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Van Hofwegen DJ, Hovde CJ, Minnich SA. Comparison of Yersinia enterocolitica DNA Methylation at Ambient and Host Temperatures. EPIGENOMES 2023; 7:30. [PMID: 38131902 PMCID: PMC10742451 DOI: 10.3390/epigenomes7040030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogenic bacteria recognize environmental cues to vary gene expression for host adaptation. Moving from ambient to host temperature, Yersinia enterocolitica responds by immediately repressing flagella synthesis and inducing the virulence plasmid (pYV)-encoded type III secretion system. In contrast, shifting from host to ambient temperature requires 2.5 generations to restore motility, suggesting a link to the cell cycle. We hypothesized that differential DNA methylation contributes to temperature-regulated gene expression. We tested this hypothesis by comparing single-molecule real-time (SMRT) sequencing of Y. enterocolitica DNA from cells growing exponentially at 22 °C and 37 °C. The inter-pulse duration ratio rather than the traditional QV scoring was the kinetic metric to compare DNA from cells grown at each temperature. All 565 YenI restriction sites were fully methylated at both temperatures. Among the 27,118 DNA adenine methylase (Dam) sites, 42 had differential methylation patterns, while 17 remained unmethylated regardless of the temperature. A subset of the differentially methylated Dam sites localized to promoter regions of predicted regulatory genes including LysR-type and PadR-like transcriptional regulators and a cyclic-di-GMP phosphodiesterase. The unmethylated Dam sites localized with a bias to the replication terminus, suggesting they were protected from Dam methylase. No cytosine methylation was detected at Dcm sites.
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Affiliation(s)
| | | | - Scott A. Minnich
- Department of Animal Veterinary and Food Science, University of Idaho, Moscow, ID 83843, USA; (D.J.V.H.); (C.J.H.)
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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: 0.5] [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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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: 2.5] [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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Viviani A, Ventimiglia M, Fambrini M, Vangelisti A, Mascagni F, Pugliesi C, Usai G. Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 2021; 210:104566. [PMID: 34718084 DOI: 10.1016/j.biosystems.2021.104566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy.
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
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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: 2.7] [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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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: 2.3] [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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Chromosomal organization of transcription: in a nutshell. Curr Genet 2017; 64:555-565. [PMID: 29184972 DOI: 10.1007/s00294-017-0785-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 01/25/2023]
Abstract
Early studies of transcriptional regulation focused on individual gene promoters defined specific transcription factors as central agents of genetic control. However, recent genome-wide data propelled a different view by linking spatially organized gene expression patterns to chromosomal dynamics. Therefore, the major problem in contemporary molecular genetics concerned with transcriptional gene regulation is to establish a unifying model that reconciles these two views. This problem, situated at the interface of polymer physics and network theory, requires development of an integrative methodology. In this review, we discuss recent achievements in classical model organism E. coli and provide some novel insights gained from studies of a bacterial plant pathogen, D. dadantii. We consider DNA topology and the basal transcription machinery as key actors of regulation, in which activation of functionally relevant genes is coupled to and coordinated with the establishment of extended chromosomal domains of coherent transcription. We argue that the spatial organization of genome plays a fundamental role in its own regulation.
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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.
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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.
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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: 1.1] [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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Gerganova V, Berger M, Zaldastanishvili E, Sobetzko P, Lafon C, Mourez M, Travers A, Muskhelishvili G. Chromosomal position shift of a regulatory gene alters the bacterial phenotype. Nucleic Acids Res 2015; 43:8215-26. [PMID: 26170236 PMCID: PMC4751926 DOI: 10.1093/nar/gkv709] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
Recent studies strongly suggest that in bacterial cells the order of genes along the chromosomal origin-to-terminus axis is determinative for regulation of the growth phase-dependent gene expression. The prediction from this observation is that positional displacement of pleiotropic genes will affect the genetic regulation and hence, the cellular phenotype. To test this prediction we inserted the origin-proximal dusB-fis operon encoding the global regulator FIS in the vicinity of replication terminus on both arms of the Escherichia coli chromosome. We found that the lower fis gene dosage in the strains with terminus-proximal dusB-fis operons was compensated by increased fis expression such that the intracellular concentration of FIS was homeostatically adjusted. Nevertheless, despite unchanged FIS levels the positional displacement of dusB-fis impaired the competitive growth fitness of cells and altered the state of the overarching network regulating DNA topology, as well as the cellular response to environmental stress, hazardous substances and antibiotics. Our finding that the chromosomal repositioning of a regulatory gene can determine the cellular phenotype unveils an important yet unexplored facet of the genetic control mechanisms and paves the way for novel approaches to manipulate bacterial physiology.
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Affiliation(s)
- Veneta Gerganova
- Jacobs University Bremen, School of Engineering and Science, Bremen, 28758, Germany
| | - Michael Berger
- Institut für Hygiene, Universitätsklinikum Münster, Münster, 48149, Germany
| | | | - Patrick Sobetzko
- Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Department of Chromosome Biology, Marburg, 35032, Germany
| | - Corinne Lafon
- SANOFI/ TSU Infectious Diseases, Toulouse, 31036, France
| | - Michael Mourez
- SANOFI/ TSU Infectious Diseases, Toulouse, 31036, France
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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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: 103] [Impact Index Per Article: 11.4] [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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Scolari VF, Sclavi B, Cosentino Lagomarsino M. The nucleoid as a smart polymer. Front Microbiol 2015; 6:424. [PMID: 26005440 PMCID: PMC4424877 DOI: 10.3389/fmicb.2015.00424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/21/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
- Vittore F Scolari
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France
| | - Bianca Sclavi
- Centre National de la Recherche Scientifique, LBPA, UMR 8113, ENS Cachan Cachan, France
| | - Marco Cosentino Lagomarsino
- Computational and Quantitative Biology, Sorbonne Universités, UPMC Univ Paris 06, UMR 7238 Paris, France ; Centre National de la Recherche Scientifique, UMR 7238 Paris, France
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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: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abstract
A periodic bias in nucleotide frequency with a period of about 11 bp is characteristic for bacterial genomes. This signal is commonly interpreted to relate to the helical pitch of negatively supercoiled DNA. Functions in supercoiling-dependent RNA transcription or as a 'structural code' for DNA packaging have been suggested. Cyanobacterial genomes showed especially strong periodic signals and, on the other hand, DNA supercoiling and supercoiling-dependent transcription are highly dynamic and underlie circadian rhythms of these phototrophic bacteria. Focusing on this phylum and dinucleotides, we find that a minimal motif of AT-tracts (AT2) yields the strongest signal. Strong genome-wide periodicity is ancestral to a clade of unicellular and polyploid species but lost upon morphological transitions into two baeocyte-forming and a symbiotic species. The signal is intermediate in heterocystous species and weak in monoploid picocyanobacteria. A pronounced 'structural code' may support efficient nucleoid condensation and segregation in polyploid cells. The major source of the AT2 signal are protein-coding regions, where it is encoded preferentially in the first and third codon positions. The signal shows only few relations to supercoiling-dependent and diurnal RNA transcription in Synechocystis sp. PCC 6803. Strong and specific signals in two distinct transposons suggest roles in transposase transcription and transpososome formation.
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Affiliation(s)
- Robert Lehmann
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany
| | - Rainer Machné
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090, Vienna, Austria
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt University, Berlin, Invalidenstraße 43, D-10115, Berlin, Germany
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