1
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Pham P, Wood EA, Dunbar EL, Cox MM, Goodman MF. Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements. Nucleic Acids Res 2024; 52:6392-6405. [PMID: 38676944 DOI: 10.1093/nar/gkae320] [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: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, $ \le$2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
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Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Emma L Dunbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
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2
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Pham P, Wood EA, Dunbar EL, Cox MM, Goodman MF. Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.01.560376. [PMID: 37873128 PMCID: PMC10592627 DOI: 10.1101/2023.10.01.560376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, ≤2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
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Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Emma L. Dunbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
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3
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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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4
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Cossa A, Trépout S, Wien F, Groen J, Le Brun E, Turbant F, Besse L, Pereiro E, Arluison V. Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator. J Struct Biol 2022; 214:107912. [PMID: 36283630 DOI: 10.1016/j.jsb.2022.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.
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Affiliation(s)
- Antoine Cossa
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Johannes Groen
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Université Paris Cité, UFR Sciences du vivant, 75006 Paris cedex, France.
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5
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Mitra D, Pande S, Chatterji A. Polymer architecture orchestrates the segregation and spatial organization of replicating E. coli chromosomes in slow growth. SOFT MATTER 2022; 18:5615-5631. [PMID: 35861071 DOI: 10.1039/d2sm00734g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The mechanism of chromosome segregation and organization in the bacterial cell cycle of E. coli is one of the least understood aspects in its life cycle. The E. coli chromosome is often modelled as a bead spring ring polymer. We introduce cross-links in the DNA-ring polymer, resulting in the formation of loops within each replicating bacterial chromosome. We use simulations to show that the chosen polymer-topology ensures its self-organization along the cell long-axis, such that various chromosomal loci get spatially localized as seen in vivo. The localization of loci arises due to entropic repulsion between polymer loops within each daughter DNA confined in a cylinder. The cellular addresses of the loci in our model are in fair agreement with those seen in experiments as given in J. A. Cass et al., Biophys. J., 2016, 110, 2597-2609. We also show that the adoption of such modified polymer architectures by the daughter DNAs leads to an enhanced propensity of their spatial segregation. Secondly, we match other experimentally reported results, including observation of the cohesion time and the ter-transition. Additionally, the contact map generated from our simulations reproduces the macro-domain like organization as seen in the experimentally obtained Hi-C map. Lastly, we have also proposed a plausible reconciliation of the 'Train Track' and the 'Replication Factory' models which provide conflicting descriptions of the spatial organization of the replication forks. Thus, we reconcile observations from complementary experimental techniques probing bacterial chromosome organization.
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6
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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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7
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Yousuf M, Iuliani I, Veetil RT, Seshasayee A, Sclavi B, Cosentino Lagomarsino M. Early fate of exogenous promoters in E. coli. Nucleic Acids Res 2020; 48:2348-2356. [PMID: 31960057 PMCID: PMC7049719 DOI: 10.1093/nar/gkz1196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/05/2019] [Accepted: 12/20/2019] [Indexed: 01/12/2023] Open
Abstract
Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory. We combine sequencing, flow cytometry and sorting, followed by microscopy to monitor gene expression and its variability after large-scale random insertions of a reporter gene in a population of Escherichia coli bacteria. We find that inserted promoters have a wide range of gene-expression variability related to their location. We find that high-expression clones carry insertions that are not correlated with H-NS binding. Conversely, binding of H-NS correlates with silencing. Finally, while most promoters show a common level of extrinsic noise, some insertions show higher noise levels. Analysis of these high-noise clones supports a scenario of switching due to transcriptional interference from divergent ribosomal promoters. Altogether, our findings point to evolutionary pathways where newly-acquired genes are not necessarily silenced, but may immediately explore a wide range of expression levels to probe the optimal ones.
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Affiliation(s)
- Malikmohamed Yousuf
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Ilaria Iuliani
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: LCQB, UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Reshma T Veetil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
- School of Life science, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru 560064, Karnataka, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India
| | - Bianca Sclavi
- LBPA, UMR 8113, CNRS, ENS Paris-Saclay, 61 Avenue du President Wilson, 94235 Cachan, France
- Current Affiliation: LCQB, UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Marco Cosentino Lagomarsino
- Sorbonne Université, Campus Pierre and Marie Curie, 4 Place Jussieu, 75005 Paris, France
- CNRS, UMR7238, 4 Place Jussieu, 75005 Paris, France
- Current Affiliation: IFOM, FIRC Institute of Molecular Oncology, Via Adamello 16, 20143 Milan, Italy
- Current Affiliation: Physics Department, University of Milan, and I.N.F.N., Via Celoria 16, 20133 Milan, Italy
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8
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Abstract
In bacteria, chromosomes are highly organized within the limited volume of the cell to form a nucleoid. Recent application of microscopy and chromosome conformation capture techniques have together provided a comprehensive understanding of the nature of this organization and the role of factors such as the structural maintenance of chromosomes (SMC) proteins in the establishment and maintenance of the same. In this chapter, we outline a microfluidics-based approach for live cell imaging of Escherichia coli chromosome dynamics in wild-type cells. This assay can be used to track the activity of the SMC complex, MukBEF, on DNA and assess the impact of perturbations such as DNA damage on chromosome organization and segregation.
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9
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Le Gall A, Cattoni DI, Nollmann M. Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy. Methods Mol Biol 2018; 1624:253-268. [PMID: 28842889 DOI: 10.1007/978-1-4939-7098-8_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The bacterial nucleoid is highly organized, yet it is dynamically remodeled by cellular processes such as transcription, replication, or segregation. Many principles of nucleoid organization have remained obscure due to the inability of conventional microscopy methods to retrieve structural information beyond the diffraction limit of light. Structured illumination microscopy has recently been shown to provide new levels of spatial details on bacterial chromosome organization by surpassing the diffraction limit. Its ease of use and fast 3D multicolor capabilities make it a method of choice for imaging fluorescently labeled specimens at the nanoscale. We describe a simple high-throughput method for imaging bacterial chromosomes using this technique.
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Affiliation(s)
- Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090, Montpellier, France.
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10
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Gaal T, Bratton BP, Sanchez-Vazquez P, Sliwicki A, Sliwicki K, Vegel A, Pannu R, Gourse RL. Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus. Genes Dev 2017; 30:2272-2285. [PMID: 27898392 PMCID: PMC5110994 DOI: 10.1101/gad.290312.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 01/20/2023]
Abstract
Gaal et al. examined the relative positions of the ribosomal RNA operons in space. The results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus. The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180° on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.
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Affiliation(s)
- Tamas Gaal
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Benjamin P Bratton
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | - Alexander Sliwicki
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kristine Sliwicki
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Andrew Vegel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Rachel Pannu
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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11
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Wlodarski M, Raciti B, Kotar J, Cosentino Lagomarsino M, Fraser GM, Cicuta P. Both genome and cytosol dynamics change in E. coli challenged with sublethal rifampicin. Phys Biol 2017; 14:015005. [PMID: 28207419 DOI: 10.1088/1478-3975/aa5b71] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
While the action of many antimicrobial drugs is well understood at the molecular level, a systems-level physiological response to antibiotics remains largely unexplored. This work considers fluctuation dynamics of both the chromosome and cytosol in Escherichia coli, and their response to sublethal treatments of a clinically important antibiotic, rifampicin. We precisely quantify the changes in dynamics of chromosomal loci and cytosolic aggregates (a rheovirus nonstructural protein known as μNS-GFP), measuring short time-scale displacements across several hours of drug exposure. To achieve this we develop an empirical method correcting for photo-bleaching and loci size effects. This procedure allows us to characterize the dynamic response to rifampicin in different growth conditions, including a customised microfluidic device. We find that sub-lethal doses of rifampicin cause a small but consistent increase in motility of both the chromosomal loci and cytosolic aggregates. Chromosomal and cytosolic responses are consistent with each other and between different growth conditions.
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Affiliation(s)
- Michal Wlodarski
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, United Kingdom
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12
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Seol Y, Neuman KC. The dynamic interplay between DNA topoisomerases and DNA topology. Biophys Rev 2016; 8:101-111. [PMID: 28510219 DOI: 10.1007/s12551-016-0240-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/03/2023] Open
Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA.
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13
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Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
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14
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Khan SR, Mahaseth T, Kouzminova EA, Cronan GE, Kuzminov A. Static and Dynamic Factors Limit Chromosomal Replication Complexity in Escherichia coli, Avoiding Dangers of Runaway Overreplication. Genetics 2016; 202:945-60. [PMID: 26801182 PMCID: PMC4788131 DOI: 10.1534/genetics.115.184697] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/17/2016] [Indexed: 12/21/2022] Open
Abstract
We define chromosomal replication complexity (CRC) as the ratio of the copy number of the most replicated regions to that of unreplicated regions on the same chromosome. Although a typical CRC of eukaryotic or bacterial chromosomes is 2, rapidly growing Escherichia coli cells induce an extra round of replication in their chromosomes (CRC = 4). There are also E. coli mutants with stable CRC∼6. We have investigated the limits and consequences of elevated CRC in E. coli and found three limits: the "natural" CRC limit of ∼8 (cells divide more slowly); the "functional" CRC limit of ∼22 (cells divide extremely slowly); and the "tolerance" CRC limit of ∼64 (cells stop dividing). While the natural limit is likely maintained by the eclipse system spacing replication initiations, the functional limit might reflect the capacity of the chromosome segregation system, rather than dedicated mechanisms, and the tolerance limit may result from titration of limiting replication factors. Whereas recombinational repair is beneficial for cells at the natural and functional CRC limits, we show that it becomes detrimental at the tolerance CRC limit, suggesting recombinational misrepair during the runaway overreplication and giving a rationale for avoidance of the latter.
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Affiliation(s)
- Sharik R Khan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Tulip Mahaseth
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Elena A Kouzminova
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Glen E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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15
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Abstract
This review provides a brief review of the current understanding of the structure-function relationship of the Escherichia coli nucleoid developed after the overview by Pettijohn focusing on the physical properties of nucleoids. Isolation of nucleoids requires suppression of DNA expansion by various procedures. The ability to control the expansion of nucleoids in vitro has led to purification of nucleoids for chemical and physical analyses and for high-resolution imaging. Isolated E. coli genomes display a number of individually intertwined supercoiled loops emanating from a central core. Metabolic processes of the DNA double helix lead to three types of topological constraints that all cells must resolve to survive: linking number, catenates, and knots. The major species of nucleoid core protein share functional properties with eukaryotic histones forming chromatin; even the structures are different from histones. Eukaryotic histones play dynamic roles in the remodeling of eukaryotic chromatin, thereby controlling the access of RNA polymerase and transcription factors to promoters. The E. coli genome is tightly packed into the nucleoid, but, at each cell division, the genome must be faithfully replicated, divided, and segregated. Nucleoid activities such as transcription, replication, recombination, and repair are all affected by the structural properties and the special conformations of nucleoid. While it is apparent that much has been learned about the nucleoid, it is also evident that the fundamental interactions organizing the structure of DNA in the nucleoid still need to be clearly defined.
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Scolari VF, Sclavi B, Cosentino Lagomarsino M. The nucleoid as a smart polymer. Front Microbiol 2015; 6:424. [PMID: 26005440 PMCID: PMC4424877 DOI: 10.3389/fmicb.2015.00424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/21/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
- Vittore F Scolari
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France
| | - Bianca Sclavi
- Centre National de la Recherche Scientifique, LBPA, UMR 8113, ENS Cachan Cachan, France
| | - Marco Cosentino Lagomarsino
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France ; Centre National de la Recherche Scientifique, UMR 7238 Paris, France
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Scolari VF, Cosentino Lagomarsino M. Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid. SOFT MATTER 2015; 11:1677-1687. [PMID: 25532064 DOI: 10.1039/c4sm02434f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework combining solely these two ingredients, in order to characterize their joint effects. Specifically, we study a simple polymer physics computational model with weak ubiquitous short-ranged self attraction and stronger sparse bridging interactions. Combining theoretical arguments and simulations, we study the general phenomenology of polymer collapse induced by these dual contributions, in the case of regularly spaced bridging. Our results distinguish a regime of classical Flory-like coil-globule collapse dictated by the interplay of excluded volume and attractive energy and a switch-like collapse where bridging interactions compete with entropy loss terms from the looped arms of a star-like rosette. Additionally, we show that bridging can induce stable compartmentalized domains. In these configurations, different "cores" of bridging proteins are kept separated by star-like polymer loops in an entropically favorable multi-domain configuration, with a mechanism that parallels micellar polysoaps. Such compartmentalized domains are stable, and do not need any intra-specific interactions driving their segregation. Domains can be stable also in the presence of uniform attraction, as long as the uniform collapse is above its theta point.
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Affiliation(s)
- Vittore F Scolari
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, 15 rue de l'École de Médecine Paris, France.
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18
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van der Valk RA, Vreede J, Crémazy F, Dame RT. Genomic Looping: A Key Principle of Chromatin Organization. J Mol Microbiol Biotechnol 2015; 24:344-59. [DOI: 10.1159/000368851] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Messerschmidt SJ, Waldminghaus T. Dynamic Organization: Chromosome Domains in Escherichia coli. J Mol Microbiol Biotechnol 2015; 24:301-15. [DOI: 10.1159/000369098] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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20
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Jin DJ, Cagliero C, Zhou YN. Role of RNA polymerase and transcription in the organization of the bacterial nucleoid. Chem Rev 2013; 113:8662-82. [PMID: 23941620 PMCID: PMC3830623 DOI: 10.1021/cr4001429] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ding Jun Jin
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| | - Cedric Cagliero
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
| | - Yan Ning Zhou
- Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory National Cancer Institute, NIH, P.O. Box B, Frederick, MD 21702
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Saha RP, Lou Z, Meng L, Harshey RM. Transposable prophage Mu is organized as a stable chromosomal domain of E. coli. PLoS Genet 2013; 9:e1003902. [PMID: 24244182 PMCID: PMC3820752 DOI: 10.1371/journal.pgen.1003902] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/06/2013] [Indexed: 11/19/2022] Open
Abstract
The E. coli chromosome is compacted by segregation into 400–500 supercoiled domains by both active and passive mechanisms, for example, transcription and DNA-protein association. We find that prophage Mu is organized as a stable domain bounded by the proximal location of Mu termini L and R, which are 37 kbp apart on the Mu genome. Formation/maintenance of the Mu ‘domain’ configuration, reported by Cre-loxP recombination and 3C (chromosome conformation capture), is dependent on a strong gyrase site (SGS) at the center of Mu, the Mu L end and MuB protein, and the E. coli nucleoid proteins IHF, Fis and HU. The Mu domain was observed at two different chromosomal locations tested. By contrast, prophage λ does not form an independent domain. The establishment/maintenance of the Mu domain was promoted by low-level transcription from two phage promoters, one of which was domain dependent. We propose that the domain confers transposition readiness to Mu by fostering topological requirements of the reaction and the proximity of Mu ends. The potential benefits to the host cell from a subset of proteins expressed by the prophage may in turn help its long-term stability. A majority of sequenced bacterial genomes harbor prophage sequences. Some prophages are viable, while others have decayed from accumulating mutations and genome rearrangements. Prophages, including defective ones, can contribute important biological properties such as antibiotic resistance, toxins, and serum resistance that increase the survival and ecological range of their hosts. We show in this study that the 37 kbp transposable prophage Mu exists in a unique configuration we call the ‘Mu domain’, where its two ends are paired, segregating the Mu sequences from those of the host chromosome. This is the largest stable chromosomal domain in E. coli mapped to date. The Mu domain configuration promotes low-level transcription from an early prophage promoter, which controls the expression of several genes, not all essential for phage growth. Some non-essential genes include DNA repair functions. We suggest that the Mu domain provides long-term survival benefits to both the prophage and the host: to the prophage in bestowing transposition-ready topological properties unique to the Mu reaction, and to the host in contributing extraneous DNA housekeeping functions.
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Affiliation(s)
- Rudra P. Saha
- Department of Molecular Biosciences & Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Zheng Lou
- Department of Molecular Biosciences & Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Luke Meng
- Department of Molecular Biosciences & Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Rasika M. Harshey
- Department of Molecular Biosciences & Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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22
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Abstract
DNA topology changes dynamically during DNA replication. Supercoiling, precatenation, catenation and knotting interplay throughout the process that is finely regulated by DNA topoisomerases. In the present article, we provide an overview of theoretical and experimental approaches to understand the interplay between various manifestations of topological constraints acting on replicating DNA molecules. Data discussed reveal that DNA entanglements (supercoils and catenanes) play an active role in preventing the formation of deleterious knots.
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Lopez-Vernaza MA, Leach DRF. WITHDRAWN: Symmetries and Asymmetries Associated with Non-Random Segregation of Sister DNA Strands in Escherichia coli. Semin Cell Dev Biol 2013:S1084-9521(13)00077-3. [PMID: 23692810 DOI: 10.1016/j.semcdb.2013.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/06/2013] [Indexed: 11/19/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.semcdb.2013.05.010. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- Manuel A Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
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24
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Lopez-Vernaza MA, Leach DRF. Symmetries and asymmetries associated with non-random segregation of sister DNA strands in Escherichia coli. Semin Cell Dev Biol 2013; 24:610-7. [PMID: 23685127 DOI: 10.1016/j.semcdb.2013.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The successful inheritance of genetic information across generations is a complex process requiring replication of the genome and its faithful segregation into two daughter cells. At each replication cycle there is a risk that new DNA strands incorporate genetic changes caused by miscopying of parental information. By contrast the parental strands retain the original information. This raises the intriguing possibility that specific cell lineages might inherit "immortal" parental DNA strands via non-random segregation. If so, this requires an understanding of the mechanisms of non-random segregation. Here, we review several aspects of asymmetry in the very symmetrical cell, Escherichia coli, in the interest of exploring the potential basis for non-random segregation of leading- and lagging-strand replicated chromosome arms. These considerations lead us to propose a model for DNA replication that integrates chromosome segregation and genomic localisation with non-random strand segregation.
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Affiliation(s)
- Manuel A Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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25
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Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription. Biochem Soc Trans 2013; 41:542-7. [DOI: 10.1042/bst20120222] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA supercoiling and NAPs (nucleoid-associated proteins) contribute to the regulation of transcription of many bacterial genes. The horizontally acquired SPI (Salmonella pathogenicity island) genes respond positively to DNA relaxation, they are activated and repressed by the Fis (factor for inversion stimulation) and H-NS (histone-like nucleoid-structuring) NAPs respectively, and are positively controlled by the OmpR global regulatory protein. The ompR gene is autoregulated and responds positively to DNA relaxation. Binding of the Fis and OmpR proteins to their targets in DNA is differentially sensitive to its topological state, whereas H-NS binds regardless of the topological state of the DNA. These data illustrate the overlapping and complex nature of NAP and DNA topological contributions to transcription control in bacteria.
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26
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Dame RT, Espéli O, Grainger DC, Wiggins PA. Multidisciplinary perspectives on bacterial genome organization and dynamics. Mol Microbiol 2012; 86:1023-30. [DOI: 10.1111/mmi.12055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2012] [Indexed: 11/30/2022]
Affiliation(s)
| | - Olivier Espéli
- CNRS; Centre de Génétique Moléculaire; Gif-sur-yvette Cedex; France
| | - David C. Grainger
- School of Biosciences; University of Birmingham; Edgbaston; Birmingham; B15 2TT; UK
| | - Paul A. Wiggins
- Department of Physics; University of Washington; Seattle; WA; USA
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27
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Benza VG, Bassetti B, Dorfman KD, Scolari VF, Bromek K, Cicuta P, Lagomarsino MC. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:076602. [PMID: 22790781 DOI: 10.1088/0034-4885/75/7/076602] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.
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Affiliation(s)
- Vincenzo G Benza
- Dipartimento di Fisica e Matematica, Università dell'Insubria, Como, Italy
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28
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Junier I, Hérisson J, Képès F. Genomic organization of evolutionarily correlated genes in bacteria: limits and strategies. J Mol Biol 2012; 419:369-86. [PMID: 22446685 DOI: 10.1016/j.jmb.2012.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 12/30/2022]
Abstract
The need for efficient molecular interplay in time and space within a cell imposes strong constraints that could be partially relaxed if relative gene positions along chromosomes were appropriate. Comparative genomics studies have demonstrated the short-scale conservation of gene proximity along bacterial chromosomes. Additionally, the long-range periodic positioning of evolutionarily correlated genes within Escherichia coli has recently been highlighted. To gain further insight into these different genetic organizations, we examined the compromise between chromosomal proximity and periodicity for all available eubacterial genomes by evaluating groups of evolutionarily correlated genes from a benchmark data set. In enterobacteria, strict chromosomal proximity is found to be limited to groups under 20 genes, whereas periodicity is significant in all groups over 50. The E. coli K12 genome bears 511 periodic genes (12% of the genome), whose orthologs are found to be periodic in all eubacterial phyla. These periodic genes predominantly function in macromolecular synthesis and spatial organization of cellular components. They are enriched in essential and housekeeping genes and tend to often be constitutively expressed. On this basis, it is argued that chromosomal proximity and periodicity are ubiquitous complementary genomic strategies that favor the build-up of local concentrations of co-functional molecules. In particular, the periodic layout may facilitate chromosome folding to spatially organize the construction of major cell components. The transition at 20 genes is reminiscent of the size of the longest operons and of topological microdomains. The range for which DNA neighborhood optimizes biochemical interactions might therefore be defined by DNA topology.
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Affiliation(s)
- Ivan Junier
- Epigenomics Project/Institute of Systems and Synthetic Biology, Genopole, CNRS, University of Evry, 91030 Evry, France.
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29
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Wang W, Li GW, Chen C, Xie XS, Zhuang X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 2011; 333:1445-9. [PMID: 21903814 DOI: 10.1126/science.1204697] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.
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Affiliation(s)
- Wenqin Wang
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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30
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Vendeville A, Larivière D, Fourmentin E. An inventory of the bacterial macromolecular components and their spatial organization. FEMS Microbiol Rev 2011; 35:395-414. [DOI: 10.1111/j.1574-6976.2010.00254.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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31
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Scolari VF, Bassetti B, Sclavi B, Lagomarsino MC. Gene clusters reflecting macrodomain structure respond to nucleoid perturbations. ACTA ACUST UNITED AC 2011; 7:878-88. [DOI: 10.1039/c0mb00213e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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32
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Booker BM, Deng S, Higgins NP. DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium. Mol Microbiol 2010; 78:1348-64. [PMID: 21143310 DOI: 10.1111/j.1365-2958.2010.07394.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteria differ from eukaryotes by having the enzyme DNA gyrase, which catalyses the ATP-dependent negative supercoiling of DNA. Negative supercoils are essential for condensing chromosomes into an interwound (plectonemic) and branched structure known as the nucleoid. Topo-1 removes excess supercoiling in an ATP-independent reaction and works with gyrase to establish a topological equilibrium where supercoils move within 10 kb domains bounded by stochastic barriers along the sequence. However, transcription changes the stochastic pattern by generating supercoil diffusion barriers near the sites of gene expression. Using supercoil-dependent Tn3 and γδ resolution assays, we studied DNA topology upstream, downstream and across highly transcribed operons. Whenever two Res sites flanked efficiently transcribed genes, resolution was inhibited and the loss in recombination efficiency was proportional to transcription level. Ribosomal RNA operons have the highest transcription rates, and resolution assays at the rrnG and rrnH operons showed inhibitory levels 40-100 times those measured in low-transcription zones. Yet, immediately upstream and downstream of RNA polymerase (RNAP) initiation and termination sites, supercoiling characteristics were similar to poorly transcribed zones. We present a model that explains why RNAP blocks plectonemic supercoil movement in the transcribed track and suggests how gyrase and TopA control upstream and downstream transcription-driven supercoiling.
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Affiliation(s)
- Betty M Booker
- Department of Biochemistry and Molecular Genetics, University of Alabama , Birmingham, AL 35294-0024, USA
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33
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Mathelier A, Carbone A. Chromosomal periodicity and positional networks of genes in Escherichia coli. Mol Syst Biol 2010; 6:366. [PMID: 20461073 PMCID: PMC2890325 DOI: 10.1038/msb.2010.21] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 03/18/2010] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli periodic gene distribution is identified for a periodic interval of 33 kb. Two positional networks of genes are discovered by studying gene periodic distribution: one is driven by metabolic genes and the other by genes involved in cellular processing and signaling. A functional core of Escherichia coli genes drives gene periodic distribution. A few chromosomal regions that preserve gene transcription profiles across environmental changes are identified. This single genome analysis approach can be taken as a footprint for a large-scale bacterial and archaeal periodic distribution analysis.
The structure of dynamic folds in microbial chromosomes is largely unknown. On the other hand, genes characterizing a functional core in Escherichia coli K12 show to be periodically distributed along the arcs, suggesting an encoded three-dimensional genomic organization helping functional activities among which are translation and, possibly, transcription. Core genes are expected to be either highly expressed or rapidly expressed when needed. Because of E. coli K12 life mode, they are especially encoded at the genomic level, with a very biased codon composition, and as a consequence, they can, at some extent, be predicted in silico. On the basis of a computational method allowing the definition of a class of genes that are organism specific, we identify a pool of core genes, some of which are conserved across many species, some depend on the environmental living conditions of the organism, some are involved in the stress response, and others have no yet identified function. This set of predicted core genes covers roughly 10% of all genes in E. coli K12 and approximates well the class of experimentally known essential genes. An important property of core genes is that they cover all the spectrum of microbial functions. This means that for any functional class of genes, some representative of the class belongs to the functional core. Consequently, we reasoned, the three-dimensional chromosomal arrangement of these genes may be important to fulfill basic functional responses. A strong periodic signal of 33 kb is detected, and the approach shows also that a periodic arrangement affects not only core genes, but in fact, all genes along the E. coli K12 chromosome, even if the signal is weaker. An analysis of functional classes of genes shows that they systematically organize into two independent positional gene networks, one driven by metabolic genes and the other by genes involved in cellular processing and signaling (Figure 5A). We conclude that functional reasons justify periodic gene organization. To explore the functional basis of the distribution, we examined the relationships between the codon bias of E. coli K12 genes and transcriptomic data for a number of different growth conditions. We could identify in a very precise manner a few chromosomal regions that preserve gene transcription profiles across environmental changes. These regions present a profile of the expression levels for their genes, which is periodic by a period of 33 kb. These finding generate new questions on evolutionary pressures imposed on the chromosome and suggest a number of insights on chromosomal superhelicity that can lead to a precise conception of experiments and to hypothesis to be tested. The theoretical analysis of functional classes of genes involved in the periodic distribution, for instance, makes clear that metabolic genes and genes involved in translation are expected to be the most affected by a disruption of the periodic chromosomal arrangement. The methodological approach is based on single genome analysis. Given either core genes or genes organized in functional classes, we analyze the detailed distribution of distances between pairs of genes through a parameterized model based on signal processing and find that these groups of genes tend to be separated by a regular integral distance characterized by a periodic interval of 33 kb. The methodology can be applied to any set of genes and can be taken as a footprint for large-scale bacterial and archaeal analysis. The structure of dynamic folds in microbial chromosomes is largely unknown. Here, we find that genes with a highly biased codon composition and characterizing a functional core in Escherichia coli K12 show to be periodically distributed along the arcs, suggesting an encoded three-dimensional genomic organization helping functional activities among which are translation and, possibly, transcription. This extends to functional classes of genes that are shown to systematically organize into two independent positional gene networks, one driven by metabolic genes and the other by genes involved in cellular processing and signaling. We conclude that functional reasons justify periodic gene organization. This finding generates new questions on evolutionary pressures imposed on the chromosome. Our methodological approach is based on single genome analysis. Given either core genes or genes organized in functional classes, we analyze the detailed distribution of distances between pairs of genes through a parameterized model based on signal processing and find that these groups of genes tend to be separated by a regular integral distance. The methodology can be applied to any set of genes and can be taken as a footprint for large-scale bacterial and archaeal analysis.
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Affiliation(s)
- Anthony Mathelier
- UPMC Univ Paris 06, FRE3214, Génomique Analytique, 15 rue de l'Ecole de Médecine, Paris, France
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34
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Junier I, Martin O, Képès F. Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput Biol 2010; 6:e1000678. [PMID: 20169181 PMCID: PMC2820526 DOI: 10.1371/journal.pcbi.1000678] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 01/12/2010] [Indexed: 12/22/2022] Open
Abstract
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close by. This is motivated by recurrent evidence that there exist physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient. The good operation of cells relies on a coordination between chromosome structure and genetic regulation which is yet to be understood. This can be seen in particular from the transcription machinery: in some eukaryotes and bacteria, transcription of highly active genes occurs within discrete foci called transcription factories, where RNA polymerases, transcription factors and their target genes co-localize. The mechanisms underlying the formation of these foci and the resulting topological structure of the chromosome remain to be elucidated. Here, we propose a thermodynamic framework based on a polymer description of DNA in which genes effectively interact through attractive forces in physical space. The formation of transcription foci then corresponds to a self-organizing process whereby the interacting genes and the non-interacting DNA form two phases that tend to separate. Numerical simulations of the model unveil a rich zoology of the topological ordering of DNA around the foci and show that regularities in the positions of the interacting genes make the spatial co-localization of multiple families of genes particularly efficient. Experimental testing of the predictions of our model should shed new light on the relation between transcriptional regulation and cellular conformations of chromosomes.
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Affiliation(s)
- Ivan Junier
- Epigenomics Project, Genopole, CNRS UPS 3201, UniverSud Paris, University of Evry, Genopole Campus 1 - Genavenir 6, Evry, France
- Institut des Systèmes Complexes Paris Île-de-France, Paris, France
| | - Olivier Martin
- Université Paris-Sud, UMR 8626 LPTMS, F-91405, Orsay, France
- Université Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, Gif/Yvette, France
| | - François Képès
- Epigenomics Project, Genopole, CNRS UPS 3201, UniverSud Paris, University of Evry, Genopole Campus 1 - Genavenir 6, Evry, France
- * E-mail:
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35
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Abstract
The regulation of self-renewal, cell diversity, and differentiation can occur by modulating symmetric and asymmetric cell divisions. Remarkably, asymmetric cell divisions can arise through multiple processes in which molecules in the cytoplasm and nucleus, as well as template "immortal" DNA strands, can segregate to one daughter cell during cell division. Explaining how these events direct distinct daughter cell fates is a major challenge to understanding how the organism is assembled and maintained for a lifetime. Numerous technical issues that are associated with assessing how distinct cell fates are executed in vivo have resulted in divergent interpretations of experimental findings. This review addresses some of these points and considers different developmental model systems that attempt to investigate how cell fate decisions are determined, as well as the molecules that guide these choices.
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Affiliation(s)
- Shahragim Tajbakhsh
- Stem Cells and Development, CNRS URA 2578, Department of Developmental Biology, Institut Pasteur, 75724 Paris Cedex 15, France.
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36
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Weiner A, Zauberman N, Minsky A. Recombinational DNA repair in a cellular context: a search for the homology search. Nat Rev Microbiol 2009; 7:748-55. [PMID: 19756013 DOI: 10.1038/nrmicro2206] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Double-strand DNA breaks (DSBs) are the most detrimental lesion that can be sustained by the genetic complement, and their inaccurate mending can be just as damaging. According to the consensual view, precise DSB repair relies on homologous recombination. Here, we review studies on DNA repair, chromatin diffusion and chromosome confinement, which collectively imply that a genome-wide search for a homologous template, generally thought to be a pivotal stage in all homologous DSB repair pathways, is improbable. The implications of this assertion for the scope and constraints of DSB repair pathways and for the ability of diverse organisms to cope with DNA damage are discussed.
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Affiliation(s)
- Allon Weiner
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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37
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Luijsterburg MS, White MF, van Driel R, Dame RT. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 2009; 43:393-418. [PMID: 19037758 DOI: 10.1080/10409230802528488] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.
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Affiliation(s)
- Martijn S Luijsterburg
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan, Amsterdam, The Netherlands
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38
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Reyes-Lamothe R, Wang X, Sherratt D. Escherichia coli and its chromosome. Trends Microbiol 2008; 16:238-45. [DOI: 10.1016/j.tim.2008.02.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 02/23/2008] [Accepted: 02/29/2008] [Indexed: 01/22/2023]
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39
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Danilova O, Reyes-Lamothe R, Pinskaya M, Sherratt D, Possoz C. MukB colocalizes with the oriC region and is required for organization of the two Escherichia coli chromosome arms into separate cell halves. Mol Microbiol 2007; 65:1485-92. [PMID: 17824928 PMCID: PMC2169520 DOI: 10.1111/j.1365-2958.2007.05881.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The circular Escherichia coli chromosome is organized by bidirectional replication into two equal left and right arms (replichores). Each arm occupies a separate cell half, with the origin of replication (oriC) at mid-cell. E. coli MukBEF belongs to the ubiquitous family of SMC protein complexes that play key roles in chromosome organization and processing. In mukBEF mutants, viability is restricted to low temperature with production of anucleate cells, reflecting chromosome segregation defects. We show that in mukB mutant cells, the two chromosome arms do not separate into distinct cell halves, but extend from pole to pole with the oriC region located at the old pole. Mutations in topA, encoding topoisomerase I, do not suppress the aberrant positioning of chromosomal loci in mukB cells, despite suppressing the temperature-sensitivity and production of anucleate cells. Furthermore, we show that MukB and the oriC region generally colocalize throughout the cell cycle, even when oriC localization is aberrant. We propose that MukBEF initiates the normal bidirectional organization of the chromosome from the oriC region.
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Affiliation(s)
| | | | | | - David Sherratt
- E-mail ; Tel. +44 (0) 1865 275 296; Fax +44 (0) 1865 275 297; Email ; Tel. +33 (0) 1 69 82 31 70; Fax +33 (0) 1 69 82 31 60
| | - Christophe Possoz
- E-mail ; Tel. +44 (0) 1865 275 296; Fax +44 (0) 1865 275 297; Email ; Tel. +33 (0) 1 69 82 31 70; Fax +33 (0) 1 69 82 31 60
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40
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Arraiano CM, Bamford J, Brüssow H, Carpousis AJ, Pelicic V, Pflüger K, Polard P, Vogel J. Recent advances in the expression, evolution, and dynamics of prokaryotic genomes. J Bacteriol 2007; 189:6093-100. [PMID: 17601780 PMCID: PMC1951890 DOI: 10.1128/jb.00612-07] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Cecilia M Arraiano
- ITQB-Instituto de Tecnologia Química e Biológical/Universidade Nova de Lisboa, Oeiras, Portugal
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41
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Abstract
The study of chromosome segregation in bacteria has gained strong insights from the use of cytology techniques. A global view of chromosome choreography during the cell cycle is emerging, highlighting as a next challenge the description of the molecular mechanisms and factors involved. Here, we review one of such factor, the FtsK DNA translocase. FtsK couples segregation of the chromosome terminus, the ter region, with cell division. It is a powerful and fast translocase that reads chromosome polarity to find the end, thereby sorting sister ter regions on either side of the division septum, and activating the last steps of segregation. Recent data have revealed the structure of the FtsK motor, how translocation is oriented by specific DNA motifs, termed KOPS, and suggests novel mechanisms for translocation and sensing chromosome polarity.
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Affiliation(s)
- Sarah Bigot
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Université Paul Sabatier--Toulouse III, 118 route de Narbonne, 31062 Toulouse Cedex, France.
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