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Benham CJ. DNA superhelicity. Nucleic Acids Res 2024; 52:22-48. [PMID: 37994702 PMCID: PMC10783518 DOI: 10.1093/nar/gkad1092] [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: 03/26/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
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Affiliation(s)
- Craig J Benham
- UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
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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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3
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Reverchon S, Meyer S, Forquet R, Hommais F, Muskhelishvili G, Nasser W. The nucleoid-associated protein IHF acts as a 'transcriptional domainin' protein coordinating the bacterial virulence traits with global transcription. Nucleic Acids Res 2021; 49:776-790. [PMID: 33337488 PMCID: PMC7826290 DOI: 10.1093/nar/gkaa1227] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 02/04/2023] Open
Abstract
Bacterial pathogenic growth requires a swift coordination of pathogenicity function with various kinds of environmental stress encountered in the course of host infection. Among the factors critical for bacterial adaptation are changes of DNA topology and binding effects of nucleoid-associated proteins transducing the environmental signals to the chromosome and coordinating the global transcriptional response to stress. In this study, we use the model phytopathogen Dickeya dadantii to analyse the organisation of transcription by the nucleoid-associated heterodimeric protein IHF. We inactivated the IHFα subunit of IHF thus precluding the IHFαβ heterodimer formation and determined both phenotypic effects of ihfA mutation on D. dadantii virulence and the transcriptional response under various conditions of growth. We show that ihfA mutation reorganises the genomic expression by modulating the distribution of chromosomal DNA supercoils at different length scales, thus affecting many virulence genes involved in both symptomatic and asymptomatic phases of infection, including those required for pectin catabolism. Altogether, we propose that IHF heterodimer is a 'transcriptional domainin' protein, the lack of which impairs the spatiotemporal organisation of transcriptional stress-response domains harbouring various virulence traits, thus abrogating the pathogenicity of D. dadantii.
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Affiliation(s)
- Sylvie Reverchon
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, F-69622, France
| | - Sam Meyer
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, F-69622, France
| | - Raphaël Forquet
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, F-69622, France
| | - Florence Hommais
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, F-69622, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - William Nasser
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240 MAP, F-69622, France
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4
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Sutthibutpong T, Matek C, Benham C, Slade GG, Noy A, Laughton C, K Doye JP, Louis AA, Harris SA. Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation. Nucleic Acids Res 2016; 44:9121-9130. [PMID: 27664220 PMCID: PMC5100592 DOI: 10.1093/nar/gkw815] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/03/2016] [Indexed: 12/14/2022] Open
Abstract
It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
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Affiliation(s)
- Thana Sutthibutpong
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Craig Benham
- UC Davis Genome Centre, Health Sciences Drive, Davis, CA 95616, USA
| | - Gabriel G Slade
- Department of Physics, São Paulo State University, Rua Cristovão, São José do Rio Preto, SP 15054-000, Brazil
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD, UK
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK .,Astbury Centre for Structural and Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
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5
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Abstract
This review focuses on more recent studies concerning the systems biology of branched-chain amino acid biosynthesis, that is, the pathway-specific and global metabolic and genetic regulatory networks that enable the cell to adjust branched-chain amino acid synthesis rates to changing nutritional and environmental conditions. It begins with an overview of the enzymatic steps and metabolic regulatory mechanisms of the pathways and descriptions of the genetic regulatory mechanisms of the individual operons of the isoleucine-leucine-valine (ilv) regulon. This is followed by more-detailed discussions of recent evidence that global control mechanisms that coordinate the expression of the operons of this regulon with one another and the growth conditions of the cell are mediated by changes in DNA supercoiling that occur in response to changes in cellular energy charge levels that, in turn, are modulated by nutrient and environmental signals. Since the parallel pathways for isoleucine and valine biosynthesis are catalyzed by a single set of enzymes, and because the AHAS-catalyzed reaction is the first step specific for valine biosynthesis but the second step of isoleucine biosynthesis, valine inhibition of a single enzyme for this enzymatic step might compromise the cell for isoleucine or result in the accumulation of toxic intermediates. The operon-specific regulatory mechanisms of the operons of the ilv regulon are discussed in the review followed by a consideration and brief review of global regulatory proteins such as integration host factor (IHF), Lrp, and CAP (CRP) that affect the expression of these operons.
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6
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Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM. The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. Nucleic Acids Res 2013; 41:5965-77. [PMID: 23620297 PMCID: PMC3695496 DOI: 10.1093/nar/gkt308] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although the right-handed double helical B-form DNA is most common under physiological conditions, DNA is dynamic and can adopt a number of alternative structures, such as the four-stranded G-quadruplex, left-handed Z-DNA, cruciform and others. Active transcription necessitates strand separation and can induce such non-canonical forms at susceptible genomic sequences. Therefore, it has been speculated that these non-B DNA motifs can play regulatory roles in gene transcription. Such conjecture has been supported in higher eukaryotes by direct studies of several individual genes, as well as a number of large-scale analyses. However, the role of non-B DNA structures in many lower organisms, in particular proteobacteria, remains poorly understood and incompletely documented. In this study, we performed the first comprehensive study of the occurrence of B DNA-non-B DNA transition-susceptible sites (non-B DNA motifs) within the context of the operon structure of the Escherichia coli genome. We compared the distributions of non-B DNA motifs in the regulatory regions of operons with those from internal regions. We found an enrichment of some non-B DNA motifs in regulatory regions, and we show that this enrichment cannot be simply explained by base composition bias in these regions. We also showed that the distribution of several non-B DNA motifs within intergenic regions separating divergently oriented operons differs from the distribution found between convergent ones. In particular, we found a strong enrichment of cruciforms in the termination region of operons; this enrichment was observed for operons with Rho-dependent, as well as Rho-independent terminators. Finally, a preference for some non-B DNA motifs was observed near transcription factor-binding sites. Overall, the conspicuous enrichment of transition-susceptible sites in these specific regulatory regions suggests that non-B DNA structures may have roles in the transcriptional regulation of specific operons within the E. coli genome.
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Affiliation(s)
- Xiangjun Du
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bethesda, MD 20894, USA
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Zhabinskaya D, Benham CJ. Theoretical analysis of competing conformational transitions in superhelical DNA. PLoS Comput Biol 2012; 8:e1002484. [PMID: 22570598 PMCID: PMC3343103 DOI: 10.1371/journal.pcbi.1002484] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 03/05/2012] [Indexed: 01/16/2023] Open
Abstract
We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcribing. We apply our model to explore the correlation between stress-induced transitions and transcriptional activity in various organisms. In higher eukaryotes we find a strong enhancement of Z-forming regions immediately 5′ to their transcription start sites (TSS), and a depletion of strand separating sites in a broad region around the TSS. The opposite patterns occur around transcript end locations. We also show that susceptibility to each type of transition is different in eukaryotes and prokaryotes. By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downstream of the TSS is not preserved, suggesting it may be under selection pressure. The stresses imposed on DNA within organisms can drive the molecule from its standard B-form double-helical structure into other conformations at susceptible sites within the sequence. We present a theoretical method to calculate this transition behavior due to stresses induced by supercoiling. We also develop a numerical algorithm that calculates the transformation probability of each base pair in a user-specified DNA sequence under stress. We apply this method to analyze the competition between transitions to strand separated and left-handed Z-form structures. We find that these two conformations are both competitive under physiological environmental conditions, and that this competition is especially sensitive to temperature. By comparing its results to experimental data we also show that the algorithm properly describes the competition between melting and Z-DNA formation. Analysis of large gene sets from various organisms shows a correlation between sites of stress-induced transitions and locations that are involved in regulating gene expression.
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Affiliation(s)
- Dina Zhabinskaya
- UC Davis Genome Center, University of California, Davis, California, United States of America.
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8
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The polypyrimidine/polypurine motif in the mouse mu opioid receptor gene promoter is a supercoiling-regulatory element. Gene 2011; 487:52-61. [PMID: 21839154 DOI: 10.1016/j.gene.2011.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 07/25/2011] [Indexed: 11/21/2022]
Abstract
The mu opioid receptor (MOR) is the principle molecular target of opioid analgesics. The polypyrimidine/polypurine (PPy/u) motif enhances the activity of the MOR gene promoter by adopting a non-B DNA conformation. Here, we report that the PPy/u motif regulates the processivity of torsional stress, which is important for endogenous MOR gene expression. Analysis by topoisomerase assays, S1 nuclease digests, and atomic force microscopy showed that, unlike homologous PPy/u motifs, the position- and orientation-induced structural strains to the mouse PPy/u element affect its ability to perturb the relaxation activity of topoisomerase, resulting in polypurine strand-nicked and catenated DNA conformations. Raman spectrum microscopy confirmed that mouse PPy/u containing-plasmid DNA molecules under the different structural strains have a different configuration of ring bases as well as altered Hoogsteen hydrogen bonds. The mouse MOR PPy/u motif drives reporter gene expression fortyfold more effectively in the sense orientation than in the antisense orientation. Furthermore, mouse neuronal cells activate MOR gene expression in response to the perturbations of topology by topoisomerase inhibitors, whereas human cells do not. These results suggest that, interestingly among homologous PPy/u motifs, the mouse MOR PPy/u motif dynamically responds to torsional stress and consequently regulates MOR gene expression in vivo.
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9
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Zhabinskaya D, Benham CJ. Theoretical analysis of the stress induced B-Z transition in superhelical DNA. PLoS Comput Biol 2011; 7:e1001051. [PMID: 21283778 PMCID: PMC3024258 DOI: 10.1371/journal.pcbi.1001051] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 12/06/2010] [Indexed: 11/19/2022] Open
Abstract
We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that occurs among all susceptible Z-forming regions at thermodynamic equilibrium in a superhelically stressed DNA of specified sequence. This method, which we call SIBZ, is similar to the SIDD algorithm that was previously developed to analyze superhelical duplex destabilization. A state of the system is determined by assigning to each base pair either the B- or the Z-conformation, accounting for the dinucleotide repeat unit of Z-DNA. The free energy of a state is comprised of the nucleation energy, the sequence-dependent B-Z transition energy, and the energy associated with the residual superhelicity remaining after the change of twist due to transition. Using this information, SIBZ calculates the equilibrium B-Z transition probability of each base pair in the sequence. This can be done at any physiologically reasonable level of negative superhelicity. We use SIBZ to analyze a variety of representative genomic DNA sequences. We show that the dominant Z-DNA forming regions in a sequence can compete in highly complex ways as the superhelicity level changes. Despite having no tunable parameters, the predictions of SIBZ agree precisely with experimental results, both for the onset of transition in plasmids containing introduced Z-forming sequences and for the locations of Z-forming regions in genomic sequences. We calculate the transition profiles of 5 kb regions taken from each of 12,841 mouse genes and centered on the transcription start site (TSS). We find a substantial increase in the frequency of Z-forming regions immediately upstream from the TSS. The approach developed here has the potential to illuminate the occurrence of Z-form regions in vivo, and the possible roles this transition may play in biological processes.
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Affiliation(s)
- Dina Zhabinskaya
- UC Davis Genome Center, University of California, Davis, Davis California, United States of America.
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10
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Vasudevaraju P, Bharathi, Garruto R, Sambamurti K, Rao K. Role of DNA dynamics in Alzheimer's disease. ACTA ACUST UNITED AC 2008; 58:136-48. [DOI: 10.1016/j.brainresrev.2008.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/14/2008] [Accepted: 01/15/2008] [Indexed: 10/22/2022]
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C8-alkynyl- and alkylamino substituted 2′-deoxyguanosines: a universal linker for nucleic acids modification. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.01.091] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Wang H, Benham CJ. Superhelical destabilization in regulatory regions of stress response genes. PLoS Comput Biol 2008; 4:e17. [PMID: 18208321 PMCID: PMC2211533 DOI: 10.1371/journal.pcbi.0040017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 12/03/2007] [Indexed: 11/18/2022] Open
Abstract
Stress-induced DNA duplex destabilization (SIDD) analysis exploits the known structural and energetic properties of DNA to predict sites that are susceptible to strand separation under negative superhelical stress. When this approach was used to calculate the SIDD profile of the entire Escherichia coli K12 genome, it was found that strongly destabilized sites occur preferentially in intergenic regions that are either known or inferred to contain promoters, but rarely occur in coding regions. Here, we investigate whether the genes grouped in different functional categories have characteristic SIDD properties in their upstream flanks. We report that strong SIDD sites in the E. coli K12 genome are statistically significantly overrepresented in the upstream regions of genes encoding transcriptional regulators. In particular, the upstream regions of genes that directly respond to physiological and environmental stimuli are more destabilized than are those regions of genes that are not involved in these responses. Moreover, if a pathway is controlled by a transcriptional regulator whose gene has a destabilized 5′ flank, then the genes (operons) in that pathway also usually contain strongly destabilized SIDD sites in their 5′ flanks. We observe this statistically significant association of SIDD sites with upstream regions of genes functioning in transcription in 38 of 43 genomes of free-living bacteria, but in only four of 18 genomes of endosymbionts or obligate parasitic bacteria. These results suggest that strong SIDD sites 5′ to participating genes may be involved in transcriptional responses to environmental changes, which are known to transiently alter superhelicity. We propose that these SIDD sites are active and necessary participants in superhelically mediated regulatory mechanisms governing changes in the global pattern of gene expression in prokaryotes in response to physiological or environmental changes. DNA in vivo experiences regulated amounts of untwisting stress. If sufficiently large, these stresses can destabilize the double helix at specific locations. These sites then become favored locations for strand separations. Gene expression and DNA replication, the two major jobs of DNA, both require the strands of the duplex to be separated. Thus, events that affect the ease of strand separation can regulate the initiation of these processes. Stress-induced DNA duplex destabilization (SIDD) has been implicated in mechanisms regulating several biological processes, including the initiation of gene expression and replication. We have developed computational methods that accurately predict the locations and extents of destabilization within genomic DNA sequences that occur in response to specified stress levels. Here, we report that the easily destabilized sites we find in the Escherichia coli K12 genome are statistically significantly overrepresented in the upstream regions of genes encoding proteins that regulate transcription. In particular, the regions upstream of genes that directly respond to physiological and environmental stimuli are more destabilized than are those regions of genes that are not involved in these responses. These results suggest that strong SIDD sites upstream of participating genes may be involved in transcriptional responses to environmental changes.
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Affiliation(s)
- Huiquan Wang
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Craig J Benham
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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13
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Yadav VK, Abraham JK, Mani P, Kulshrestha R, Chowdhury S. QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes. Nucleic Acids Res 2007; 36:D381-5. [PMID: 17962308 PMCID: PMC2238983 DOI: 10.1093/nar/gkm781] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Emerging evidence indicates the importance of G-quadruplex motifs as drug targets. [Stuart A. Borman, Ascent of quadruplexes-nucleic acid structures become promising drug targets. Chem. Eng. News, 2007;85, 12-17], which stems from the fact that these motifs are present in a surprising number of promoters wherein their role in controlling gene expression has been demonstrated for a few. We present a compendium of quadruplex motifs, with particular focus on their occurrence and conservation in promoters-QuadBase. It is composed of two parts (EuQuad and ProQuad). EuQuad gives information on quadruplex motifs present within 10 kb of transcription starts sites in 99 980 human, chimpanzee, rat and mouse genes. ProQuad contains quadruplex information of 146 prokaryotes. Apart from gene-specific searches for quadruplex motifs, QuadBase has a number of other modules. 'Orthologs Analysis' queries for conserved motifs across species based on a selected reference organism; 'Pattern Search' can be used to fetch specific motifs of interest from a selected organism using user-defined criteria for quadruplex motifs, i.e. stem, loop size, etc. 'Pattern Finder' tool can search for motifs in any given sequence. QuadBase is freely available to users from non-profit organization at http://quadbase.igib.res.in/.
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Affiliation(s)
- Vinod Kumar Yadav
- G. N. Ramachandran Knowledge Centre for Genome Informatics and Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, New Delhi 110 007, India
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14
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Mielke SP, Grønbech-Jensen N, Krishnan VV, Fink WH, Benham CJ. Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA. J Chem Phys 2007; 123:124911. [PMID: 16392531 DOI: 10.1063/1.2038767] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The topological state of DNA in vivo is dynamically regulated by a number of processes that involve interactions with bound proteins. In one such process, the tracking of RNA polymerase along the double helix during transcription, restriction of rotational motion of the polymerase and associated structures, generates waves of overtwist downstream and undertwist upstream from the site of transcription. The resulting superhelical stress is often sufficient to drive double-stranded DNA into a denatured state at locations such as promoters and origins of replication, where sequence-specific duplex opening is a prerequisite for biological function. In this way, transcription and other events that actively supercoil the DNA provide a mechanism for dynamically coupling genetic activity with regulatory and other cellular processes. Although computer modeling has provided insight into the equilibrium dynamics of DNA supercoiling, to date no model has appeared for simulating sequence-dependent DNA strand separation under the nonequilibrium conditions imposed by the dynamic introduction of torsional stress. Here, we introduce such a model and present results from an initial set of computer simulations in which the sequences of dynamically superhelical, 147 base pair DNA circles were systematically altered in order to probe the accuracy with which the model can predict location, extent, and time of stress-induced duplex denaturation. The results agree both with well-tested statistical mechanical calculations and with available experimental information. Additionally, we find that sites susceptible to denaturation show a propensity for localizing to supercoil apices, suggesting that base sequence determines locations of strand separation not only through the energetics of interstrand interactions, but also by influencing the geometry of supercoiling.
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Affiliation(s)
- Steven P Mielke
- Biophysics Graduate Group, University of California, Davis, California 95616, USA.
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15
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Sohanpal BK, Friar S, Roobol J, Plumbridge JA, Blomfield IC. Multiple co-regulatory elements and IHF are necessary for the control of fimB expression in response to sialic acid and N-acetylglucosamine in Escherichia coli K-12. Mol Microbiol 2007; 63:1223-36. [PMID: 17238917 DOI: 10.1111/j.1365-2958.2006.05583.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Expression of the FimB recombinase, and hence the OFF-to-ON switching of type 1 fimbriation in Escherichia coli, is inhibited by sialic acid (Neu(5)Ac) and by GlcNAc. NanR (Neu(5)Ac-responsive) and NagC (GlcNAc-6P-responsive) activate fimB expression by binding to operators (O(NR) and O(NC1) respectively) located more than 600 bp upstream of the fimB promoter within the large (1.4 kb) nanC-fimB intergenic region. Here it is demonstrated that NagC binding to a second site (O(NC2)), located 212 bp closer to fimB, also controls fimB expression, and that integration host factor (IHF), which binds midway between O(NC1) and O(NC2), facilitates NagC binding to its two operator sites. In contrast, IHF does not enhance the ability of NanR to activate fimB expression in the wild-type background. Neither sequences up to 820 bp upstream of O(NR), nor those 270 bp downstream of O(NC2), are required for activation by NanR and NagC. However, placing the NanR, IHF and NagC binding sites closer to the fimB promoter enhances the ability of the regulators to activate fimB expression. These results support a refined model for how two potentially key indicators of host inflammation, Neu(5)Ac and GlcNAc, regulate type 1 fimbriation.
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Affiliation(s)
- Baljinder K Sohanpal
- Biomedical Research Group, Department of Biosciences, University of Kent, Kent, UK
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16
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Abstract
The various conformations of DNA--the A, B, and Z forms, the protein-induced DNA kink, and the G-quartet form--are thought to play important biological roles in processes such as DNA replication, gene expression and regulation, and the repair of DNA damage. The investigation of local DNA conformational changes associated with biological events is therefore essential for understanding the function of DNA. In this Minireview, we discuss the use of photochemical dehalogenation of 5-halouracil-containing DNA to probe the structure of DNA. Hydrogen abstraction by the resultant uracil-5-yl radicals is atom-specific and highly dependent on the structure of the DNA, suggesting that this photochemical approach could be applied as a probe of DNA conformations in living cells.
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Affiliation(s)
- Yan Xu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
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17
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Aeling KA, Opel ML, Steffen NR, Tretyachenko-Ladokhina V, Hatfield GW, Lathrop RH, Senear DF. Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy. J Biol Chem 2006; 281:39236-48. [PMID: 17035240 DOI: 10.1074/jbc.m606363200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex.
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Affiliation(s)
- Kimberly A Aeling
- Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, School of Medicine, University of California 92697, USA
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18
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Rawal P, Kummarasetti VBR, Ravindran J, Kumar N, Halder K, Sharma R, Mukerji M, Das SK, Chowdhury S. Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res 2006; 16:644-55. [PMID: 16651665 PMCID: PMC1457047 DOI: 10.1101/gr.4508806] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The role of nonlinear DNA in replication, recombination, and transcription has become evident in recent years. Although several studies have predicted and characterized regulatory elements at the sequence level, very few have investigated DNA structure as regulatory motifs. Here, using G-quadruplex or G4 DNA motifs as a model, we have researched the role of DNA structure in transcription on a genome-wide scale. Analyses of >61,000 open reading frames (ORFs) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported by conserved G4 motifs in promoters of orthologous genes across phylogenetically distant organisms. We hypothesized a regulatory role of G4 DNA during supercoiling stress, when duplex destabilization may result in G4 formation. This is in line with our observations from target site analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (P<0.001) association of G4 motifs with target sites of global regulators FIS and Lrp and the sigma factor RpoD (sigma70). These factors together control >1000 genes in the early growth phase and are believed to be induced by supercoiled DNA. We also predict G4 motif-induced supercoiling sensitivity for >30 operons in E. coli, and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation in E. coli.
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Affiliation(s)
- Pooja Rawal
- G.N. Ramachandran Knowledge Centre for Genome Informatics
| | | | | | - Nirmal Kumar
- G.N. Ramachandran Knowledge Centre for Genome Informatics
| | | | - Rakesh Sharma
- G.N. Ramachandran Knowledge Centre for Genome Informatics
- Environmental Biotechnology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi 110 007, India
| | - Mitali Mukerji
- G.N. Ramachandran Knowledge Centre for Genome Informatics
- Functional Genomics Unit
| | | | - Shantanu Chowdhury
- G.N. Ramachandran Knowledge Centre for Genome Informatics
- Proteomics and Structural Biology Unit
- Corresponding author.E-mail ; fax 91-11-2766-7471
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19
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Xu Y, Sugiyama H. Die photochemische Untersuchung verschiedener DNA-Strukturen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200501962] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Ak P, Benham CJ. Susceptibility to superhelically driven DNA duplex destabilization: a highly conserved property of yeast replication origins. PLoS Comput Biol 2005; 1:e7. [PMID: 16103908 PMCID: PMC1183513 DOI: 10.1371/journal.pcbi.0010007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Accepted: 05/10/2005] [Indexed: 12/03/2022] Open
Abstract
Strand separation is obligatory for several DNA functions, including replication. However, local DNA properties such as A+T content or thermodynamic stability alone do not determine the susceptibility to this transition in vivo. Rather, superhelical stresses provide long-range coupling among the transition behaviors of all base pairs within a topologically constrained domain. We have developed methods to analyze superhelically induced duplex destabilization (SIDD) in genomic DNA that take into account both this long-range stress-induced coupling and sequence-dependent local thermodynamic stability. Here we apply this approach to examine the SIDD properties of 39 experimentally well-characterized autonomously replicating DNA sequences (ARS elements), which function as replication origins in the yeast Saccharomyces cerevisiae. We find that these ARS elements have a strikingly increased susceptibility to SIDD relative to their surrounding sequences. On average, these ARS elements require 4.78 kcal/mol less free energy to separate than do their immediately surrounding sequences, making them more than 2,000 times easier to open. Statistical analysis shows that the probability of this strong an association between SIDD sites and ARS elements arising by chance is approximately 4 × 10−10. This local enhancement of the propensity to separate to single strands under superhelical stress has obvious implications for origin function. SIDD properties also could be used, in conjunction with other known origin attributes, to identify putative replication origins in yeast, and possibly in other metazoan genomes. Several DNA functions require the two strands of the DNA duplex to transiently separate. Examples include the initiation of gene expression and of DNA replication. Here the authors examine the strand separation properties of the DNA duplex at autonomously replicating sequences (ARS elements), which are the potential replication origins in yeast. In vivo, susceptibility to strand separation does not depend only on local DNA properties such as adenine plus thymine content or thermodynamic stability. Rather, stresses imposed on the DNA in vivo couple together the strand-opening behaviors of all base pairs that experience them. The authors use computational methods for analyzing stress-driven strand separation to examine the susceptibility to opening of 39 experimentally well-characterized ARS elements. They show that these ARS elements have strikingly increased susceptibilities to stress-induced separation relative to the surrounding sequences. On average, these ARS elements require 4.78 kcal/mol less free energy to separate than do surrounding sequences, making them more than 2,000 times easier to open. This enhanced susceptibility to stress-driven strand separation has obvious implications for the mechanisms that begin the process of replication. This property is also shared by bacterial and viral replication start points, suggesting that it may be a general attribute of replication origins.
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Affiliation(s)
- Prashanth Ak
- UC Davis Genome Center, University of California, Davis, USA.
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21
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Benham CJ, Bi C. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J Comput Biol 2005; 11:519-43. [PMID: 15579230 DOI: 10.1089/cmb.2004.11.519] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We present a method for calculating predicted locations and extents of stress-induced DNA duplex destabilization (SIDD) as functions of base sequence and stress level in long DNA molecules. The base pair denaturation energies are assigned individually, so the influences of near neighbors, methylated bases, adducts, or lesions can be included. Sample calculations indicate that copolymeric energetics give results that are close to those derived when full near-neighbor energetics are used; small but potentially informative differences occur only in the calculated SIDD properties of moderately destabilized regions. The method presented here for analyzing long sequences calculates the destabilization properties within windows of fixed length N, with successive windows displaced by an offset distance d(o). The final values of the relevant destabilization parameters for each base pair are calculated as weighted averages of the values computed for each window in which that base pair appears. This approach implicitly assumes that the strength of the direct coupling between remote base pairs that is induced by the imposed stress attenuates with their separation distance. This strategy enables calculations of the destabilization properties of DNA sequences of any length, up to and including complete chromosomes. We illustrate its utility by calculating the destabilization properties of the entire E. coli genomic DNA sequence. A preliminary analysis of the results shows that promoters are associated with SIDD regions in a highly statistically significant manner, suggesting that SIDD attributes may prove useful in the computational prediction of promoter locations in prokaryotes.
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Affiliation(s)
- Craig J Benham
- UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA.
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22
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Champ PC, Maurice S, Vargason JM, Camp T, Ho PS. Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Res 2004; 32:6501-10. [PMID: 15598822 PMCID: PMC545456 DOI: 10.1093/nar/gkh988] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An analysis of the human chromosome 22 genomic sequence shows that both Z-DNA forming regions (ZDRs) and promoter sites for nuclear factor-I (NFI) are correlated with the locations of known and predicted genes across the chromosome and accumulate around the transcriptional start sites of the known genes. Thus, the occurrence of Z-DNA across human genomic sequences mirrors that of a known eukaryotic transcription factor. In addition, 43 of the 383 fully annotated chromosomal genes have ZDRs within 2 nucleosomes upstream of strong NFIs. This suggests a distinct class of human genes that may potentially be transcriptionally regulated by a mechanism that couples Z-DNA with NFI activation, similar to the mechanism previously elucidated for the human colony stimulation factor-I promoter [Liu et al. (2001) Cell, 106, 309-318]. The results from this study will facilitate the design of experimental studies to test the generality of this mechanism for other genes in the cell.
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Affiliation(s)
- P Christoph Champ
- Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331, USA
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23
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Polonskaya Z, Benham CJ, Hearing J. Role for a region of helically unstable DNA within the Epstein–Barr virus latent cycle origin of DNA replication oriP in origin function. Virology 2004; 328:282-91. [PMID: 15464848 DOI: 10.1016/j.virol.2004.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Revised: 05/27/2004] [Accepted: 07/23/2004] [Indexed: 11/26/2022]
Abstract
The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component of oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication.
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Affiliation(s)
- Zhanna Polonskaya
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
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24
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Wang H, Noordewier M, Benham CJ. Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Res 2004; 14:1575-84. [PMID: 15289476 PMCID: PMC509266 DOI: 10.1101/gr.2080004] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present the first analysis of stress-induced DNA duplex destabilization (SIDD) in a complete chromosome, the Escherichia coli K12 genome. We used a newly developed method to calculate the locations and extents of stress-induced destabilization to single-base resolution at superhelix density sigma = -0.06. We find that SIDD sites in this genome show a statistically highly significant tendency to avoid coding regions. And among intergenic regions, those that either contain documented promoters or occur between divergently transcribing coding regions, and hence may be inferred to contain promoters, are associated with strong SIDD sites in a statistically highly significant manner. Intergenic regions located between convergently transcribing genes, which are inferred not to contain promoters, are not significantly enriched for destabilized sites. Statistical analysis shows that a strongly destabilized intergenic region has an 80% chance of containing a promoter, whereas an intergenic region that does not contain a strong SIDD site has only a 24% chance. We describe how these observations may illuminate specific mechanisms of regulation, and assist in the computational identification of promoter locations in prokaryotes.
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Affiliation(s)
- Huiquan Wang
- UC Davis Genome Center, University of California, Davis, California 95616, USA
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25
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Abstract
Nucleic acids are characterized by a vast structural variability. Secondary structural conformations include the main polymorphs A, B, and Z, cruciforms, intrinsic curvature, and multistranded motifs. DNA secondary motifs are stabilized and regulated by the primary base sequence, contextual effects, environmental factors, as well as by high-order DNA packaging modes. The high-order modes are, in turn, affected by secondary structures and by the environment. This review is concerned with the flow of structural information among the hierarchical structural levels of DNA molecules, the intricate interplay between the various factors that affect these levels, and the regulation and physiological significance of DNA high-order structures.
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Affiliation(s)
- Abraham Minsky
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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Opel ML, Aeling KA, Holmes WM, Johnson RC, Benham CJ, Hatfield GW. Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism. Mol Microbiol 2004; 53:665-74. [PMID: 15228542 DOI: 10.1111/j.1365-2958.2004.04147.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The leuV operon of Escherichia coli encodes three of the four genes for the tRNA1Leu isoacceptors. Transcription from this and other stable RNA promoters is known to be affected by a cis-acting UP element and by Fis protein interactions with the carboxyl-terminal domain of the alpha-subunits of RNA polymerase. In this report, we suggest that transcription from the leuV promoter also is activated by a Fis-mediated, DNA supercoiling-dependent mechanism similar to the IHF-mediated mechanism described previously for the ilvP(G) promoter (S. D. Sheridan et al., 1998, J Biol Chem 273: 21298-21308). We present evidence that Fis binding results in the translocation of superhelical energy from the promoter-distal portion of a supercoiling-induced DNA duplex destabilized (SIDD) region to the promoter-proximal portion of the leuV promoter that is unwound within the open complex. A mutant Fis protein, which is defective in contacting the carboxyl-terminal domain of the alpha-subunits of RNA polymerase, remains competent for stimulating open complex formation, suggesting that this DNA supercoiling-dependent component of Fis-mediated activation occurs in the absence of specific protein interactions between Fis and RNA polymerase. Fis-mediated translocation of superhelical energy from upstream binding sites to the promoter region may be a general feature of Fis-mediated activation of transcription at stable RNA promoters, which often contain A+T-rich upstream sequences.
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Affiliation(s)
- Michael L Opel
- Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
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27
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Abstract
Various modified guanine derivatives were synthesized and introduced into G(4) of d(CGCGCG)(2) to evaluate their capacity to stabilize Z-form DNA. It was found that the incorporation of 8-methylguanosine (m(8)rG) in oligonucleotides stabilizes the Z form more dramatically than does the incorporation of 8-methyl-2'-deoxyguanosine (m(8)G). This enhancement is ascribed to a reduction in the entropic penalty, which arises from the introduction of hydrophilic groups in solvent-exposed regions. The incorporation of m(8)rG into DNA sequences markedly stabilizes the Z form even in the absence of NaCl. The Z-DNA stabilizer allows oligonucleotides with a wide range of sequences to be converted to the Z form. It could be a powerful tool for examining the molecular basis of many types of Z-form-specific reactions at the molecular level under physiological salt conditions.
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Affiliation(s)
- Yan Xu
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda, Tokyo 101-0062, Japan
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28
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Abstract
Because the level of DNA superhelicity varies with the cellular energy charge, it can change rapidly in response to a wide variety of altered nutritional and environmental conditions. This is a global alteration, affecting the entire chromosome and the expression levels of all operons whose promoters are sensitive to superhelicity. In this way, the global pattern of gene expression may be dynamically tuned to changing needs of the cell under a wide variety of circumstances. In this article, we propose a model in which chromosomal superhelicity serves as a global regulator of gene expression in Escherichia coli, tuning expression patterns across multiple operons, regulons, and stimulons to suit the growth state of the cell. This model is illustrated by the DNA supercoiling-dependent mechanisms that coordinate basal expression levels of operons of the ilv regulon both with one another and with cellular growth conditions.
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Affiliation(s)
- G Wesley Hatfield
- Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, California 92697, USA.
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29
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Oyoshi T, Kawai K, Sugiyama H. Efficient C2'alpha-hydroxylation of deoxyribose in protein-induced Z-form DNA. J Am Chem Soc 2003; 125:1526-31. [PMID: 12568612 DOI: 10.1021/ja028388g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA local conformations are thought to play an important biological role in processes such as gene expression by altering DNA-protein interactions. Although left-handed Z-form DNA is one of the best-characterized and significant local structures of DNA, having been extensively investigated for more than two decades, the biological relevance of Z-form DNA remains unclear. This is presumably due to the lack of a versatile detection method in a living cell. Previously, we demonstrated that the incorporation of a methyl group at the guanine C8 position (m(8)G) dramatically stabilizes the Z-form of short oligonucleotides in a variety of sequences. To develop a photochemical method to detect Z-form DNA, we examined the photoreaction of 5-iodouracil-containing Z-form d(CGCG(I)UGCG)(ODN 1)/d(Cm(8)GCAm(8)GCG)(ODN 2) in 2 M NaCl and found stereospecific C2'alpha-hydroxylation occurred at G(4) to provide d(CGCrGUGCG), 5. Recently, Rich and co-workers [Schwartz et al. Science 1999, 284, 1841. Schwartz et al. Nat. Struct. Biol. 2001, 8, 761] found that an ubiquitous RNA editing enzyme, adenosine deaminase 1 (ADAR1), and tumor-associated protein DML-1 specifically bind to Z-form DNA. In the present study, we investigate the photoreactivity of octanucleotide ODN 1-2 in Z-form induced by Zalpha, which is the NH(2)-terminal domain of ADAR1 responsible for tight binding of ADAR1. Detailed product analysis revealed that the C2'alpha-hydroxylated products 5 and 6 produced significantly higher yields in Z-form ODN 1-2 induced by Zalpha compared with that in 2 M NaCl. Upon treatment with ribonuclease T1, 5 and 6 were quantitatively hydrolyzed at the 3'-phosphodiester bond of the rG residue to provide d(UGCG) as a common hydrolyzed fragment on the 3' side. Quantitative analysis demonstrated that the amount of photochemically formed 5 and 6 from ODN 1-2 directly correlated with the proportion of Z-form induced by Zalpha or NaCl. These results suggest that this photochemical and enzymatic procedure can be used as a specific probe for the existence of local Z-form structure in cellular DNA.
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Affiliation(s)
- Takanori Oyoshi
- Division of Biofunctional Molecules, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda, Tokyo 101-0062, Japan
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30
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Sheridan SD, Opel ML, Hatfield GW. Activation and repression of transcription initiation by a distant DNA structural transition. Mol Microbiol 2001; 40:684-90. [PMID: 11359573 DOI: 10.1046/j.1365-2958.2001.02416.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Negative superhelical tension can drive local transitions to alternative DNA structures. Long regions of DNA may contain several sites that are susceptible to forming alternative structures. Their relative propensities to undergo transition are ordered according to the energies required for their formation. These energies have two components - the energy needed to drive the transition and the energy relieved by the partial relaxation of superhelicity that the transition provides. This coupling can cause a complex competition among the possible transitions, in which the formation of one energetically favourable alternative structure may inhibit the formation of another within the same domain. In principle, DNA structural competitions can affect the structural and energetic requirements for the initiation of transcription at distant promoter sites. We have tested this possibility by examining the effects of structural transitions on transcription initiation from promoter sites in the same superhelical domain. Specifically, we describe the effects of the presence of a Z-DNA-forming DNA sequence on the basal levels of expression of two supercoiling-sensitive promoters of Escherichia coli, ilvPG and gyrA. We demonstrate transcriptional repression of the ilvPG promoter and activation of the gyrA promoter. We present evidence that this regulation is effected by the superhelically induced B- to Z-DNA transition in a manner that is both orientation and distance independent. We discuss the mechanism of topological coupling between left-handed Z-DNA and the regulation of promoter activity. We also discuss the possibility that the coupling of DNA structural transitions and transcriptional activity might be used as a general regulatory mechanism for gene expression.
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Affiliation(s)
- S D Sheridan
- Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
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31
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Opel ML, Arfin SM, Hatfield GW. The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons. Mol Microbiol 2001; 39:1109-15. [PMID: 11251829 DOI: 10.1111/j.1365-2958.2001.02309.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Transcriptional activities of closely spaced divergent promoters are affected by the accumulation of local negative superhelicity in the region between transcribing RNA polymerase molecules (transcriptional coupling). The effect of this transcription-induced DNA supercoiling on these promoters depends on their intrinsic properties. As the global superhelical density of the chromosome is controlled by the energy charge of the cell, which is affected by environmental stresses and transitions from one growth state to another, the transcriptional coupling that occurs between divergently transcribed promoters is likely to serve a physiological purpose. Here, we suggest that transcriptional coupling between the divergent promoters of the ilvYC operon of Escherichia coli serves to co-ordinate the expression of this operon with other operons of the ilv regulon during metabolic adjustments associated with growth state transitions. As DNA supercoiling-dependent transcriptional coupling between the promoters of other divergently transcribed operons is investigated, additional global gene regulatory mechanisms and physiological roles are sure to emerge.
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Affiliation(s)
- M L Opel
- Departments of Microbiology and Molecular Genetics and Biological Chemistry, College of Medicine, University of California, Irvine, CA 92697, USA
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32
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Kulić I. Single and multiple topologically driven structural transitions in DNA. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 2000; 62:7123-7134. [PMID: 11102069 DOI: 10.1103/physreve.62.7123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2000] [Revised: 06/03/2000] [Indexed: 05/23/2023]
Abstract
We derive some exact general results concerning the behavior of topological absorbers (i.e., sequences undergoing topologically driven structural transitions) in closed circular DNA molecules. Starting from the formal physical framework that covers all known structural transitions, like those from standard B-DNA to nonstandard conformers Z-DNA, H-DNA, cruciform-DNA, melt-DNA or others, we develop a reduced state space description that leads to an analytically simplified "black box" view of absorbers. The latter contains only a single state variable-the total sequence unwinding u describing the topological state of the absorber. We show that the statistical mechanics of u is determined by the (one-dimensional) absorption free energy function G(abs) and find explicit expressions for G(abs) and for moments <u(n)> in terms of the standard experimental observable-the absorption function alpha:=<u>. The reduced state space method is then applied to systems consisting of several interacting topologically coupled absorbers and a formula predicting their collective behavior (superposition) in terms of their individual absorptions is derived. Using these results we formulate and discuss solution methods for two basic types of inverse problems that turn out to be fundamental for future absorber construction.
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Affiliation(s)
- I Kulić
- Institut für Theoretische Physik 1, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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33
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Arfin SM, Long AD, Ito ET, Tolleri L, Riehle MM, Paegle ES, Hatfield GW. Global gene expression profiling in Escherichia coli K12. The effects of integration host factor. J Biol Chem 2000; 275:29672-84. [PMID: 10871608 DOI: 10.1074/jbc.m002247200] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have used nylon membranes spotted in duplicate with full-length polymerase chain reaction-generated products of each of the 4,290 predicted Escherichia coli K12 open reading frames (ORFs) to measure the gene expression profiles in otherwise isogenic integration host factor IHF(+) and IHF(-) strains. Our results demonstrate that random hexamer rather than 3' ORF-specific priming of cDNA probe synthesis is required for accurate measurement of gene expression levels in bacteria. This is explained by the fact that the currently available set of 4,290 unique 3' ORF-specific primers do not hybridize to each ORF with equal efficiency and by the fact that widely differing degradation rates (steady-state levels) are observed for the 25-base pair region of each message complementary to each ORF-specific primer. To evaluate the DNA microarray data reported here, we used a linear analysis of variance (ANOVA) model appropriate for our experimental design. These statistical methods allowed us to identify and appropriately correct for experimental variables that affect the reproducibility and accuracy of DNA microarray measurements and allowed us to determine the statistical significance of gene expression differences between our IHF(+) and IHF(-) strains. Our results demonstrate that small differences in gene expression levels can be accurately measured and that the significance of differential gene expression measurements cannot be assessed simply by the magnitude of the fold difference. Our statistical criteria, supported by excellent agreement between previously determined effects of IHF on gene expression and the results reported here, have allowed us to identify new genes regulated by IHF with a high degree of confidence.
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Affiliation(s)
- S M Arfin
- Department of Biological Chemistry, College of Medicine, University of California, Irvine, 92697, USA
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Rhee KY, Opel M, Ito E, Hung SP, Arfin SM, Hatfield GW. Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli. Proc Natl Acad Sci U S A 1999; 96:14294-9. [PMID: 10588699 PMCID: PMC24430 DOI: 10.1073/pnas.96.25.14294] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The twin-domain model [Liu, L. F. & Wang, J. C. (1987) Proc. Natl. Acad. Sci. USA 84, 7024-7027] suggests that closely spaced, divergent, superhelically sensitive promoters can affect the transcriptional activity of one another by transcriptionally induced negative DNA supercoiling generated in the divergent promoter region. This gene arrangement is observed for many LysR-type-regulated operons in bacteria. We have examined the effects of divergent transcription in the prototypic LysR-type system, the ilvYC operon of Escherichia coli. Double-reporter constructs with the lacZ gene under transcriptional control of the ilvC promoter and the galK gene under control of the divergent ilvY promoter were used to demonstrate that a down-promoter mutation in the ilvY promoter severely decreases in vivo transcription from the ilvC promoter. However, a down-promoter mutation in the ilvC promoter only slightly affects transcription from the ilvY promoter. In vitro transcription assays with DNA topoisomers showed that transcription from the ilvC promoter increases over the entire range of physiological superhelical densities, whereas transcription initiation from the ilvY promoter exhibits a broad optimum at a midphysiological superhelical density. Evidence that this promoter coupling is DNA supercoiling-dependent is provided by the observation that a novobiocin-induced decrease in global negative superhelicity results in an increase in ilvY promoter activity and a decrease in ilvC promoter activity predicted by the in vitro data. We suggest that this transcriptional coupling is important for coordinating basal level expression of the ilvYC operon with the nutritional and environmental conditions of cell growth.
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Affiliation(s)
- K Y Rhee
- Department of Microbiology, College of Medicine, University of California, Irvine, CA 92697, USA
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