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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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2
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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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Muskhelishvili G, Sobetzko P, Mehandziska S, Travers A. Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors. Biomolecules 2021; 11:biom11070924. [PMID: 34206477 PMCID: PMC8301835 DOI: 10.3390/biom11070924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
The coordination of bacterial genomic transcription involves an intricate network of interdependent genes encoding nucleoid-associated proteins (NAPs), DNA topoisomerases, RNA polymerase subunits and modulators of transcription machinery. The central element of this homeostatic regulatory system, integrating the information on cellular physiological state and producing a corresponding transcriptional response, is the multi-subunit RNA polymerase (RNAP) holoenzyme. In this review article, we argue that recent observations revealing DNA topoisomerases and metabolic enzymes associated with RNAP supramolecular complex support the notion of structural coupling between transcription machinery, DNA topology and cellular metabolism as a fundamental device coordinating the spatiotemporal genomic transcription. We analyse the impacts of various combinations of RNAP holoenzymes and global transcriptional regulators such as abundant NAPs, on genomic transcription from this viewpoint, monitoring the spatiotemporal patterns of couplons—overlapping subsets of the regulons of NAPs and RNAP sigma factors. We show that the temporal expression of regulons is by and large, correlated with that of cognate regulatory genes, whereas both the spatial organization and temporal expression of couplons is distinctly impacted by the regulons of NAPs and sigma factors. We propose that the coordination of the growth phase-dependent concentration gradients of global regulators with chromosome configurational dynamics determines the spatiotemporal patterns of genomic expression.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Natural Sciences, Agricultural University of Georgia, David Aghmashenebeli Alley 24, Tbilisi 0159, Georgia
- Correspondence:
| | - Patrick Sobetzko
- Department of Chromosome Biology, Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043 Marburg, Germany;
| | - Sanja Mehandziska
- School of Engineering and Science, Campus Ring 1, Jacobs University Bremen, 28759 Bremen, Germany;
| | - 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
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4
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Japaridze A, Yang W, Dekker C, Nasser W, Muskhelishvili G. DNA sequence-directed cooperation between nucleoid-associated proteins. iScience 2021; 24:102408. [PMID: 33997690 PMCID: PMC8099737 DOI: 10.1016/j.isci.2021.102408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/05/2021] [Accepted: 04/06/2021] [Indexed: 02/01/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilizing higher-order nucleoprotein complexes in the bacterial chromosome. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding site arrangements. We find that spatial organization of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiation within the bacterial chromosome. The location of protein binding sites along DNA is important for 3D organization FIS protein forms DNA loops while H-NS forms compact DNA plectonemes FIS DNA loops inhibit H-NS from spreading over the DNA FIS and H-NS competition creates regions of ‘open’ and ‘closed’ DNA
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Affiliation(s)
- Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Georgi Muskhelishvili
- School of Natural Sciences, Agricultural University of Georgia, Davit Aghmashenebeli Alley 240, 0159 Tbilisi, Georgia
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Travers A, Muskhelishvili G. Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0016-2019. [PMID: 32056535 PMCID: PMC11168577 DOI: 10.1128/ecosalplus.esp-0016-2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Indexed: 12/22/2022]
Abstract
In this article, we summarize our current understanding of the bacterial genetic regulation brought about by decades of studies using the Escherichia coli model. It became increasingly evident that the cellular genetic regulation system is organizationally closed, and a major challenge is to describe its circular operation in quantitative terms. We argue that integration of the DNA analog information (i.e., the probability distribution of the thermodynamic stability of base steps) and digital information (i.e., the probability distribution of unique triplets) in the genome provides a key to understanding the organizational logic of genetic control. During bacterial growth and adaptation, this integration is mediated by changes of DNA supercoiling contingent on environmentally induced shifts in intracellular ionic strength and energy charge. More specifically, coupling of dynamic alterations of the local intrinsic helical repeat in the structurally heterogeneous DNA polymer with structural-compositional changes of RNA polymerase holoenzyme emerges as a fundamental organizational principle of the genetic regulation system. We present a model of genetic regulation integrating the genomic pattern of DNA thermodynamic stability with the gene order and function along the chromosomal OriC-Ter axis, which acts as a principal coordinate system organizing the regulatory interactions in the genome.
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Affiliation(s)
- Andrew Travers
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
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Chechetkin VR, Lobzin VV. Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique. J Theor Biol 2017; 426:162-179. [PMID: 28552553 DOI: 10.1016/j.jtbi.2017.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 04/23/2017] [Accepted: 05/23/2017] [Indexed: 12/15/2022]
Abstract
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT). DDFT serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding. The method is versatile and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy. The latter characteristic is closely related to the replication and transcription and can also be used for the assessment of temperature or supercoiling effects on the chromosome folding. We tested the method on the genome of E. coli K-12 and found good correspondence with the annotated domains/units established experimentally. As a brief illustration of further abilities of DDFT, the study of large-scale genome organization for bacteriophage PHIX174 and bacterium Caulobacter crescentus was also added. The combined experimental, modeling, and bioinformatic DDFT analysis should yield more complete knowledge on the chromosome architecture and genome organization.
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Affiliation(s)
- V R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilov str., 32, Moscow 119334, Russia; Theoretical Department of Division for Perspective Investigations, Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI), Moscow, Troitsk District 108840, Russia.
| | - V V Lobzin
- School of Physics, University of Sydney, Sydney, NSW 2006, Australia.
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7
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Japaridze A, Renevey S, Sobetzko P, Stoliar L, Nasser W, Dietler G, Muskhelishvili G. Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein. J Biol Chem 2017; 292:7607-7618. [PMID: 28316324 PMCID: PMC5418058 DOI: 10.1074/jbc.m117.780239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/11/2017] [Indexed: 11/28/2022] Open
Abstract
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.
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Affiliation(s)
- Aleksandre Japaridze
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | - Sylvain Renevey
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | | | | | - William Nasser
- UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003 INSA Lyon, Villeurbanne F-69621, France, and
| | - Giovanni Dietler
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland,
| | - Georgi Muskhelishvili
- Jacobs University, D-28759 Bremen, Germany, .,Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159 Tbilisi, Republik of Georgia
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8
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Genes on a Wire: The Nucleoid-Associated Protein HU Insulates Transcription Units in Escherichia coli. Sci Rep 2016; 6:31512. [PMID: 27545593 PMCID: PMC4992867 DOI: 10.1038/srep31512] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/21/2016] [Indexed: 01/06/2023] Open
Abstract
The extent to which chromosomal gene position in prokaryotes affects local gene expression remains an open question. Several studies have shown that chromosomal re-positioning of bacterial transcription units does not alter their expression pattern, except for a general decrease in gene expression levels from chromosomal origin to terminus proximal positions, which is believed to result from gene dosage effects. Surprisingly, the question as to whether this chromosomal context independence is a cis encoded property of a bacterial transcription unit, or if position independence is a property conferred by factors acting in trans, has not been addressed so far. For this purpose, we established a genetic test system assessing the chromosomal positioning effects by means of identical promoter-fluorescent reporter gene fusions inserted equidistantly from OriC into both chromosomal replichores of Escherichia coli K-12. Our investigations of the reporter activities in mutant cells lacking the conserved nucleoid associated protein HU uncovered various drastic chromosomal positional effects on gene transcription. In addition we present evidence that these positional effects are caused by transcriptional activity nearby the insertion site of our reporter modules. We therefore suggest that the nucleoid-associated protein HU is functionally insulating transcription units, most likely by constraining transcription induced DNA supercoiling.
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9
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Finzi L, Dunlap D. Supercoiling biases the formation of loops involved in gene regulation. Biophys Rev 2016; 8:65-74. [PMID: 28510212 DOI: 10.1007/s12551-016-0211-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/17/2016] [Indexed: 11/25/2022] Open
Abstract
The function of DNA as a repository of genetic information is well-known. The post-genomic effort is to understand how this information-containing filament is chaperoned to manage its compaction and topological states. Indeed, the activities of enzymes that transcribe, replicate, or repair DNA are regulated to a large degree by access. Proteins that act at a distance along the filament by binding at one site and contacting another site, perhaps as part of a bigger complex, create loops that constitute topological domains and influence regulation. DNA loops and plectonemes are not necessarily spontaneous, especially large loops under tension for which high energy is required to bring their ends together, or small loops that require accessory proteins to facilitate DNA bending. However, the torsion in stiff filaments such as DNA dramatically modulates the topology, driving it from extended and genetically accessible to more looped and compact, genetically secured forms. Furthermore, there are accessory factors that bias the response of the DNA filament to supercoiling. For example, small molecules like polyamines, which neutralize the negative charge repulsions along the phosphate backbone, enhance flexibility and promote writhe over twist in response to torsion. Such increased flexibility likely pushes the topological equilibrium from twist toward writhe at tensions thought to exist in vivo. A predictable corollary is that stiffening DNA antagonizes looping and bending. Certain sequences are known to be more or less flexible or to exhibit curvature, and this may affect interactions with binding proteins. In vivo all of these factors operate simultaneously on DNA that is generally negatively supercoiled to some degree. Therefore, in order to better understand gene regulation that involves protein-mediated DNA loops, it is critical to understand the thermodynamics and kinetics of looping in DNA that is under tension, negatively supercoiled, and perhaps exposed to molecules that alter elasticity. Recent experiments quantitatively reveal how much negatively supercoiling DNA lowers the free energy of looping, possibly biasing the operation of genetic switches.
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Affiliation(s)
- Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr. N.E., Atlanta, GA, 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr. N.E., Atlanta, GA, 30322, USA.
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Nigatu D, Henkel W, Sobetzko P, Muskhelishvili G. Relationship between digital information and thermodynamic stability in bacterial genomes. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2016; 2016:4. [PMID: 26877724 PMCID: PMC4740571 DOI: 10.1186/s13637-016-0037-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/19/2016] [Indexed: 02/06/2023]
Abstract
Ever since the introduction of the Watson-Crick model, numerous efforts have been made to fully characterize the digital information content of the DNA. However, it became increasingly evident that variations of DNA configuration also provide an “analog” type of information related to the physicochemical properties of the DNA, such as thermodynamic stability and supercoiling. Hence, the parallel investigation of the digital information contained in the base sequence with associated analog parameters is very important for understanding the coding capacity of the DNA. In this paper, we represented analog information by its thermodynamic stability and compare it with digital information using Shannon and Gibbs entropy measures on the complete genome sequences of several bacteria, including Escherichia coli (E. coli), Bacillus subtilis (B. subtilis), Streptomyces coelicolor (S. coelicolor), and Salmonella typhimurium (S. typhimurium). Furthermore, the link to the broader classes of functional gene groups (anabolic and catabolic) is examined. Obtained results demonstrate the couplings between thermodynamic stability and digital sequence organization in the bacterial genomes. In addition, our data suggest a determinative role of the genome-wide distribution of DNA thermodynamic stability in the spatial organization of functional gene groups.
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Affiliation(s)
- Dawit Nigatu
- Transmission Systems Group, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, Bremen, 28759 Germany
| | - Werner Henkel
- Transmission Systems Group, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, Bremen, 28759 Germany
| | - Patrick Sobetzko
- Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, Mehrzweckgebäude, Marburg, 35043 Germany
| | - Georgi Muskhelishvili
- Microbiologie, Adaptation, Pathogénie, UMR5240 CNRS-UCBL-INSA-BayerCropScience, Lyon, France ; Jacobs University Bremen, Campus Ring 1, Bremen, 28759 Germany
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Travers A, Muskhelishvili G. DNA structure and function. FEBS J 2015; 282:2279-95. [PMID: 25903461 DOI: 10.1111/febs.13307] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/26/2015] [Accepted: 04/21/2015] [Indexed: 12/11/2022]
Abstract
The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.
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Affiliation(s)
- Andrew Travers
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Biochemistry, University of Cambridge, UK
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12
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Chromosomal "stress-response" domains govern the spatiotemporal expression of the bacterial virulence program. mBio 2015; 6:e00353-15. [PMID: 25922390 PMCID: PMC4436070 DOI: 10.1128/mbio.00353-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies strongly suggest that the gene expression sustaining both normal and pathogenic bacterial growth is governed by the structural dynamics of the chromosome. However, the mechanistic device coordinating the chromosomal configuration with selective expression of the adaptive traits remains largely unknown. We used a holistic approach exploring the inherent relationships between the physicochemical properties of the DNA and the expression of adaptive traits, including virulence factors, in the pathogen Dickeya dadantii (formerly Erwinia chrysanthemi). In the transcriptomes obtained under adverse conditions encountered during bacterial infection, we explored the patterns of chromosomal DNA sequence organization, supercoil dynamics, and gene expression densities, together with the long-range regulatory impacts of the abundant DNA architectural proteins implicated in pathogenicity control. By integrating these data, we identified transient chromosomal domains of coherent gene expression featuring distinct couplings between DNA thermodynamic stability, supercoil dynamics, and virulence traits. We infer that the organization of transient chromosomal domains serving specific functions acts as a fundamental device for versatile adjustment of the pathogen to environmental stress. We believe that the identification of chromosomal “stress-response” domains harboring distinct virulence traits and mediating the cellular adaptive behavior provides a breakthrough in understanding the control mechanisms of bacterial pathogenicity.
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Muskhelishvili G, Travers A. Order from the Order: How a Spatiotemporal Genetic Program Is Encoded in a 2-D Genetic Map of the Bacterial Chromosome. J Mol Microbiol Biotechnol 2015; 24:332-43. [DOI: 10.1159/000368852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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14
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Travers A. Dynamic DNA underpins chromosome dynamics. Biophys J 2014; 105:2235-7. [PMID: 24268134 DOI: 10.1016/j.bpj.2013.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/01/2013] [Indexed: 11/16/2022] Open
Abstract
A recent article by Meyer and co-workers provides a detailed description of the dynamics of base-step conformational transitions and of the first steps to the basepair opening. These results underpin the essential role that DNA dynamics place in the DNA structural transitions that accompany the active processes of transcription, replication, and recombination in bacterial and eukaryotic chromatin.
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Affiliation(s)
- Andrew Travers
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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15
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Muskhelishvili G, Travers A. Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell Mol Life Sci 2013; 70:4555-67. [PMID: 23771629 PMCID: PMC11113758 DOI: 10.1007/s00018-013-1394-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 11/29/2022]
Abstract
Understanding genetic regulation is a problem of fundamental importance. Recent studies have made it increasingly evident that, whereas the cellular genetic regulation system embodies multiple disparate elements engaged in numerous interactions, the central issue is the genuine function of the DNA molecule as information carrier. Compelling evidence suggests that the DNA, in addition to the digital information of the linear genetic code (the semantics), encodes equally important continuous, or analog, information that specifies the structural dynamics and configuration (the syntax) of the polymer. These two DNA information types are intrinsically coupled in the primary sequence organisation, and this coupling is directly relevant to regulation of the genetic function. In this review, we emphasise the critical need of holistic integration of the DNA information as a prerequisite for understanding the organisational complexity of the genetic regulation system.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany,
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Abstract
The Topological Aspects of DNA Function and Protein Folding international meeting provided an interdisciplinary forum for biological scientists, physicists and mathematicians to discuss recent developments in the application of topology to the study of DNA and protein structure. It had 111 invited participants, 48 talks and 21 posters. The present article discusses the importance of topology and introduces the articles from the meeting's speakers.
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Sobetzko P, Glinkowska M, Travers A, Muskhelishvili G. DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle. MOLECULAR BIOSYSTEMS 2013; 9:1643-51. [PMID: 23493878 DOI: 10.1039/c3mb25515h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The chromosomal DNA polymer constituting the cellular genetic material is primarily a device for coding information. Whilst the gene sequences comprise the digital (discontinuous) linear code, physiological alterations of the DNA superhelical density generate in addition analog (continuous) three-dimensional information essential for regulation of both chromosome compaction and gene expression. Insight into the relationship between the DNA analog information and the digital linear code is of fundamental importance for understanding genetic regulation. Our previous study in the model organism Escherichia coli suggested that the chromosomal gene order and a spatiotemporal gradient of DNA superhelicity associated with DNA replication determine the growth phase-dependent gene transcription. In this study we reveal a general gradient of DNA thermodynamic stability correlated with the polarity of chromosomal replication and manifest in the spatiotemporal pattern of gene transcription during the bacterial growth cycle. Furthermore, by integrating the physical and dynamic features of the transcribed sequences with their functional content we identify spatiotemporal domains of gene expression encompassing different functions. We thus provide both an insight into the organisational principle of the bacterial growth program and a novel holistic methodology for exploring chromosomal dynamics.
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Affiliation(s)
- Patrick Sobetzko
- Jacobs University Bremen, School of Engineering and Science, Campus Ring 1, D-28759 Bremen, Germany
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