1
|
Pham P, Wood EA, Dunbar EL, Cox M, Goodman M. 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 PMCID: PMC11194060 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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Fukute J, Maki K, Adachi T. The nucleolar shell provides anchoring sites for DNA untwisting. Commun Biol 2024; 7:83. [PMID: 38263258 PMCID: PMC10805735 DOI: 10.1038/s42003-023-05750-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: 08/18/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024] Open
Abstract
DNA underwinding (untwisting) is a crucial step in transcriptional activation. DNA underwinding occurs between the site where torque is generated by RNA polymerase (RNAP) and the site where the axial rotation of DNA is constrained. However, what constrains DNA axial rotation in the nucleus is yet unknown. Here, we show that the anchorage to the nuclear protein condensates constrains DNA axial rotation for DNA underwinding in the nucleolus. In situ super-resolution imaging of underwound DNA reveal that underwound DNA accumulates in the nucleolus, a nuclear condensate with a core-shell structure. Specifically, underwound DNA is distributed in the nucleolar core owing to RNA polymerase I (RNAPI) activities. Furthermore, underwound DNA in the core decreases when nucleolar shell components are prevented from binding to their recognition structure, G-quadruplex (G4). Taken together, these results suggest that the nucleolar shell provides anchoring sites that constrain DNA axial rotation for RNAPI-driven DNA underwinding in the core. Our findings will contribute to understanding how nuclear protein condensates make up constraints for the site-specific regulation of DNA underwinding and transcription.
Collapse
Affiliation(s)
- Jumpei Fukute
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan
| | - Koichiro Maki
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan.
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan.
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Sakyo, Kyoto, Japan.
- Department of Medicine and Medical Science, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan.
| | - Taiji Adachi
- Laboratory of Cellular and Molecular Biomechanics, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
- Laboratory of Biomechanics, Institute for Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, Japan
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Sakyo, Kyoto, Japan
- Department of Medicine and Medical Science, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto, Japan
| |
Collapse
|
4
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
5
|
Boulas I, Bruno L, Rimsky S, Espeli O, Junier I, Rivoire O. Assessing in vivo the impact of gene context on transcription through DNA supercoiling. Nucleic Acids Res 2023; 51:9509-9521. [PMID: 37667073 PMCID: PMC10570042 DOI: 10.1093/nar/gkad688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023] Open
Abstract
Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. Our results are explained if TopoI and gyrase both act specifically, respectively upstream and downstream of the gene, with antagonistic effects of TopoI, which can repress initiation while facilitating elongation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation.
Collapse
Affiliation(s)
- Ihab Boulas
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Lisa Bruno
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Sylvie Rimsky
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Ivan Junier
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Gulliver, ESPCI, CNRS, Université PSL, Paris, France
| |
Collapse
|
6
|
Joyeux M. Models of topological barriers and molecular motors of bacterial DNA. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2120626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France
| |
Collapse
|
7
|
Conin B, Billault-Chaumartin I, El Sayyed H, Quenech'Du N, Cockram C, Koszul R, Espéli O. Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome. Nucleic Acids Res 2022; 50:2635-2650. [PMID: 35212387 PMCID: PMC8934667 DOI: 10.1093/nar/gkac105] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/07/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022] Open
Abstract
In bacteria, chromosome segregation occurs progressively from the origin to terminus within minutes of replication of each locus. Between replication and segregation, sister loci are held in an apparent cohesive state by topological links. The decatenation activity of topoisomerase IV (Topo IV) is required for segregation of replicated loci, yet little is known about the structuring of the chromosome maintained in a cohesive state. In this work, we investigated chromosome folding in cells with altered decatenation activities. Within minutes after Topo IV inactivation, massive chromosome reorganization occurs, associated with increased in contacts between nearby loci, likely trans-contacts between sister chromatids, and in long-range contacts between the terminus and distant loci. We deciphered the respective roles of Topo III, MatP and MukB when TopoIV activity becomes limiting. Topo III reduces short-range inter-sister contacts suggesting its activity near replication forks. MatP, the terminus macrodomain organizing system, and MukB, the Escherichia coli SMC, promote long-range contacts with the terminus. We propose that the large-scale conformational changes observed under these conditions reveal defective decatenation attempts involving the terminus area. Our results support a model of spatial and temporal partitioning of the tasks required for sister chromosome segregation.
Collapse
Affiliation(s)
- Brenna Conin
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France.,Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France.,Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Ingrid Billault-Chaumartin
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Hafez El Sayyed
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Nicole Quenech'Du
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| | - Charlotte Cockram
- Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France
| | - Romain Koszul
- Institut Pasteur, Université de Paris, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015Paris, France
| | - Olivier Espéli
- Center for Interdisciplinary Research in Biology (CIRB), Collége de France, CNRS, INSERM, Université PSL, Paris, France
| |
Collapse
|
8
|
Xu W, Yan Y, Artsimovitch I, Dunlap D, Finzi L. Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops. Nucleic Acids Res 2022; 50:2826-2835. [PMID: 35188572 PMCID: PMC8934669 DOI: 10.1093/nar/gkac093] [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: 10/07/2021] [Revised: 12/22/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022] Open
Abstract
Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. During transcription, RNA polymerase generates supercoiling that may facilitate passage through such barriers. We monitored E. coli RNA polymerase progress along templates in conditions that prevented, or favored, 400 bp LacI-mediated DNA looping. Tethered particle motion measurements revealed that RNA polymerase paused longer at unlooped LacI obstacles or those barring entry to a loop than those barring exit from the loop. Enhanced dissociation of a LacI roadblock by the positive supercoiling generated ahead of a transcribing RNA polymerase within a torsion-constrained DNA loop may be responsible for this reduction in pause time. In support of this idea, RNA polymerase transcribed 6-fold more slowly through looped DNA and paused at LacI obstacles for 66% less time on positively supercoiled compared to relaxed templates, especially under increased tension (torque). Positive supercoiling propagating ahead of polymerase facilitated elongation along topologically complex, protein-coated templates.
Collapse
Affiliation(s)
- Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
| |
Collapse
|
9
|
Tripathi S, Brahmachari S, Onuchic JN, Levine H. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic Acids Res 2021; 50:1269-1279. [PMID: 34951454 PMCID: PMC8860607 DOI: 10.1093/nar/gkab1252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.
Collapse
Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.,Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
| | | | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Physics and Astronomy, Department of Chemistry, & Department of Biosciences, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
| |
Collapse
|
10
|
Joyeux M, Junier I. Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome. Biophys J 2020; 119:1215-1225. [PMID: 32822585 PMCID: PMC7420610 DOI: 10.1016/j.bpj.2020.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 11/29/2022] Open
Abstract
Bacterial genomes have been shown to be partitioned into several-kilobase-long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors. Both in vivo and in vitro experiments have been performed to question the nature of the topological barriers at play, leading to several predictions on possible molecular actors. Here, we address the question of topological barriers using polymer models of supercoiled DNA chains that are constrained such as to mimic the action of predicted molecular actors. More specifically, we determine under which conditions DNA-bridging proteins may act as topological barriers. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. As a result, we find that DNA-bridging proteins must exert rather strong constraints on their binding sites; they must block the diffusion of the excess of twist through the two binding sites on the DNA molecule and, simultaneously, prevent the rotation of one DNA segment relative to the other one. Importantly, not all DNA-bridging proteins satisfy this second condition. For example, single bridges formed by proteins that bind DNA nonspecifically, like H-NS dimers, are expected to fail with this respect. Our findings might also explain, in the case of specific DNA-bridging proteins like LacI, why multiple bridges are required to create stable independent topological domains. Strikingly, when the relative rotation of the DNA segments is not prevented, relaxation results in complex intrication of the two domains. Moreover, although the value of the torsional stress in each domain may vary, their differential is preserved. Our work also predicts that nucleoid-associated proteins known to wrap DNA must form higher protein-DNA complexes to efficiently work as topological barriers.
Collapse
Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS, Université Grenoble Alpes, Grenoble, France.
| | - Ivan Junier
- TIMC-IMAG, CNRS, Université Grenoble Alpes, Grenoble, France
| |
Collapse
|
11
|
Kim S, Beltran B, Irnov I, Jacobs-Wagner C. Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling. Cell 2020; 179:106-119.e16. [PMID: 31539491 DOI: 10.1016/j.cell.2019.08.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/14/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022]
Abstract
Genes are often transcribed by multiple RNA polymerases (RNAPs) at densities that can vary widely across genes and environmental conditions. Here, we provide in vitro and in vivo evidence for a built-in mechanism by which co-transcribing RNAPs display either collaborative or antagonistic dynamics over long distances (>2 kb) through transcription-induced DNA supercoiling. In Escherichia coli, when the promoter is active, co-transcribing RNAPs translocate faster than a single RNAP, but their average speed is not altered by large variations in promoter strength and thus RNAP density. Environmentally induced promoter repression reduces the elongation efficiency of already-loaded RNAPs, causing premature termination and quick synthesis arrest of no-longer-needed proteins. This negative effect appears independent of RNAP convoy formation and is abrogated by topoisomerase I activity. Antagonistic dynamics can also occur between RNAPs from divergently transcribed gene pairs. Our findings may be broadly applicable given that transcription on topologically constrained DNA is the norm across organisms.
Collapse
Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA.
| | - Bruno Beltran
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Irnov Irnov
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06536, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
| |
Collapse
|
12
|
Joyeux M. Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling. Biophys J 2020; 118:2141-2150. [PMID: 31629479 PMCID: PMC7202931 DOI: 10.1016/j.bpj.2019.09.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this work, we investigate the interplay of these two mechanisms with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime in which the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing.
Collapse
Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
| |
Collapse
|
13
|
Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194515. [PMID: 32113983 DOI: 10.1016/j.bbagrm.2020.194515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 02/07/2020] [Accepted: 02/20/2020] [Indexed: 01/04/2023]
Abstract
Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a LineWeaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition. Next, we estimate the fraction of time in locked states and number of transcription events prior to locking, which we validate by measurements under Gyrase inhibition. Replacing the gene of interest by one with slower transcription rate decreases the fraction of time in locked states due to PSB. Finally, we combine data from both constructs to infer a range of possible transcription initiation locking kinetics in a chromosomal location, obtainable by tuning the transcription rate. We validate with measurements of transcription activity at different induction levels. This strategy for dissecting transcription initiation locking kinetics due to PSB can contribute to resolve the transcriptional programs of E. coli and in the engineering of synthetic genetic circuits.
Collapse
|
14
|
Dages S, Zhi X, Leng F. Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli. FEBS Lett 2020; 594:791-798. [PMID: 31639222 PMCID: PMC10857741 DOI: 10.1002/1873-3468.13643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/30/2019] [Accepted: 10/18/2019] [Indexed: 01/07/2023]
Abstract
Previously, we demonstrated that transcription-coupled DNA supercoiling (TCDS) potently activated or inhibited nearby promoters in Escherichia coli even in the presence of all four DNA topoisomerases, suggesting that DNA topoisomerases are not the only factors regulating TCDS. A different mechanism exists to confine this localized DNA supercoiling. Using an in vivo system containing the TCDS-activated leu-500 promoter (Pleu-500 ), we find that the nucleoid-associated Fis protein potently inhibits the TCDS-mediated activation of Pleu-500 . We also find that deletion of the fis gene significantly enhances TCDS-mediated inhibition of transcription of three genes purH, yieP, and yrdA divergently coupled to different rrn operons in the early log phase. These results suggest that Fis protein forms DNA topological barriers upon binding to its recognition sites, blocks TCDS diffusion, and potently inhibits the TCDS-activated Pleu-500 .
Collapse
Affiliation(s)
- Samantha Dages
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Xiaoduo Zhi
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| |
Collapse
|
15
|
Chedin F, Benham CJ. Emerging roles for R-loop structures in the management of topological stress. J Biol Chem 2020; 295:4684-4695. [PMID: 32107311 DOI: 10.1074/jbc.rev119.006364] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.
Collapse
Affiliation(s)
- Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616 .,Genome Center, University of California, Davis, California 95616
| | - Craig J Benham
- Genome Center, University of California, Davis, California 95616 .,Departments of Mathematics and Biomedical Engineering, University of California, Davis, California 95616
| |
Collapse
|
16
|
Abstract
How genomes are organized within cells and how the 3D architecture of a genome influences cellular functions are significant questions in biology. A bacterial genomic DNA resides inside cells in a highly condensed and functionally organized form called nucleoid (nucleus-like structure without a nuclear membrane). The Escherichia coli chromosome or nucleoid is composed of the genomic DNA, RNA, and protein. The nucleoid forms by condensation and functional arrangement of a single chromosomal DNA with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling. Although a high-resolution structure of a bacterial nucleoid is yet to come, five decades of research has established the following salient features of the E. coli nucleoid elaborated below: 1) The chromosomal DNA is on the average a negatively supercoiled molecule that is folded as plectonemic loops, which are confined into many independent topological domains due to supercoiling diffusion barriers; 2) The loops spatially organize into megabase size regions called macrodomains, which are defined by more frequent physical interactions among DNA sites within the same macrodomain than between different macrodomains; 3) The condensed and spatially organized DNA takes the form of a helical ellipsoid radially confined in the cell; and 4) The DNA in the chromosome appears to have a condition-dependent 3-D structure that is linked to gene expression so that the nucleoid architecture and gene transcription are tightly interdependent, influencing each other reciprocally. Current advents of high-resolution microscopy, single-molecule analysis and molecular structure determination of the components are expected to reveal the total structure and function of the bacterial nucleoid.
Collapse
Affiliation(s)
- Subhash C. Verma
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (SCV); (SLA)
| | - Zhong Qian
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sankar L. Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (SCV); (SLA)
| |
Collapse
|
17
|
Growth Phase-Dependent Chromosome Condensation and Heat-Stable Nucleoid-Structuring Protein Redistribution in Escherichia coli under Osmotic Stress. J Bacteriol 2019; 201:JB.00469-19. [PMID: 31481544 DOI: 10.1128/jb.00469-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
The heat-stable nucleoid-structuring (H-NS) protein is a global transcriptional regulator implicated in coordinating the expression of over 200 genes in Escherichia coli, including many involved in adaptation to osmotic stress. We have applied superresolved microscopy to quantify the intracellular and spatial reorganization of H-NS in response to a rapid osmotic shift. We found that H-NS showed growth phase-dependent relocalization in response to hyperosmotic shock. In stationary phase, H-NS detached from a tightly compacted bacterial chromosome and was excluded from the nucleoid volume over an extended period of time. This behavior was absent during rapid growth but was induced by exposing the osmotically stressed culture to a DNA gyrase inhibitor, coumermycin. This chromosomal compaction/H-NS exclusion phenomenon occurred in the presence of either potassium or sodium ions and was independent of the presence of stress-responsive sigma factor σS and of the H-NS paralog StpA.IMPORTANCE The heat-stable nucleoid-structuring (H-NS) protein coordinates the expression of over 200 genes in E. coli, with a large number involved in both bacterial virulence and drug resistance. We report on the novel observation of a dynamic compaction of the bacterial chromosome in response to exposure to high levels of salt. This stress response results in the detachment of H-NS proteins and their subsequent expulsion to the periphery of the cells. We found that this behavior is related to mechanical properties of the bacterial chromosome, in particular, to how tightly twisted and coiled is the chromosomal DNA. This behavior might act as a biomechanical response to stress that coordinates the expression of genes involved in adapting bacteria to a salty environment.
Collapse
|
18
|
Xia Y, Zheng KW, He YD, Liu HH, Wen CJ, Hao YH, Tan Z. Transmission of dynamic supercoiling in linear and multi-way branched DNAs and its regulation revealed by a fluorescent G-quadruplex torsion sensor. Nucleic Acids Res 2019; 46:7418-7424. [PMID: 29982790 PMCID: PMC6101514 DOI: 10.1093/nar/gky534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/31/2018] [Indexed: 01/20/2023] Open
Abstract
DNA supercoiling is an important regulator of gene activity. The transmission of transcription-generated supercoiling wave along a DNA helix provides a way for a gene being transcribed to communicate with and regulate its neighboring genes. Currently, the dynamic behavior of supercoiling transmission remains unclear owing to the lack of a suitable tool for detecting the dynamics of supercoiling transmission. In this work, we established a torsion sensor that quantitatively monitors supercoiling transmission in real time in DNA. Using this sensor, we studied the transmission of transcriptionally generated negative supercoiling in linear and multi-way DNA duplexes. We found that transcription-generated dynamic supercoiling not only transmits along linear DNA duplex but also equally diverges at and proceeds through multi-way DNA junctions. We also show that such a process is regulated by DNA–protein interactions and non-canonical DNA structures in the path of supercoiling transmission. These results imply a transcription-coupled mechanism of dynamic supercoiling-mediated intra- and inter-chromosomal signal transduction pathway and their regulation in DNA.
Collapse
Affiliation(s)
- Ye Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Ke-Wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Hong-He Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Cui-Jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yu-Hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| |
Collapse
|
19
|
Yan Y, Ding Y, Leng F, Dunlap D, Finzi L. Protein-mediated loops in supercoiled DNA create large topological domains. Nucleic Acids Res 2019. [PMID: 29538766 PMCID: PMC5961096 DOI: 10.1093/nar/gky153] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure. To characterize the extent of constrained supercoiling, 400 bp, lac repressor-secured loops were formed in extensively over- or under-wound DNA under gentle tension in a magnetic tweezer. The protein-mediated loops constrained variable amounts of supercoiling that often exceeded the maximum writhe expected for a 400 bp plectoneme. Loops with such high levels of supercoiling appear to be entangled with flanking domains. Thus, loop-mediating proteins operating on supercoiled substrates can establish topological domains that may coordinate gene regulation and other DNA transactions across spans in the genome that are larger than the separation between the binding sites.
Collapse
Affiliation(s)
- Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Yue Ding
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| |
Collapse
|
20
|
Yan Y, Leng F, Finzi L, Dunlap D. Protein-mediated looping of DNA under tension requires supercoiling. Nucleic Acids Res 2019; 46:2370-2379. [PMID: 29365152 PMCID: PMC5861448 DOI: 10.1093/nar/gky021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/12/2018] [Indexed: 02/06/2023] Open
Abstract
Protein-mediated DNA looping is ubiquitous in chromatin organization and gene regulation, but to what extent supercoiling or nucleoid associated proteins promote looping is poorly understood. Using the lac repressor (LacI), a paradigmatic loop-mediating protein, we measured LacI-induced looping as a function of either supercoiling or the concentration of the HU protein, an abundant nucleoid protein in Escherichia coli. Negative supercoiling to physiological levels with magnetic tweezers easily drove the looping probability from 0 to 100% in single DNA molecules under slight tension that likely exists in vivo. In contrast, even saturating (micromolar) concentrations of HU could not raise the looping probability above 30% in similarly stretched DNA or 80% in DNA without tension. Negative supercoiling is required to induce significant looping of DNA under any appreciable tension.
Collapse
Affiliation(s)
- Yan Yan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - Fenfei Leng
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, GA 30322, USA
| |
Collapse
|
21
|
Oliveira SMD, Goncalves NSM, Kandavalli VK, Martins L, Neeli-Venkata R, Reyelt J, Fonseca JM, Lloyd-Price J, Kranz H, Ribeiro AS. Chromosome and plasmid-borne P LacO3O1 promoters differ in sensitivity to critically low temperatures. Sci Rep 2019; 9:4486. [PMID: 30872616 PMCID: PMC6418193 DOI: 10.1038/s41598-019-39618-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/28/2019] [Indexed: 12/31/2022] Open
Abstract
Temperature shifts trigger genome-wide changes in Escherichia coli's gene expression. We studied if chromosome integration impacts on a gene's sensitivity to these shifts, by comparing the single-RNA production kinetics of a PLacO3O1 promoter, when chromosomally-integrated and when single-copy plasmid-borne. At suboptimal temperatures their induction range, fold change, and response to decreasing temperatures are similar. At critically low temperatures, the chromosome-integrated promoter becomes weaker and noisier. Dissection of its initiation kinetics reveals longer lasting states preceding open complex formation, suggesting enhanced supercoiling buildup. Measurements with Gyrase and Topoisomerase I inhibitors suggest hindrance to escape supercoiling buildup at low temperatures. Consistently, similar phenomena occur in energy-depleted cells by DNP at 30 °C. Transient, critically-low temperatures have no long-term consequences, as raising temperature quickly restores transcription rates. We conclude that the chromosomally-integrated PLacO3O1 has higher sensitivity to low temperatures, due to longer-lasting super-coiled states. A lesser active, chromosome-integrated native lac is shown to be insensitive to Gyrase overexpression, even at critically low temperatures, indicating that the rate of escaping positive supercoiling buildup is temperature and transcription rate dependent. A genome-wide analysis supports this, since cold-shock genes exhibit atypical supercoiling-sensitivities. This phenomenon might partially explain the temperature-sensitivity of some transcriptional programs of E. coli.
Collapse
Affiliation(s)
- Samuel M D Oliveira
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Nadia S M Goncalves
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Vinodh K Kandavalli
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Leonardo Martins
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
- CA3 CTS/UNINOVA. Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Caparica, Portugal
| | - Ramakanth Neeli-Venkata
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland
| | - Jan Reyelt
- Gene Bridges, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Jose M Fonseca
- CA3 CTS/UNINOVA. Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Caparica, Portugal
| | - Jason Lloyd-Price
- Biostatistics Department, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Harald Kranz
- Gene Bridges, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics and Multi-Scaled Biodata Analysis and Modelling Research Community, Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 7, 33720, Tampere, Finland.
- CA3 CTS/UNINOVA. Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Caparica, Portugal.
| |
Collapse
|
22
|
Mawhinney MT, Liu R, Lu F, Maksimoska J, Damico K, Marmorstein R, Lieberman PM, Urbanc B. CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy. J Mol Biol 2018; 430:759-776. [PMID: 29409905 DOI: 10.1016/j.jmb.2018.01.012] [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] [Received: 08/04/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 11/26/2022]
Abstract
The CTCF protein has emerged as a key architectural protein involved in genome organization. Although hypothesized to initiate DNA looping, direct evidence of CTCF-induced DNA loop formation is still missing. Several studies have shown that the 11 zinc finger (11 ZF) domain of CTCF is actively involved in DNA binding. We here use atomic force microscopy to examine the effect of the 11 ZF domain comprising residues 266-579 (11 ZF CTCF) and the 3 ZF domain comprising residues 402-494 (6-8 ZF CTCF) of human CTCF on the DNA morphology. Our results show that both domains alter the DNA architecture from the relaxed morphology observed in control DNA samples to compact circular complexes, meshes, and networks, offering important insights into the multivalent character of the 11 ZF CTCF domain. Atomic force microscopy images reveal quasi-circular DNA/CTCF complexes, which are destabilized upon replacing the 11 ZF CTCF by the 6-8 ZF CTCF domain, highlighting the role of the 11 ZF motif in loop formation. Intriguingly, the formation of circular DNA/CTCF complexes is dominated by non-specific binding, whereby contour length and height profiles suggest a single DNA molecule twice wrapped around the protein.
Collapse
Affiliation(s)
| | - Runcong Liu
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - Fang Lu
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Jasna Maksimoska
- The Wistar Institute, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin Damico
- The Wistar Institute, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- The Wistar Institute, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA; Faculty of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana, Slovenia.
| |
Collapse
|
23
|
Zheng KW, He YD, Liu HH, Li XM, Hao YH, Tan Z. Superhelicity Constrains a Localized and R-Loop-Dependent Formation of G-Quadruplexes at the Upstream Region of Transcription. ACS Chem Biol 2017; 12:2609-2618. [PMID: 28846373 DOI: 10.1021/acschembio.7b00435] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcription induces formation of intramolecular G-quadruplex structures at the upstream region of a DNA duplex by an upward transmission of negative supercoiling through the DNA. Currently the regulation of such G-quadruplex formation remains unclear. Using plasmid as a model, we demonstrate that while it is the dynamic negative supercoiling generated by a moving RNA polymerase that triggers a formation of a G-quadruplex, the constitutional superhelicity determines the potential and range of the formation of a G-quadruplex by constraining the propagation of the negative supercoiling. G-quadruplex formation is maximal in negatively supercoiled and nearly abolished in relaxed plasmids while being moderate in nicked and linear ones. The formation of a G-quadruplex strongly correlates with the presence of an R-loop. Preventing R-loop formation virtually abolished G-quadruplex formation even in the negatively supercoiled plasmid. Enzymatic action and protein binding that manipulate supercoiling or its propagation all impact the formation of G-quadruplexes. Because chromosomes and plasmids in cells in their natural form are maintained in a supercoiled state, our findings reveal a physical basis that justifies the formation and regulation of G-quadruplexes in vivo. The structural features involved in G-quadruplex formation may all serve as potential targets in clinical and therapeutic applications.
Collapse
Affiliation(s)
- Ke-wei Zheng
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yi-de He
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hong-he Liu
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xin-min Li
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yu-hua Hao
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Zheng Tan
- State
Key Laboratory of Membrane Biology, Institute of Zoology, ‡University of Chinese
Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| |
Collapse
|
24
|
Tardin C. The mechanics of DNA loops bridged by proteins unveiled by single-molecule experiments. Biochimie 2017; 142:80-92. [PMID: 28804000 DOI: 10.1016/j.biochi.2017.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/06/2017] [Indexed: 12/28/2022]
Abstract
Protein-induced DNA bridging and looping is a common mechanism for various and essential processes in bacterial chromosomes. This mechanism is preserved despite the very different bacterial conditions and their expected influence on the thermodynamic and kinetic characteristics of the bridge formation and stability. Over the last two decades, single-molecule techniques carried out on in vitro DNA systems have yielded valuable results which, in combination with theoretical works, have clarified the effects of different parameters of nucleoprotein complexes on the protein-induced DNA bridging and looping process. In this review, I will outline the features that can be measured for such processes with various single-molecule techniques in use in the field. I will then describe both the experimental results and the theoretical models that illuminate the contribution of the DNA molecule itself as well as that of the bridging proteins in the DNA looping mechanism at play in the nucleoid of E. coli.
Collapse
Affiliation(s)
- Catherine Tardin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France.
| |
Collapse
|
25
|
Chen Y, Gao T, Wang Y, Yang G. Investigating the Influence of Magnesium Ions on p53-DNA Binding Using Atomic Force Microscopy. Int J Mol Sci 2017; 18:ijms18071585. [PMID: 28754018 PMCID: PMC5536072 DOI: 10.3390/ijms18071585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
p53 is a tumor suppressor protein that plays a significant role in apoptosis and senescence, preserving genomic stability, and preventing oncogene expression. Metal ions, such as magnesium and zinc ions, have important influences on p53–DNA interactions for stabilizing the structure of the protein and enhancing its affinity to DNA. In the present study, we systematically investigated the interaction of full length human protein p53 with DNA in metal ion solution by atomic force microscopy (AFM). The p53–DNA complexes at various p53 concentrations were scanned by AFM and their images are used to measure the dissociation constant of p53–DNA binding by a statistical method. We found that the dissociation constant of p53 binding DNA is 328.02 nmol/L in physiological buffer conditions. The influence of magnesium ions on p53–DNA binding was studied by AFM at various ion strengths through visualization. We found that magnesium ions significantly stimulate the binding of the protein to DNA in a sequence-independent manner, different from that stimulated by zinc. Furthermore, the high concentrations of magnesium ions can promote p53 aggregation and even lead to the formation of self-assembly networks of DNA and p53 proteins. We propose an aggregation and self-assembly model based on the present observation and discuss its biological meaning.
Collapse
Affiliation(s)
- Yang Chen
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Tianyong Gao
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Yanwei Wang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
26
|
Zhi X, Dages S, Dages K, Liu Y, Hua ZC, Makemson J, Leng F. Transient and dynamic DNA supercoiling potently stimulates the leu-500 promoter in Escherichia coli. J Biol Chem 2017; 292:14566-14575. [PMID: 28696257 DOI: 10.1074/jbc.m117.794628] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/23/2017] [Indexed: 01/11/2023] Open
Abstract
The inactive prokaryotic leu-500 promoter (Pleu-500) contains a single A-to-G point mutation in the -10 region of the leucine operon promoter, which causes leucine auxotrophy. This promoter can be activated by (-) DNA supercoiling in Escherichia coli topA strains. However, whether this activation arises from global, permanent, or transient, dynamic supercoiling is still not fully understood. In this article, using a newly established in vivo system carrying a pair of divergently coupled promoters, i.e. an IPTG-inducible promoter and Pleu-500 that control the expression of lacZ and luc (the firefly luciferase gene), respectively, we demonstrate that transient, dynamic (-) DNA supercoiling provided by divergent transcription in both wild-type and topA strains can potently activate Pleu-500 We found that this activation depended on the promoter strength and the length of RNA transcripts, which are functional characteristics of transcription-coupled DNA supercoiling (TCDS) precisely predicted by the twin-supercoiled domain model of transcription in which a (+) supercoiled domain is produced ahead of the RNA polymerase and a (-) supercoiled domain behind it. We also demonstrate that TCDS can be generated on topologically open DNA molecules, i.e. linear DNA molecules, in Escherichia coli, suggesting that topological boundaries or barriers are not required for the production of TCDS in vivo This work demonstrates that transient, dynamic TCDS by RNA polymerases is a major chromosome remodeling force in E. coli and greatly influences the nearby, coupled promoters/transcription.
Collapse
Affiliation(s)
- Xiaoduo Zhi
- From the Biomolecular Sciences Institute and.,Departments of Chemistry & Biochemistry and
| | - Samantha Dages
- From the Biomolecular Sciences Institute and.,Departments of Chemistry & Biochemistry and
| | - Kelley Dages
- From the Biomolecular Sciences Institute and.,Departments of Chemistry & Biochemistry and
| | - Yingting Liu
- From the Biomolecular Sciences Institute and.,Departments of Chemistry & Biochemistry and.,the School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Zi-Chun Hua
- the School of Life Sciences, Nanjing University, Nanjing 210023, Jiangsu, China
| | - John Makemson
- Biological Sciences, Florida International University, Miami, Florida 33199 and
| | - Fenfei Leng
- From the Biomolecular Sciences Institute and .,Departments of Chemistry & Biochemistry and
| |
Collapse
|
27
|
Leng F. Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. Biophys Rev 2017; 8:123-133. [PMID: 28510217 DOI: 10.1007/s12551-016-0239-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/27/2016] [Indexed: 12/18/2022] Open
Abstract
Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (-) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop. These constrained (-) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.
Collapse
Affiliation(s)
- Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.
| |
Collapse
|
28
|
Noy A, Maxwell A, Harris SA. Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA. Biophys J 2017; 112:523-531. [PMID: 28108011 PMCID: PMC5300792 DOI: 10.1016/j.bpj.2016.12.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/09/2016] [Accepted: 12/16/2016] [Indexed: 11/29/2022] Open
Abstract
We have explored the interdependence of the binding of a DNA triplex and a repressor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations. We observe that the interaction between the two ligands through their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences.
Collapse
Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, United Kingdom
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, United Kingdom
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom.
| |
Collapse
|
29
|
Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:145-155. [PMID: 28035245 PMCID: PMC5153831 DOI: 10.1007/s12551-016-0241-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 01/09/2023] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
Collapse
Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
| |
Collapse
|
30
|
Perez PJ, Olson WK. Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops. Biophys Rev 2016; 8:135-144. [PMID: 28133491 PMCID: PMC5267335 DOI: 10.1007/s12551-016-0209-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/13/2016] [Indexed: 11/26/2022] Open
Abstract
Genomic DNA is vastly longer than the space allotted to it in a cell. The molecule must fold with a level of organization that satisfies the imposed spatial constraints as well as allows for the processing of genetic information. Key players in this organization include the negative supercoiling of DNA, which facilitates the unwinding of the double-helical molecule, and the associations of DNA with proteins, which partition the DNA into isolated loops, or domains. In order to gain insight into the principles of genome organization and to visualize the folding of spatially constrained DNA, we have developed new computational methods to identify the preferred three-dimensional pathways of protein-mediated DNA loops and to characterize the topological properties of these structures. Here we focus on the levels of supercoiling and the spatial arrangements of DNA in model nucleoprotein systems with two topological domains. We construct these systems by anchoring DNA loops in opposing orientations on a common protein-DNA assembly, namely the Lac repressor protein with two bound DNA operators. The linked pieces of DNA form a covalently closed circle such that the protein attaches to two widely spaced sites along the DNA. We examine the effects of operator spacing, loop orientation, and long-range contacts on overall chain configuration and topology and discuss our findings in the context of classic experiments on the effects of supercoiling and operator spacing on Lac repressor-mediated looping and recent work on the role of proteins as barriers that divide genomes into independent topological domains.
Collapse
Affiliation(s)
- Pamela J. Perez
- Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Wilma K. Olson
- Rutgers, The State University of New Jersey, Piscataway, NJ USA
| |
Collapse
|
31
|
Muskhelishvili G, Travers A. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Biophys Rev 2016; 8:5-22. [PMID: 28510220 PMCID: PMC5425797 DOI: 10.1007/s12551-016-0237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.
Collapse
Affiliation(s)
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
| |
Collapse
|
32
|
Mogil LS, Becker NA, Maher LJ. Supercoiling Effects on Short-Range DNA Looping in E. coli. PLoS One 2016; 11:e0165306. [PMID: 27783696 PMCID: PMC5081198 DOI: 10.1371/journal.pone.0165306] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E. coli strains characterized by different levels of global supercoiling: wild type, gyrase mutant (gyrB226), and topoisomerase mutant (ΔtopA10). DNA looping in each strain was measured by assaying repression of the endogenous lac operon, and repression of ten reporter constructs with DNA loop sizes between 70-85 base pairs. Our data are most simply interpreted as supporting the hypothesis that negative supercoiling facilitates gene repression by small DNA-protein loops in living bacteria.
Collapse
MESH Headings
- DNA Gyrase/genetics
- DNA Gyrase/metabolism
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- Electrophoresis, Agar Gel
- Escherichia coli/genetics
- Genes, Reporter
- Lac Operon/genetics
- Mutation
- Nucleic Acid Conformation
Collapse
Affiliation(s)
- Lauren S. Mogil
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
- Biochemistry and Molecular Biology track, Mayo Graduate School, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
| | - Nicole A. Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America
- * E-mail:
| |
Collapse
|
33
|
Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:233-243. [PMID: 27738452 PMCID: PMC5039213 DOI: 10.1007/s12551-016-0208-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 12/31/2022] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
Collapse
Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
| |
Collapse
|
34
|
Leng F. Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects. Biophys Rev 2016; 8:197-207. [PMID: 28510223 DOI: 10.1007/s12551-016-0204-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022] Open
Abstract
Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (-) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop. These constrained (-) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.
Collapse
Affiliation(s)
- Fenfei Leng
- Biomolecular Sciences Institute and Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.
| |
Collapse
|
35
|
Fulcrand G, Chapagain P, Dunlap D, Leng F. Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS Lett 2016; 590:613-8. [PMID: 26878689 DOI: 10.1002/1873-3468.12094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/04/2016] [Accepted: 02/09/2016] [Indexed: 01/08/2023]
Abstract
Escherichia coli lactose repressor (LacI), a tetrameric protein, is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. It specifically binds to the O1, O2, and O3 operators of the lac promoter, forms DNA loops, and regulates transcription of the lac operon. In this article, utilizing combined techniques of DNA-nicking assay and AFM imaging, we directly observed a 91 bp LacI-mediated, negatively supercoiled DNA loop mimicking the DNA loop between the O1 and O3 operators in the lac promoter.
Collapse
Affiliation(s)
- Geraldine Fulcrand
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Physics, Florida International University, Miami, FL, USA
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA, USA
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.,Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| |
Collapse
|
36
|
Fulcrand G, Dages S, Zhi X, Chapagain P, Gerstman BS, Dunlap D, Leng F. DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. Sci Rep 2016; 6:19243. [PMID: 26763930 PMCID: PMC4725879 DOI: 10.1038/srep19243] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/10/2015] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the lac operon and forms a DNA loop to repress transcription from the adjacent lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (−) supercoils within the 401-bp DNA loop of the lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the lac operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (−) supercoils within the 401-bp DNA loop of the lac promoter. These constrained (−) supercoils enhance LacI’s DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of lacZYA in the lac operon under varying growth conditions.
Collapse
Affiliation(s)
- Geraldine Fulcrand
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| | - Samantha Dages
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| | - Xiaoduo Zhi
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| | - Prem Chapagain
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Physics, Florida International University, Miami, FL 33199
| | - Bernard S Gerstman
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Physics, Florida International University, Miami, FL 33199
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA 30322
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199.,Department of Chemistry &Biochemistry, Florida International University, Miami, FL 33199
| |
Collapse
|
37
|
Lagomarsino MC, Espéli O, Junier I. From structure to function of bacterial chromosomes: Evolutionary perspectives and ideas for new experiments. FEBS Lett 2015; 589:2996-3004. [PMID: 26171924 DOI: 10.1016/j.febslet.2015.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 12/11/2022]
Abstract
The link between chromosome structure and function is a challenging open question because chromosomes in vivo are highly dynamic and arduous to manipulate. Here, we examine several promising approaches to tackle this question specifically in bacteria, by integrating knowledge from different sources. Toward this end, we first provide a brief overview of experimental tools that have provided insights into the description of the bacterial chromosome, including genetic, biochemical and fluorescence microscopy techniques. We then explore the possibility of using comparative genomics to isolate functionally important features of chromosome organization, exploiting the fact that features shared between phylogenetically distant bacterial species reflect functional significance. Finally, we discuss possible future perspectives from the field of experimental evolution. Specifically, we propose novel experiments in which bacteria could be screened and selected on the basis of the structural properties of their chromosomes.
Collapse
Affiliation(s)
| | - Olivier Espéli
- CIRB-Collège de France, CNRS UMR 7241, INSERM U1050, Paris, France
| | - Ivan Junier
- Laboratoire Adaptation et Pathogénie des Micro-organismes - UMR 5163, Université Grenoble 1, CNRS, BP 170, F-38042 Grenoble Cedex 9, France; Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
38
|
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
|
39
|
Chong S, Chen C, Ge H, Xie XS. Mechanism of transcriptional bursting in bacteria. Cell 2014; 158:314-326. [PMID: 25036631 DOI: 10.1016/j.cell.2014.05.038] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 03/17/2014] [Accepted: 05/08/2014] [Indexed: 11/18/2022]
Abstract
Transcription of highly expressed genes has been shown to occur in stochastic bursts. But the origin of such ubiquitous phenomenon has not been understood. Here, we present the mechanism in bacteria. We developed a high-throughput, in vitro, single-molecule assay to follow transcription on individual DNA templates in real time. We showed that positive supercoiling buildup on a DNA segment by transcription slows down transcription elongation and eventually stops transcription initiation. Transcription can be resumed upon gyrase binding to the DNA segment. Furthermore, using single-cell mRNA counting fluorescence in situ hybridization (FISH), we found that duty cycles of transcriptional bursting depend on the intracellular gyrase concentration. Together, these findings prove that transcriptional bursting of highly expressed genes in bacteria is primarily caused by reversible gyrase dissociation from and rebinding to a DNA segment, changing the supercoiling level of the segment.
Collapse
Affiliation(s)
- Shasha Chong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chongyi Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hao Ge
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China; Beijing International Center for Mathematical Research (BICMR), Peking University, Beijing 100871, China
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China.
| |
Collapse
|
40
|
Abstract
Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling between them. Furthermore, in single DNA molecules stretched and twisted with magnetic tweezers, levels of superhelical density confined in CI-mediated DNA loops ranged from -15% or +11%. Finally, in DNA under tensions that may occur in vivo, supercoiling lowered the free energy of loop formation and was essential for DNA looping. Supercoiling-enhanced looping can influence the maintenance of lysogeny in the λ repressor system; it can encode sensitivity to the energy level of the cell and creates independent topological domains of distinct superhelical density.
Collapse
|
41
|
Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells. Proc Natl Acad Sci U S A 2014; 111:E4449-57. [PMID: 25288735 DOI: 10.1073/pnas.1410764111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic gene regulation involves complex patterns of long-range DNA-looping interactions between enhancers and promoters, but how these specific interactions are achieved is poorly understood. Models that posit other DNA loops--that aid or inhibit enhancer-promoter contact--are difficult to test or quantitate rigorously in eukaryotic cells. Here, we use the well-characterized DNA-looping proteins Lac repressor and phage λ CI to measure interactions between pairs of long DNA loops in E. coli cells in the three possible topological arrangements. We find that side-by-side loops do not affect each other. Nested loops assist each other's formation consistent with their distance-shortening effect. In contrast, alternating loops, where one looping element is placed within the other DNA loop, inhibit each other's formation, thus providing clear support for the loop domain model for insulation. Modeling shows that combining loop assistance and loop interference can provide strong specificity in long-range interactions.
Collapse
|
42
|
Lim CJ, Kenney LJ, Yan J. Single-molecule studies on the mechanical interplay between DNA supercoiling and H-NS DNA architectural properties. Nucleic Acids Res 2014; 42:8369-78. [PMID: 24990375 PMCID: PMC4117784 DOI: 10.1093/nar/gku566] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Escherichia coli H-NS protein is a major nucleoid-associated protein that is involved in chromosomal DNA packaging and gene regulatory functions. These biological processes are intimately related to the DNA supercoiling state and thus suggest a direct relationship between H-NS binding and DNA supercoiling. Here, we show that H-NS, which has two distinct DNA-binding modes, is able to differentially regulate DNA supercoiling. H-NS DNA-stiffening mode caused by nucleoprotein filament formation is able to suppress DNA plectoneme formation during DNA supercoiling. In contrast, when H-NS is in its DNA-bridging mode, it is able to promote DNA plectoneme formation during DNA supercoiling. In addition, the DNA-bridging mode is able to block twists diffusion thus trapping DNA in supercoiled domains. Overall, this work reveals the mechanical interplay between H-NS and DNA supercoiling which provides insights to H-NS organization of chromosomal DNA based on its two distinct DNA architectural properties.
Collapse
Affiliation(s)
- Ci Ji Lim
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore Mechanobiology Institute, Singapore Department of Physics, National University of Singapore, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, Singapore Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, USA Department of Biological Sciences, National University of Singapore, Singapore
| | - Jie Yan
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore Mechanobiology Institute, Singapore Department of Physics, National University of Singapore, Singapore
| |
Collapse
|
43
|
Olszewski P, Szambowska A, Barałska S, Narajczyk M, Węgrzyn G, Glinkowska M. A dual promoter system regulating λ DNA replication initiation. Nucleic Acids Res 2014; 42:4450-62. [PMID: 24500197 PMCID: PMC3985674 DOI: 10.1093/nar/gku103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Transcription and DNA replication are tightly regulated to ensure coordination of gene expression with growth conditions and faithful transmission of genetic material to progeny. A large body of evidence has accumulated, indicating that encounters between protein machineries carrying out DNA and RNA synthesis occur in vivo and may have important regulatory consequences. This feature may be exacerbated in the case of compact genomes, like the one of bacteriophage λ, used in our study. Transcription that starts at the rightward pR promoter and proceeds through the λ origin of replication and downstream of it was proven to stimulate the initiation of λ DNA replication. Here, we demonstrate that the activity of a convergently oriented pO promoter decreases the efficiency of transcription starting from pR. Our results show, however, that a lack of the functional pO promoter negatively influences λ phage and λ-derived plasmid replication. We present data, suggesting that this effect is evoked by the enhanced level of the pR-driven transcription, occurring in the presence of the defective pO, which may result in the impeded formation of the replication initiation complex. Our data suggest that the cross talk between the two promoters regulates λ DNA replication and coordinates transcription and replication processes.
Collapse
Affiliation(s)
- Paweł Olszewski
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland, Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza 59, 80-308 Gdańsk, Poland and Laboratory of Electron Microscopy, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | | | | | | | | | | |
Collapse
|
44
|
Gowetski DB, Kodis EJ, Kahn JD. Rationally designed coiled-coil DNA looping peptides control DNA topology. Nucleic Acids Res 2013; 41:8253-65. [PMID: 23825092 PMCID: PMC3783159 DOI: 10.1093/nar/gkt553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein–DNA nanostructures.
Collapse
Affiliation(s)
- Daniel B Gowetski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | | | | |
Collapse
|
45
|
Fulcrand G, Zhi X, Leng F. Transcription-coupled DNA supercoiling in defined protein systems and in E. coli topA mutant strains. IUBMB Life 2013; 65:615-22. [PMID: 23757201 DOI: 10.1002/iub.1179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 04/16/2013] [Indexed: 11/09/2022]
Abstract
Transcription by RNA polymerases can stimulate (-) DNA supercoiling both in vitro and in Escherichia coli topA strains. This phenomenon has been successfully explained by a "twin-supercoiled-domain" model of transcription in which (+) supercoils are produced in front of the transcribing RNA polymerase and (-) supercoils behind it. Previously, it has been shown that certain sequence-specific DNA-binding proteins potently stimulate transcription-coupled DNA supercoiling (TCDS) in an in vitro protein system. These results are consistent with a topological barrier model where certain nucleoprotein complexes can form topological barriers that impede the diffusion and merger of independent chromosomal supercoil domains. Indeed, recent biochemical and single-molecule results demonstrated the existence of nucleoprotein-based DNA topological barriers, which are capable of dividing a DNA molecule into different topological domains. Additionally, recent in vivo studies showed that a transcriptional ensemble (including the transcribing RNA polymerase and the RNA transcript) alone is sufficient to cause a change in local DNA superhelicity. This topological change in local chromosome structure should have a great impact on the conformation and function of critical DNA sequence elements, such as promoters and DNA replication origins. In this article, we will also review recent progress by which TCDS is a critical stimulating force to activate transcription initiation from weak promoters, such as the Salmonella typhimurium leu-500 promoter.
Collapse
Affiliation(s)
- Geraldine Fulcrand
- Department of Chemistry and Biochemistry, Florida International University, FL 33199, USA
| | | | | |
Collapse
|
46
|
Zhi X, Leng F. Dependence of transcription-coupled DNA supercoiling on promoter strength in Escherichia coli topoisomerase I deficient strains. Gene 2012. [PMID: 23201416 DOI: 10.1016/j.gene.2012.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA in vitro and in vivo. This phenomenon has been nicely explained by a "twin-supercoiled-domain" model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In Escherichia coli topA strains, DNA gyrase selectively converts the positively supercoiled domain into negative supercoils to produce hypernegatively supercoiled DNA. In this article, in order to examine whether promoter strength affects transcription-coupled DNA supercoiling (TCDS), we developed a two-plasmid system in which a linear, non-supercoiled plasmid was used to express lac repressor constitutively while a circular plasmid was used to gage TCDS in E. coli cells. Using this two-plasmid system, we found that TCDS in topA strains is dependent on promoter strength. We also demonstrated that transcription-coupled hypernegative supercoiling of plasmid DNA did not need the expression of a membrane-insertion protein for strong promoters; however, it might require co-transcriptional synthesis of a polypeptide. Furthermore, we found that for weak promoters the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. Our results can be explained by the "twin-supercoiled-domain" model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA.
Collapse
MESH Headings
- Base Sequence
- Blotting, Western
- DNA Topoisomerases, Type I/genetics
- DNA Topoisomerases, Type I/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Plasmids/genetics
- Promoter Regions, Genetic/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
Collapse
Affiliation(s)
- Xiaoduo Zhi
- Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | | |
Collapse
|
47
|
Vanderlinden W, Blunt M, David CC, Moucheron C, Kirsch-De Mesmaeker A, De Feyter S. Mesoscale DNA Structural Changes on Binding and Photoreaction with Ru[(TAP)2PHEHAT]2+. J Am Chem Soc 2012; 134:10214-21. [DOI: 10.1021/ja303091q] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Willem Vanderlinden
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Matthew Blunt
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Charlotte C. David
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| | - Cécile Moucheron
- Department of Chemistry, Laboratory
of Organic Chemistry and Photochemistry, Université Libre de Bruxelles, Avenue Franklin D. Roosevelt 50,
1050 Brussels, Belgium
| | - Andrée Kirsch-De Mesmaeker
- Department of Chemistry, Laboratory
of Organic Chemistry and Photochemistry, Université Libre de Bruxelles, Avenue Franklin D. Roosevelt 50,
1050 Brussels, Belgium
| | - Steven De Feyter
- Department of Chemistry, Laboratory
of Photochemistry and Spectroscopy, Division of Molecular Imaging
and Photonics, KU Leuven, Celestijnenlaan
200F, 3001 Leuven, Belgium
| |
Collapse
|