trends Cell Biol 2021; 31:671-685. [PMID: 33771451 PMCID: PMC8286288 DOI: 10.1016/j.tcb.2021.03.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023]
Abstract
Phase separation is emerging as a paradigm to explain the self-assembly and organization of membraneless bodies in the cell. Recent advances show that this principle also extends to nucleoprotein complexes, including DNA-based structures. We discuss here recent observations on the role of phase separation in genome organization across the evolutionary spectrum from bacteria to mammals. These findings suggest that molecular interactions amongst DNA-binding proteins evolved to form a variety of biomolecular condensates with distinct material properties that affect genome organization and function. We suggest that phase separation contributes to genome organization across evolution and that the resulting phase behavior of genomes may underlie regulatory mechanisms and disease.
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Affiliation(s)
- Marina Feric
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA; National Institute of General Medical Sciences, NIH, Bethesda, MD, USA.
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, USA.
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40
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Kaljević J, Saaki TNV, Govers SK, Remy O, van Raaphorst R, Lamot T, Laloux G. Chromosome choreography during the non-binary cell cycle of a predatory bacterium. Curr Biol 2021; 31:3707-3720.e5. [PMID: 34256020 PMCID: PMC8445325 DOI: 10.1016/j.cub.2021.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022]
Abstract
In bacteria, the dynamics of chromosome replication and segregation are tightly coordinated with cell-cycle progression and largely rely on specific spatiotemporal arrangement of the chromosome. Whereas these key processes are mostly investigated in species that divide by binary fission, they remain mysterious in bacteria producing larger number of descendants. Here, we establish the predatory bacterium Bdellovibrio bacteriovorus as a model to investigate the non-binary processing of a circular chromosome. We found that its single chromosome is highly compacted in a polarized nucleoid that excludes freely diffusing proteins during the non-proliferative stage of the cell cycle. A binary-like cycle of DNA replication and asymmetric segregation is followed by multiple asynchronous rounds of replication and progressive ParABS-dependent partitioning, uncoupled from cell division. Finally, we provide the first evidence for an on-off behavior of the ParB protein, which localizes at the centromere in a cell-cycle-regulated manner. Altogether, our findings support a model of complex chromosome choreography leading to the generation of variable, odd, or even numbers of offspring and highlight the adaptation of conserved mechanisms to achieve non-binary reproduction. The Bdellovibrio chromosome is polarized, with ori located near the invasive pole The highly compacted nucleoid excludes cytosolic proteins in non-replicative cells Replication and segregation of chromosomes are uncoupled from cell division The centromeric protein ParB localizes at parS in a cell-cycle-dependent manner
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Affiliation(s)
- Jovana Kaljević
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Terrens N V Saaki
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Sander K Govers
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ophélie Remy
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | | | - Thomas Lamot
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium.
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Lioy VS, Junier I, Lagage V, Vallet I, Boccard F. Distinct Activities of Bacterial Condensins for Chromosome Management in Pseudomonas aeruginosa. Cell Rep 2021; 33:108344. [PMID: 33147461 DOI: 10.1016/j.celrep.2020.108344] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/11/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022] Open
Abstract
Three types of structurally related structural maintenance of chromosomes (SMC) complexes, referred to as condensins, have been identified in bacteria. Smc-ScpAB is present in most bacteria, whereas MukBEF is found in enterobacteria and MksBEF is scattered over the phylogenic tree. The contributions of these condensins to chromosome management were characterized in Pseudomonas aeruginosa, which carries both Smc-ScpAB and MksBEF. In this bacterium, SMC-ScpAB controls chromosome disposition by juxtaposing chromosome arms. In contrast, MksBEF is critical for chromosome segregation in the absence of the main segregation system, and it affects the higher-order architecture of the chromosome by promoting DNA contacts in the megabase range. Strikingly, our results reveal a prevalence of Smc-ScpAB over MksBEF involving a coordination of their activities with chromosome replication. They also show that E. coli MukBEF can substitute for MksBEF in P. aeruginosa while prevailing over Smc-ScpAB. Our results reveal a hierarchy between activities of bacterial condensins on the same chromosome.
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Affiliation(s)
- Virginia S Lioy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ivan Junier
- CNRS, Université Grenoble Alpes, TIMC-IMAG, 38000 Grenoble, France
| | - Valentine Lagage
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Isabelle Vallet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Frédéric Boccard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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42
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Ferrándiz MJ, Hernández P, de la Campa AG. Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae. PLoS Genet 2021; 17:e1009542. [PMID: 33930020 PMCID: PMC8115823 DOI: 10.1371/journal.pgen.1009542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/12/2021] [Accepted: 04/10/2021] [Indexed: 02/02/2023] Open
Abstract
Streptococcus pneumoniae is a major cause of disease and death that develops resistance to multiple antibiotics. DNA topoisomerase I (TopoI) is a novel pneumococcal drug target. TopoI is the sole type-I pneumococcal topoisomerase that regulates supercoiling homeostasis in this bacterium. In this study, a direct in vitro interaction between TopoI and RNA polymerase (RNAP) was detected by surface plasmon resonance. To understand the interplay between transcription and supercoiling regulation in vivo, genome-wide association of RNAP and TopoI was studied by ChIP-Seq. RNAP and TopoI were enriched at the promoters of 435 and 356 genes, respectively. Higher levels of expression were consistently measured in those genes whose promoters recruit both RNAP and TopoI, in contrast with those enriched in only one of them. Both enzymes occupied a narrow region close to the ATG codon. In addition, RNAP displayed a regular distribution throughout the coding regions. Likewise, the summits of peaks called with MACS tool, mapped around the ATG codon in both cases. However, RNAP showed a broader distribution towards ATG-downstream positions. Remarkably, inhibition of RNAP with rifampicin prevented the localization of TopoI at promoters and, vice versa, inhibition of TopoI with seconeolitsine prevented the binding of RNAP to promoters. This indicates a functional interplay between RNAP and TopoI. To determine the molecular factors responsible for RNAP and TopoI co-recruitment, we looked for DNA sequence motifs. We identified a motif corresponding to a -10-extended promoter for TopoI and for RNAP. Furthermore, RNAP was preferentially recruited to genes co-directionally oriented with replication, while TopoI was more abundant in head-on genes. TopoI was located in the intergenic regions of divergent genes pairs, near the promoter of the head-on gene of the pair. These results suggest a role for TopoI in the formation/stability of the RNAP-DNA complex at the promoter and during transcript elongation. Streptococcus pneumoniae is a main cause of pneumonia, meningitis and sepsis. Antibiotic resistance in this bacterium has spread worldwide, compromising medical treatment. Therefore, the development of new drugs directed to novel targets is necessary. DNA topology is essential for the regulation of replication and gene expression. Topology is regulated and maintained by DNA topoisomerases, carrying out nicking-closing reactions. Type I and type II topoisomerases act on single-stranded and double-stranded DNA, respectively. Although type II topoisomerases are the target of clinically used antibiotics, there are no clinical antibiotics directed against type I topoisomerases. Seconeolitsine, a new drug targeting topoisomerase I, is effective against bacteria that have a single type I topoisomerase, such as Streptococcus pneumoniae and Mycobacterium tuberculosis. In this report, we studied the role of topoisomerase I in transcription. We found that topoisomerase I and RNA polymerase physically interact in vitro and co-localize at gene promoters in vivo. Binding of each of these enzymes to promoters was prevented by the specific inhibition of the other enzyme, supporting a role for topoisomerase I in RNA polymerase transcription.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Pablo Hernández
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail:
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43
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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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44
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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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45
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Locatelli E, Bianco V, Malgaretti P. Activity-Induced Collapse and Arrest of Active Polymer Rings. PHYSICAL REVIEW LETTERS 2021; 126:097801. [PMID: 33750170 DOI: 10.1103/physrevlett.126.097801] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
We investigate, using numerical simulations, the conformations of isolated active ring polymers. We find that their behavior depends crucially on their size: Short rings (N≲100) swell, whereas longer rings (N≳200) collapse, at sufficiently high activity. By investigating the nonequilibrium process leading to the steady state, we find a universal route driving both outcomes; we highlight the central role of steric interactions, at variance with linear chains, and of topology conservation. We further show that the collapsed rings are arrested by looking at different observables, all underlining the presence of an extremely long timescales at the steady state, associated with the internal dynamics of the collapsed section. Finally, we found that in some circumstances the collapsed state spins about its axis.
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Affiliation(s)
| | - Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Complutense University of Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
| | - Paolo Malgaretti
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
- IV Institute for Theoretical Physics, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Helmholtz Institut Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Fürther Strasse 248, 90429 Nürnberg, Germany
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46
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Jewett AI, Stelter D, Lambert J, Saladi SM, Roscioni OM, Ricci M, Autin L, Maritan M, Bashusqeh SM, Keyes T, Dame RT, Shea JE, Jensen GJ, Goodsell DS. Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. J Mol Biol 2021; 433:166841. [PMID: 33539886 DOI: 10.1016/j.jmb.2021.166841] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/01/2023]
Abstract
Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.
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Affiliation(s)
- Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | | | - Jason Lambert
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Shyam M Saladi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Ludovic Autin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Maritan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Saeed M Bashusqeh
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Tom Keyes
- Department of Chemistry, Boston University, MA, USA
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Joan-Emma Shea
- Departments of Chemistry and Biochemistry and Physics, University of California, Santa Barbara, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
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47
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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48
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Abstract
Acetylation was initially discovered as a post-translational modification (PTM) on the unstructured, highly basic N-terminal tails of eukaryotic histones in the 1960s. Histone acetylation constitutes part of the "histone code", which regulates chromosome compaction and various DNA processes such as gene expression, recombination, and DNA replication. In bacteria, nucleoid-associated proteins (NAPs) are responsible these functions in that they organize and compact the chromosome and regulate some DNA processes. The highly conserved DNABII family of proteins are considered functional homologues of eukaryotic histones despite having no sequence or structural conservation. Within the past decade, a growing interest in Nε-lysine acetylation led to the discovery that hundreds of bacterial proteins are acetylated with diverse cellular functions, in direct contrast to the original thought that this was a rare phenomenon. Similarly, other previously undiscovered bacterial PTMs, like serine, threonine, and tyrosine phosphorylation, have also been characterized. In this review, the various PTMs that were discovered among DNABII family proteins, specifically histone-like protein (HU) orthologues, from large-scale proteomic studies are discussed. The functional significance of these modifications and the enzymes involved are also addressed. The discovery of novel PTMs on these proteins begs this question: is there a histone-like code in bacteria?
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Affiliation(s)
- Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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49
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Efficiency and Robustness of Processes Driven by Nucleoid Exclusion in Escherichia coli. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32894477 DOI: 10.1007/978-3-030-46886-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The internal spatial organization of prokaryotic organisms, including Escherichia coli, is essential for the proper functioning of processes such as cell division. One source of this organization in E. coli is the nucleoid, which causes the exclusion of macromolecules - e.g. protein aggregates and the chemotaxis network - from midcell. Similarly, following DNA replication, the nucleoid(s) assist in placing the Z-ring at midcell. These processes need to be efficient in optimal conditions and robust to suboptimal conditions. After reviewing recent findings on these topics, we make use of past data to study the efficiency of the spatial constraining of Z-rings, chemotaxis networks, and protein aggregates, as a function of the nucleoid(s) morphology. Also, we compare the robustness of these processes to nonoptimal temperatures. We show that Z-rings, Tsr clusters, and protein aggregates have temperature-dependent spatial distributions along the major cell axis that are consistent with the nucleoid(s) morphology and the volume-exclusion phenomenon. Surprisingly, the consequences of the changes in nucleoid size with temperature are most visible in the kurtosis of these spatial distributions, in that it has a statistically significant linear correlation with the mean nucleoid length and, in the case of Z-rings, with the distance between nucleoids prior to cell division. Interestingly, we also find a negative, statistically significant linear correlation between the efficiency of these processes at the optimal condition and their robustness to suboptimal conditions, suggesting a trade-off between these traits.
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50
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Anand D, Schumacher D, Søgaard-Andersen L. SMC and the bactofilin/PadC scaffold have distinct yet redundant functions in chromosome segregation and organization in Myxococcus xanthus. Mol Microbiol 2020; 114:839-856. [PMID: 32738827 DOI: 10.1111/mmi.14583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/22/2020] [Indexed: 12/20/2022]
Abstract
In bacteria, ParABS systems and structural maintenance of chromosome (SMC) condensin-like complexes are important for chromosome segregation and organization. The rod-shaped Myxococcus xanthus cells have a unique chromosome arrangement in which a scaffold composed of the BacNOP bactofilins and PadC positions the essential ParB∙parS segregation complexes and the DNA segregation ATPase ParA in the subpolar regions. We identify the Smc and ScpAB subunits of the SMC complex in M. xanthus and demonstrate that SMC is conditionally essential, with Δsmc or ΔscpAB mutants being temperature sensitive. Inactivation of SMC caused defects in chromosome segregation and organization. Lack of the BacNOP/PadC scaffold also caused chromosome segregation defects but this scaffold is not essential for viability. Inactivation of SMC was synthetic lethal with lack of the BacNOP/PadC scaffold. Lack of SMC interfered with formation of the BacNOP/PadC scaffold while lack of this scaffold did not interfere with chromosome association by SMC. Altogether, our data support that three systems function together to enable chromosome segregation in M. xanthus. ParABS constitutes the basic and essential machinery. SMC and the BacNOP/PadC scaffold have different yet redundant roles in chromosome segregation with SMC supporting individualization of daughter chromosomes and BacNOP/PadC making the ParABS system operate more robustly.
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Affiliation(s)
- Deepak Anand
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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