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Yao Q, Zhu L, Shi Z, Banerjee S, Chen C. Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression. Nat Struct Mol Biol 2025; 32:48-61. [PMID: 39152238 DOI: 10.1038/s41594-024-01377-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 07/24/2024] [Indexed: 08/19/2024]
Abstract
DNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise. Using ATMP-seq, we directly visualized transcription-dependent negative and positive twin-supercoiled domains around genes and mapped kilobase-resolution DNA supercoiling throughout the human genome. Remarkably, we discovered megabase-scale supercoiling domains (SDs) across all chromosomes that are modulated mainly by topoisomerases I and IIβ. Transcription activities, but not the consequent supercoiling accumulation in the local region, contribute to SD formation, indicating the long-range propagation of transcription-generated supercoiling. Genome-wide SDs colocalize with A/B compartments in both human and Drosophila cells but are distinct from topologically associating domains (TADs), with negative supercoiling accumulation at TAD boundaries. Furthermore, genome-wide DNA supercoiling varies between cell states and types and regulates human gene expression, underscoring the importance of supercoiling dynamics in chromatin regulation and function.
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MESH Headings
- Humans
- DNA, Superhelical/metabolism
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- Genome, Human
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type I/chemistry
- DNA Topoisomerases, Type I/genetics
- Animals
- Gene Expression Regulation
- Chromatin/metabolism
- Chromatin/chemistry
- DNA Topoisomerases, Type II/metabolism
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/chemistry
- Cell Nucleus/metabolism
- Transcription, Genetic
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Affiliation(s)
- Qian Yao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Linying Zhu
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhen Shi
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Subhadra Banerjee
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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2
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Li S, Vemuri C, Chen C. DNA topology: A central dynamic coordinator in chromatin regulation. Curr Opin Struct Biol 2024; 87:102868. [PMID: 38878530 PMCID: PMC11283972 DOI: 10.1016/j.sbi.2024.102868] [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: 12/21/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 07/29/2024]
Abstract
Double helical DNA winds around nucleosomes, forming a beads-on-a-string array that further contributes to the formation of high-order chromatin structures. The regulatory components of the chromatin, interacting intricately with DNA, often exploit the topological tension inherent in the DNA molecule. Recent findings shed light on, and simultaneously complicate, the multifaceted roles of DNA topology (also known as DNA supercoiling) in various aspects of chromatin regulation. Different studies may emphasize the dynamics of DNA topological tension across different scales, interacting with diverse chromatin factors such as nucleosomes, nucleic acid motors that propel DNA-tracking processes, and DNA topoisomerases. In this review, we consolidate recent studies and establish connections between distinct scientific discoveries, advancing our current understanding of chromatin regulation mediated by the supercoiling tension of the double helix. Additionally, we explore the implications of DNA topology and DNA topoisomerases in human diseases, along with their potential applications in therapeutic interventions.
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Affiliation(s)
- Shuai Li
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Charan Vemuri
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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3
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Norris V, Kayser C, Muskhelishvili G, Konto-Ghiorghi Y. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiol Rev 2023; 47:fuac049. [PMID: 36549664 DOI: 10.1093/femsre/fuac049] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.
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Affiliation(s)
- Vic Norris
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Clara Kayser
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - Yoan Konto-Ghiorghi
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
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4
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Schmidt P, Brandt D, Busche T, Kalinowski J. Characterization of Bacterial Transcriptional Regulatory Networks in Escherichia coli through Genome-Wide In Vitro Run-Off Transcription/RNA-seq (ROSE). Microorganisms 2023; 11:1388. [PMID: 37374890 DOI: 10.3390/microorganisms11061388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The global characterization of transcriptional regulatory networks almost exclusively uses in vivo conditions, thereby providing a snapshot on multiple regulatory interactions at the same time. To complement these approaches, we developed and applied a method for characterizing bacterial promoters genome-wide by in vitro transcription coupled to transcriptome sequencing specific for native 5'-ends of transcripts. This method, called ROSE (run-off transcription/RNA-sequencing), only requires chromosomal DNA, ribonucleotides, RNA polymerase (RNAP) core enzyme, and a specific sigma factor, recognizing the corresponding promoters, which have to be analyzed. ROSE was performed on E. coli K-12 MG1655 genomic DNA using Escherichia coli RNAP holoenzyme (including σ70) and yielded 3226 transcription start sites, 2167 of which were also identified in in vivo studies, and 598 were new. Many new promoters not yet identified by in vivo experiments might be repressed under the tested conditions. Complementary in vivo experiments with E. coli K-12 strain BW25113 and isogenic transcription factor gene knockout mutants of fis, fur, and hns were used to test this hypothesis. Comparative transcriptome analysis demonstrated that ROSE could identify bona fide promoters that were apparently repressed in vivo. In this sense, ROSE is well-suited as a bottom-up approach for characterizing transcriptional networks in bacteria and ideally complementary to top-down in vivo transcriptome studies.
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Affiliation(s)
- Pascal Schmidt
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - David Brandt
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
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5
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Brochu J, Vlachos-Breton É, Irsenco D, Drolet M. Characterization of a pathway of genomic instability induced by R-loops and its regulation by topoisomerases in E. coli. PLoS Genet 2023; 19:e1010754. [PMID: 37141391 DOI: 10.1371/journal.pgen.1010754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/16/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
The prototype enzymes of the ubiquitous type IA topoisomerases (topos) family are Escherichia coli topo I (topA) and topo III (topB). Topo I shows preference for relaxation of negative supercoiling and topo III for decatenation. However, as they could act as backups for each other or even share functions, strains lacking both enzymes must be used to reveal the roles of type IA enzymes in genome maintenance. Recently, marker frequency analysis (MFA) of genomic DNA from topA topB null mutants revealed a major RNase HI-sensitive DNA peak bordered by Ter/Tus barriers, sites of replication fork fusion and termination in the chromosome terminus region (Ter). Here, flow cytometry for R-loop-dependent replication (RLDR), MFA, R-loop detection with S9.6 antibodies, and microscopy were used to further characterize the mechanism and consequences of over-replication in Ter. It is shown that the Ter peak is not due to the presence of a strong origin for RLDR in Ter region; instead RLDR, which is partly inhibited by the backtracking-resistant rpoB*35 mutation, appears to contribute indirectly to Ter over-replication. The data suggest that RLDR from multiple sites on the chromosome increases the number of replication forks trapped at Ter/Tus barriers which leads to RecA-dependent DNA amplification in Ter and to a chromosome segregation defect. Overproducing topo IV, the main cellular decatenase, does not inhibit RLDR or Ter over-replication but corrects the chromosome segregation defect. Furthermore, our data suggest that the inhibition of RLDR by topo I does not require its C-terminal-mediated interaction with RNA polymerase. Overall, our data reveal a pathway of genomic instability triggered by R-loops and its regulation by various topos activities at different steps.
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Affiliation(s)
- Julien Brochu
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Canada
| | - Émilie Vlachos-Breton
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Canada
| | - Dina Irsenco
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Canada
| | - Marc Drolet
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Canada
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6
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Martin L, Neguembor MV, Cosma MP. Women’s contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization. Front Mol Biosci 2023; 10:1155825. [PMID: 37051322 PMCID: PMC10083264 DOI: 10.3389/fmolb.2023.1155825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 03/28/2023] Open
Abstract
One of the biggest paradoxes in biology is that human genome is roughly 2 m long, while the nucleus containing it is almost one million times smaller. To fit into the nucleus, DNA twists, bends and folds into several hierarchical levels of compaction. Still, DNA has to maintain a high degree of accessibility to be readily replicated and transcribed by proteins. How compaction and accessibility co-exist functionally in human cells is still a matter of debate. Here, we discuss how the torsional stress of the DNA helix acts as a buffer, regulating both chromatin compaction and accessibility. We will focus on chromatin supercoiling and on the emerging role of topoisomerases as pivotal regulators of genome organization. We will mainly highlight the major breakthrough studies led by women, with the intention of celebrating the work of this group that remains a minority within the scientific community.
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Affiliation(s)
- Laura Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Technical Contact, Guangzhou, China
- *Correspondence: Maria Victoria Neguembor, ; Maria Pia Cosma,
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- ICREA, Barcelona, Spain
- Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Lead Contact, Guangzhou, China
- *Correspondence: Maria Victoria Neguembor, ; Maria Pia Cosma,
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7
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Behle A, Dietsch M, Goldschmidt L, Murugathas W, Berwanger L, Burmester J, Yao L, Brandt D, Busche T, Kalinowski J, Hudson E, Ebenhöh O, Axmann I, Machné R. Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis. Nucleic Acids Res 2022; 50:12790-12808. [PMID: 36533444 PMCID: PMC9825172 DOI: 10.1093/nar/gkac1132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5'/3' gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.
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Affiliation(s)
| | | | - Louis Goldschmidt
- Institut f. Quantitative u. Theoretische Biologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Wandana Murugathas
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lutz C Berwanger
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jonas Burmester
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lun Yao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm, Sweden
| | - David Brandt
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Tobias Busche
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm, Sweden
| | - Oliver Ebenhöh
- Institut f. Quantitative u. Theoretische Biologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany,Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ilka M Axmann
- Institut f. Synthetische Mikrobiologie, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Rainer Machné
- To whom correspondence should be addressed. Tel: +49 211 81 12923;
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8
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Jaishankar J, Keshav A, Jayaram B, Chavan S, Srivastava P. Characterization of divergent promoters PmaiA and Phyd from Gordonia: Co-expression and regulation by CRP. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194843. [PMID: 35840055 DOI: 10.1016/j.bbagrm.2022.194843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Divergent promoters are often responsible for controlling gene expression of related genes of the same pathway or for coordinating regulation at different time points. There are relatively few reports on characterization of divergent promoters in bacteria. In the present study, microarray profiling was carried out to analyze gene expression during growth of Gordonia sp. IITR100, which led to the identification of 35 % of adjacent gene candidates that are divergently transcribed. We focus here on the in-depth characterization of one such pair of genes. Two divergent promoters, PmaiA and Phyd, drive the expression of genes encoding maleate cis-trans isomerase (maiA) and hydantoinase (hyd), respectively. Our findings reveal asymmetric promoter activity with higher activity in the reverse orientation (Phyd) as compared to the forward orientation (PmaiA). Minimal promoter region for each orientation was identified by deletion mapping. Deletion of a 5'-untranslated region of each gene resulted in an increase in promoter activity. A putative binding site for CRP (Catabolite Repressor Protein) transcription regulator was also identified in the 80 bp common regulatory region between the -35 hexamers of the two promoters. The results of this study suggest that CRP-mediated repression of PmaiA occurs only in the cells grown in glucose. Phyd, on the other hand, is not repressed by CRP. However, deletion of the CRP binding site located between -95 to -110 upstream to the transcription start site of the maiA gene resulted in increased activity of PmaiA and decreased activity of Phyd. A single CRP binding site, therefore, affects the two promoters differently.
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Affiliation(s)
- Jananee Jaishankar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Aditi Keshav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Bijjiga Jayaram
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Sourabh Chavan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India.
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Muskhelishvili G, Sobetzko P, Travers A. Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle? Biomolecules 2022; 12:biom12060831. [PMID: 35740956 PMCID: PMC9221221 DOI: 10.3390/biom12060831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/25/2023] Open
Abstract
In this article we describe the bacterial growth cycle as a closed, self-reproducing, or autopoietic circuit, reestablishing the physiological state of stationary cells initially inoculated in the growth medium. In batch culture, this process of self-reproduction is associated with the gradual decline in available metabolic energy and corresponding change in the physiological state of the population as a function of "travelled distance" along the autopoietic path. We argue that this directional alteration of cell physiology is both reflected in and supported by sequential gene expression along the chromosomal OriC-Ter axis. We propose that during the E. coli growth cycle, the spatiotemporal order of gene expression is established by coupling the temporal gradient of supercoiling energy to the spatial gradient of DNA thermodynamic stability along the chromosomal OriC-Ter axis.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Natural Sciences, Biology Program, Agricultural University of Georgia, 0159 Tbilisi, Georgia
- Correspondence:
| | - Patrick Sobetzko
- Synmikro, Loewe Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
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10
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Relationship between the Chromosome Structural Dynamics and Gene Expression—A Chicken and Egg Dilemma? Microorganisms 2022; 10:microorganisms10050846. [PMID: 35630292 PMCID: PMC9144111 DOI: 10.3390/microorganisms10050846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Prokaryotic transcription was extensively studied over the last half-century. A great deal of data has been accumulated regarding the control of gene expression by transcription factors regulating their target genes by binding at specific DNA sites. However, there is a significant gap between the mechanistic description of transcriptional control obtained from in vitro biochemical studies and the complexity of transcriptional regulation in the context of the living cell. Indeed, recent studies provide ample evidence for additional levels of complexity pertaining to the regulation of transcription in vivo, such as, for example, the role of the subcellular localization and spatial organization of different molecular components involved in the transcriptional control and, especially, the role of chromosome configurational dynamics. The question as to how the chromosome is dynamically reorganized under the changing environmental conditions and how this reorganization is related to gene expression is still far from being clear. In this article, we focus on the relationships between the chromosome structural dynamics and modulation of gene expression during bacterial adaptation. We argue that spatial organization of the bacterial chromosome is of central importance in the adaptation of gene expression to changing environmental conditions and vice versa, that gene expression affects chromosome dynamics.
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11
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Kiselev S, Markelova N, Masulis I. Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification. Front Mol Biosci 2021; 8:610453. [PMID: 33748186 PMCID: PMC7967276 DOI: 10.3389/fmolb.2021.610453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding regulatory RNAs (ncRNAs) comprise specialized group of essential genetically encoded biological molecules involved in the wide variety of cellular metabolic processes. The progressive increase in the number of newly identified ncRNAs and the defining of their genome location indicate their predominant nesting in intergenic regions and expression under the control of their own regulatory elements. At the same time, the regulation of ncRNA's transcription cannot be considered in isolation from the processes occurring in the immediate genetic environment. A number of experimental data indicate the notable impact of positional regulation of gene expression mediated by dynamic temporal DNA rearrangements accompanying transcription events in the vicinity of neighboring genes. This issue can be perceived as particularly significant for divergently transcribed ncRNAs being actually subjected to double regulatory pressure. Based on available results of RNAseq experiments for Escherichia coli, we screened out divergent ncRNAs and the adjacent genes for the exact positions of transcription start sites (TSSs) and relative efficiency of RNA production. This analysis revealed extension or shortening of some previously annotated ncRNAs resulting in modified secondary structure, confirmed stable expression of four ncRNAs annotated earlier as putative, and approved the possibility of expression of divergently transcribed ncRNAs containing repetitive extragenic palindromic (REP) elements. The biogenesis of secreted ncRNAs from divergently transcribed ffs, chiX, ralA, and ryhB is discussed taking into account positions of TSSs. Refinement of TSSs for the neighboring genes renders some ncRNAs as true antisense overlapping with 5'UTR of divergently transcribed mRNAs.
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12
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Inniss NL, Morrison DA. ComWΔ6 Stimulates Transcription of Pneumococcal Competence Genes in vitro. Front Mol Biosci 2020; 7:61. [PMID: 32435654 PMCID: PMC7218084 DOI: 10.3389/fmolb.2020.00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/24/2020] [Indexed: 11/28/2022] Open
Abstract
The alternative streptococcal σ-factor and master competence regulator, σX, stimulates transcription from competence promoters, in vitro. As the only known alternative σ-factor in streptococci, σX expression is tightly controlled in each species and has a specific physiological role. Pneumococcal transformation also requires the DNA binding activity of ComW, a known σX activator and stabilizer. Mutations to the housekeeping σ factor, σA, partially alleviate the ComW requirement, suggesting that ComW is a key player in the σ factor swap during the pneumococcal competence response. However, there is no evidence of a direct ComW - RNA polymerase interaction. Furthermore, if and how ComW functions directly at combox promoters is still unknown. Here we report that a DNA-binding ComW variant, ComΔ6, can stimulate transcription from σX promoters in vitro.
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Affiliation(s)
| | - Donald A. Morrison
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL, United States
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13
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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: 1.2] [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 .
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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
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14
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Defez R, Valenti A, Andreozzi A, Romano S, Ciaramella M, Pesaresi P, Forlani S, Bianco C. New Insights into Structural and Functional Roles of Indole-3-acetic acid (IAA): Changes in DNA Topology and Gene Expression in Bacteria. Biomolecules 2019; 9:biom9100522. [PMID: 31547634 PMCID: PMC6843775 DOI: 10.3390/biom9100522] [Citation(s) in RCA: 6] [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: 07/24/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 12/11/2022] Open
Abstract
: Indole-3-acetic acid (IAA) is a major plant hormone that affects many cellular processes in plants, bacteria, yeast, and human cells through still unknown mechanisms. In this study, we demonstrated that the IAA-treatment of two unrelated bacteria, the Ensifer meliloti 1021 and Escherichia coli, harboring two different host range plasmids, influences the supercoiled state of the two plasmid DNAs in vivo. Results obtained from in vitro assays show that IAA interacts with DNA, leading to DNA conformational changes commonly induced by intercalating agents. We provide evidence that IAA inhibits the activity of the type IA topoisomerase, which regulates the DNA topological state in bacteria, through the relaxation of the negative supercoiled DNA. In addition, we demonstrate that the treatment of E. meliloti cells with IAA induces the expression of some genes, including the ones related to nitrogen fixation. In contrast, these genes were significantly repressed by the treatment with novobiocin, which reduces the DNA supercoiling in bacterial cells. Taking into account the overall results reported, we hypothesize that the IAA action and the DNA structure/function might be correlated and involved in the regulation of gene expression. This work points out that checking whether IAA influences the DNA topology under physiological conditions could be a useful strategy to clarify the mechanism of action of this hormone, not only in plants but also in other unrelated organisms.
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Affiliation(s)
- Roberto Defez
- Istituto di Bioscienze e BioRisorse, via P. Castellino 111, 80131 Naples, Italy.
| | - Anna Valenti
- Istituto di Bioscienze e BioRisorse, via P. Castellino 111, 80131 Naples, Italy.
| | - Anna Andreozzi
- Istituto di Bioscienze e BioRisorse, via P. Castellino 111, 80131 Naples, Italy.
| | - Silvia Romano
- Istituto di Bioscienze e BioRisorse, via P. Castellino 111, 80131 Naples, Italy.
| | - Maria Ciaramella
- Istituto di Bioscienze e BioRisorse, via P. Castellino 111, 80131 Naples, Italy.
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy.
| | - Sara Forlani
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy.
| | - Carmen Bianco
- Istituto di Bioscienze e BioRisorse, via P. Castellino 111, 80131 Naples, Italy.
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15
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Rivera-Osorio A, Osorio A, Poggio S, Dreyfus G, Camarena L. Architecture of divergent flagellar promoters controlled by CtrA in Rhodobacter sphaeroides. BMC Microbiol 2018; 18:129. [PMID: 30305031 PMCID: PMC6180460 DOI: 10.1186/s12866-018-1264-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhodobacter sphaeroides has two sets of flagellar genes, fla1 and fla2, that are responsible for the synthesis of two different flagellar structures. The expression of the fla2 genes is under control of CtrA. In several α-proteobacteria CtrA is also required for the expression of the flagellar genes, but the architecture of CtrA-dependent promoters has only been studied in detail in Caulobacter crescentus. In many cases the expression of fla genes originates from divergent promoters located a few base pairs apart, suggesting a particular arrangement of the cis-acting sites. RESULTS Here we characterized several control regions of the R. sphaeroides fla2 genes and analyzed in detail two regions containing the divergent promoters flgB2p-fliI2p, and fliL2p-fliF2p. Binding sites for CtrA of these promoters were identified in silico and tested by site directed mutagenesis. We conclude that each one of these promoter regions has a particular arrangement, either a single CtrA binding site for activation of fliL2p and fliF2p, or two independent sites for activation of flgB2p and fliI2p. ChIP experiments confirmed that CtrA binds to the control region containing the flgB2 and fliI2 promoters, supporting the notion that CtrA directly controls the expression of the fla2 genes. The flgB and fliI genes are syntenic and show a short intercistronic region in closely related bacterial species. We analyzed these regions and found that the arrangement of the CtrA binding sites varies considerably. CONCLUSIONS The results in this work reveal the arrangement of the fla2 divergent promoters showing that CtrA promotes transcriptional activation using more than a single architecture.
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Affiliation(s)
- Anet Rivera-Osorio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Aurora Osorio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Sebastian Poggio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
| | - Georges Dreyfus
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México.
| | - Laura Camarena
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México.
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Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli. Sci Rep 2018; 8:14759. [PMID: 30282997 PMCID: PMC6170449 DOI: 10.1038/s41598-018-33089-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
The E. coli gyrA promoter (PgyrA) is a DNA supercoiling sensitive promoter, stimulated by relaxation of DNA templates, and inhibited by (−) DNA supercoiling in bacteria. However, whether PgyrA can be inhibited by transient and localized transcription-coupled DNA supercoiling (TCDS) has not been fully examined. In this paper, using different DNA templates including the E. coli chromosome, we show that transient and localized TCDS strongly inhibits PgyrA in E. coli. This result can be explained by a twin-supercoiled domain model of transcription in which (+) and (−) supercoiled domains are generated around the transcribing RNA polymerase. We also find that fluoroquinolones, such as ciprofloxacin, can substantially increase the expression of the firefly luciferase under the control of the PgyrA coupled to a divergent IPTG-inducible promoter in the presence of IPTG. This stimulation of PgyrA by fluoroquinolones can be also explained by the twin-supercoiled domain model of transcription. This unique property of TCDS may be configured into a high throughput-screening (HTS) assay to identify antimicrobial compounds targeting bacterial DNA gyrase.
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Tinkering with Osmotically Controlled Transcription Allows Enhanced Production and Excretion of Ectoine and Hydroxyectoine from a Microbial Cell Factory. Appl Environ Microbiol 2018; 84:AEM.01772-17. [PMID: 29101191 DOI: 10.1128/aem.01772-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/28/2017] [Indexed: 12/21/2022] Open
Abstract
Ectoine and hydroxyectoine are widely synthesized by members of the Bacteria and a few members of the Archaea as potent osmostress protectants. We have studied the salient features of the osmostress-responsive promoter directing the transcription of the ectoine/hydroxyectoine biosynthetic gene cluster from the plant-root-associated bacterium Pseudomonas stutzeri by transferring it into Escherichia coli, an enterobacterium that does not produce ectoines naturally. Using ect-lacZ reporter fusions, we found that the heterologous ect promoter reacted with exquisite sensitivity in its transcriptional profile to graded increases in sustained high salinity, responded to a true osmotic signal, and required the buildup of an osmotically effective gradient across the cytoplasmic membrane for its induction. The involvement of the -10, -35, and spacer regions of the sigma-70-type ect promoter in setting promoter strength and response to osmotic stress was assessed through site-directed mutagenesis. Moderate changes in the ect promoter sequence that increase its resemblance to housekeeping sigma-70-type promoters of E. coli afforded substantially enhanced expression, both in the absence and in the presence of osmotic stress. Building on this set of ect promoter mutants, we engineered an E. coli chassis strain for the heterologous production of ectoines. This synthetic cell factory lacks the genes for the osmostress-responsive synthesis of trehalose and the compatible solute importers ProP and ProU, and it continuously excretes ectoines into the growth medium. By combining appropriate host strains and different plasmid variants, excretion of ectoine, hydroxyectoine, or a mixture of both compounds was achieved under mild osmotic stress conditions.IMPORTANCE Ectoines are compatible solutes, organic osmolytes that are used by microorganisms to fend off the negative consequences of high environmental osmolarity on cellular physiology. An understanding of the salient features of osmostress-responsive promoters directing the expression of the ectoine/hydroxyectoine biosynthetic gene clusters is lacking. We exploited the ect promoter from an ectoine/hydroxyectoine-producing soil bacterium for such a study by transferring it into a surrogate bacterial host. Despite the fact that E. coli does not synthesize ectoines naturally, the ect promoter retained its exquisitely sensitive osmotic control, indicating that osmoregulation of ect transcription is an inherent feature of the promoter and its flanking sequences. These sequences were narrowed to a 116-bp DNA fragment. Ectoines have interesting commercial applications. Building on data from a site-directed mutagenesis study of the ect promoter, we designed a synthetic cell factory that secretes ectoine, hydroxyectoine, or a mixture of both compounds into the growth medium.
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