Genomes and Genes
Summary: Circular duplex DNA isolated from viruses, bacteria and mitochondria in supercoiled or supertwisted form. This superhelical DNA is endowed with free energy. During transcription, the magnitude of RNA initiation is proportional to the DNA superhelicity.
- Liu Z, Zechiedrich E, Chan H. Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action. Biophys J. 2006;90:2344-55 pubmed
- Mielke S, Grønbech Jensen N, Krishnan V, Fink W, Benham C. Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA. J Chem Phys. 2005;123:124911 pubmed
- Sari L, Andricioaei I. Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Res. 2005;33:6621-34 pubmedTopoisomerases are enzymes of quintessence to the upkeep of superhelical DNA, and are vital for replication, transcription and recombination...
- Crut A, Koster D, Seidel R, Wiggins C, Dekker N. Fast dynamics of supercoiled DNA revealed by single-molecule experiments. Proc Natl Acad Sci U S A. 2007;104:11957-62 pubmed..These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA. ..
- Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners D, Roca J. DNA knots reveal a chiral organization of DNA in phage capsids. Proc Natl Acad Sci U S A. 2005;102:9165-9 pubmed..These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed. ..
- Mukherjee A, Sokunbi A, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res. 2008;36:3956-68 pubmed publisher..We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA. ..
- Du Q, Kotlyar A, Vologodskii A. Kinking the double helix by bending deformation. Nucleic Acids Res. 2008;36:1120-8 pubmed..Our results suggest that strong DNA bending initiates kink formation while preserving base pairing. ..
- Travers A, Muskhelishvili G. DNA supercoiling - a global transcriptional regulator for enterobacterial growth?. Nat Rev Microbiol. 2005;3:157-69 pubmed
- Pease P, Levy O, Cost G, Gore J, Ptacin J, Sherratt D, et al. Sequence-directed DNA translocation by purified FtsK. Science. 2005;307:586-90 pubmed..coli chromosome, as it does in vivo. Our results imply that FtsK is a bidirectional motor that changes direction in response to short, asymmetric directing DNA sequences. ..
- Leo E, Gould K, Pan X, Capranico G, Sanderson M, Palumbo M, et al. Novel symmetric and asymmetric DNA scission determinants for Streptococcus pneumoniae topoisomerase IV and gyrase are clustered at the DNA breakage site. J Biol Chem. 2005;280:14252-63 pubmed..However, both pneumococcal enzymes cleaved an E. coli gyrase site suggesting overlap in gyrase determinants. We propose a model for the cleavage complex of topo IV/gyrase that accommodates the unique -2A/+6T and other preferences. ..
- Koster D, Croquette V, Dekker C, Shuman S, Dekker N. Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature. 2005;434:671-4 pubmed..We propose a model for topoisomerization in which the torque drives the DNA rotation over a rugged periodic energy landscape in which the topoisomerase has a small but quantifiable probability to religate the DNA once per turn. ..
- Ye F, Brauer T, Niehus E, Drlica K, Josenhans C, Suerbaum S. Flagellar and global gene regulation in Helicobacter pylori modulated by changes in DNA supercoiling. Int J Med Microbiol. 2007;297:65-81 pubmed..These data indicate that global supercoiling changes may help coordinate temporal (growth phase-related) regulation of flagellar biosynthesis and other cellular functions in Helicobacter. ..
- Kouzine F, Levens D. Supercoil-driven DNA structures regulate genetic transactions. Front Biosci. 2007;12:4409-23 pubmed..The dynamic response of DNA to supercoiling forces contributes to control of genes such as c-myc whose physiological levels must be precisely regulated. ..
- Kelly A, Conway C, O Cróinín T, Smith S, Dorman C. DNA supercoiling and the Lrp protein determine the directionality of fim switch DNA inversion in Escherichia coli K-12. J Bacteriol. 2006;188:5356-63 pubmed..Thus, Lrp is not merely an architectural element organizing the fim invertasome, it collaborates with DNA supercoiling to determine the directionality of the DNA inversion event. ..
- Blot N, Mavathur R, Geertz M, Travers A, Muskhelishvili G. Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Rep. 2006;7:710-5 pubmed..We infer that a homeostatic mechanism organizing the supercoiling sensitivity is coordinating the growth-phase-dependent transcription of the genome. ..
- Wells R. Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci. 2007;32:271-8 pubmed..Thus, the convergence of biochemical, genetic and genomic studies has demonstrated a new paradigm implicating the non-B DNA conformations as the mutagenesis specificity determinants, not the sequences as such. ..
- Salceda J, Fernandez X, Roca J. Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA. EMBO J. 2006;25:2575-83 pubmed..We conclude that topoisomerase II is the main modulator of DNA topology in chromatin fibers. The nonessential topoisomerase I then assists DNA relaxation where chromatin structure impairs DNA juxtaposition but allows twist diffusion. ..
- Aoe K, Kiura K, Ueoka H, Tabata M, Chikamori M, Kohara H, et al. Cisplatin down-regulates topoisomerase I activity in lung cancer cell lines. Anticancer Res. 2004;24:3893-7 pubmed..Accordingly, pretreatment with cisplatin will have an impact on the sensitivity to SN-38. ..
- Samul R, Leng F. Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains. J Mol Biol. 2007;374:925-35 pubmed
- Becker N, Kahn J, Maher L. Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Res. 2007;35:3988-4000 pubmed..These results suggest that host nucleoid proteins can directly facilitate or inhibit DNA looping in bacteria. ..
- Valjavec Gratian M, Henderson T, Hill T. Tus-mediated arrest of DNA replication in Escherichia coli is modulated by DNA supercoiling. Mol Microbiol. 2005;58:758-73 pubmed..We propose that increased negative supercoiling enhances DnaB unwinding activity, thereby reducing the duration of the Tus-DnaB interaction and leading to decreased Tus activity. ..
- Bishop T. Molecular dynamics simulations of a nucleosome and free DNA. J Biomol Struct Dyn. 2005;22:673-86 pubmed..The long wavelength variations suggest 146 basepairs is a natural length of DNA to wrap around the histone core. ..
- Ruthenburg A, Graybosch D, Huetsch J, Verdine G. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J Biol Chem. 2005;280:26177-84 pubmed..We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling. ..
- Deng S, Stein R, Higgins N. Organization of supercoil domains and their reorganization by transcription. Mol Microbiol. 2005;57:1511-21 pubmed..Domain structure is subsequently reorganized by RNA transcription. Examples of transcription-dependent chromosome remodelling are also emerging from eukaryotic cell systems. ..
- Mayán Santos M, Martínez Robles M, Hernandez P, Krimer D, Schvartzman J. DNA is more negatively supercoiled in bacterial plasmids than in minichromosomes isolated from budding yeast. Electrophoresis. 2007;28:3845-53 pubmed..In E. coli, the observation that cell growth as well as ColE1 plasmid copy number decrease when DNA relaxes suggests that supercoiling could affect cell viability by regulating the initiation of both transcription and replication. ..
- Kar S, Edgar R, Adhya S. Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc Natl Acad Sci U S A. 2005;102:16397-402 pubmed..We propose that, as in eukaryotes, the nucleoid architecture dictates the global transcription profile and, consequently, the behavior pattern in bacteria. ..
- Yin Z, Jayaram M, Pathania S, Harshey R. The Mu transposase interwraps distant DNA sites within a functional transpososome in the absence of DNA supercoiling. J Biol Chem. 2005;280:6149-56 pubmed..We discuss the contribution of both MuA and DNA supercoiling to the 5-noded Mu synapse built at the 3-way junction...
- McClendon A, Osheroff N. The geometry of DNA supercoils modulates topoisomerase-mediated DNA cleavage and enzyme response to anticancer drugs. Biochemistry. 2006;45:3040-50 pubmed
- Preisler A, Mraheil M, Heisig P. Role of novel gyrA mutations in the suppression of the fluoroquinolone resistance genotype of vaccine strain Salmonella Typhimurium vacT (gyrA D87G). J Antimicrob Chemother. 2006;57:430-6 pubmed publisher..The data point to a combination of at least one non-gyrA mutation and novel gyrA mutation(s) as the basis for the unusual fluoroquinolone susceptibility of vacT...
- Benham C, Bi C. The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J Comput Biol. 2004;11:519-43 pubmed
- Fierro Fernández M, Hernandez P, Krimer D, Schvartzman J. Replication fork reversal occurs spontaneously after digestion but is constrained in supercoiled domains. J Biol Chem. 2007;282:18190-6 pubmed
- Furuyama T, Henikoff S. Centromeric nucleosomes induce positive DNA supercoils. Cell. 2009;138:104-13 pubmed publisher..The mutual incompatibility of nucleosomes with opposite topologies could explain how centromeres are efficiently maintained as unique loci on chromosomes. ..
- Fierro Fernández M, Hernandez P, Krimer D, Stasiak A, Schvartzman J. Topological locking restrains replication fork reversal. Proc Natl Acad Sci U S A. 2007;104:1500-5 pubmed..We propose that this topological locking of replication intermediates provides a biological safety mechanism that protects DNA molecules against extensive fork reversals. ..
- McClendon A, Dickey J, Osheroff N. Ability of viral topoisomerase II to discern the handedness of supercoiled DNA: bimodal recognition of DNA geometry by type II enzymes. Biochemistry. 2006;45:11674-80 pubmed
- Swigon D, Coleman B, Olson W. Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci U S A. 2006;103:9879-84 pubmed
- McClendon A, Rodriguez A, Osheroff N. Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks. J Biol Chem. 2005;280:39337-45 pubmed..These properties suggest that human topoisomerase IIalpha has the potential to alleviate torsional stress ahead of replication forks in an efficient and safe manner. ..
- Travers A, Muskhelishvili G. A common topology for bacterial and eukaryotic transcription initiation?. EMBO Rep. 2007;8:147-51 pubmed..The apparent differences in the details of regulation probably represent alternative methods of fine-tuning similar underlying processes. ..
- Shusterman R, Gavrinyov T, Krichevsky O. Internal dynamics of superhelical DNA. Phys Rev Lett. 2008;100:098102 pubmed..Biopolymers 34, 639 (1994)10.1002/bip.360340506], but also in the short time range corresponding to the segmental motion within the DNA coil. ..
- Moulin L, Rahmouni A, Boccard F. Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli. Mol Microbiol. 2005;55:601-10 pubmed..These results correlate the ability of a DNA sequence to be cleaved by DNA gyrase with topological insulator activity. Implications of the asymmetry in supercoil diffusion for the control of DNA topology are discussed. ..
- Hardy C, Cozzarelli N. A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure. Mol Microbiol. 2005;57:1636-52 pubmed..We suggest that at least H-NS, Fis and perhaps TktA assist directly in the supercoiling of domains by forming topological barriers on the E. coli chromosome. ..
- Lopez C, Yang S, Deibler R, Ray S, Pennington J, Digate R, et al. A role for topoisomerase III in a recombination pathway alternative to RuvABC. Mol Microbiol. 2005;58:80-101 pubmed..These data are consistent with a role for topoisomerase III in disentangling recombination intermediates as an alternative to RuvABC to maintain the stability of the genome. ..
- Koster D, Palle K, Bot E, Bjornsti M, Dekker N. Antitumour drugs impede DNA uncoiling by topoisomerase I. Nature. 2007;448:213-7 pubmed..This combination of single-molecule and in vivo data suggests a cytotoxic mechanism for camptothecins, in which the accumulation of positive supercoils ahead of the replication machinery induces potentially lethal DNA lesions. ..
- Lushnikov A, Potaman V, Oussatcheva E, Sinden R, Lyubchenko Y. DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis. Biochemistry. 2006;45:152-8 pubmed..This suggests no preferential orientation of the DNA cognate site within the complex, suggesting that the central part of the DNA binding site does not form strong sequence specific contacts with the protein. ..
- Guo F, Adhya S. Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc Natl Acad Sci U S A. 2007;104:4309-14 pubmed..A negatively superhelical DNA can be modeled to wrap around this left-handed HUalphabeta multimer...
- Ercolini E, Valle F, Adamcik J, Witz G, Metzler R, De Los Rios P, et al. Fractal dimension and localization of DNA knots. Phys Rev Lett. 2007;98:058102 pubmed..60 within error. In (ii), we find nu approximately 0.66, a value between the 3D and 2D (nu=3/4) exponents. Evidence is also presented for the localization of knot crossings in 2D under weak adsorption conditions. ..
- Nollmann M, Stone M, Bryant Z, Gore J, Crisona N, Hong S, et al. Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque. Nat Struct Mol Biol. 2007;14:264-71 pubmed..A third mode is responsible for the ATP-independent relaxation of negative supercoils. We present a branched kinetic model that quantitatively accounts for all of our single-molecule results and agrees with existing biochemical data. ..
- Schvartzman J, Stasiak A. A topological view of the replicon. EMBO Rep. 2004;5:256-61 pubmed
- Conter A. Plasmid DNA supercoiling and survival in long-term cultures of Escherichia coli: role of NaCl. J Bacteriol. 2003;185:5324-7 pubmed
- Stone M, Bryant Z, Crisona N, Smith S, Vologodskii A, Bustamante C, et al. Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci U S A. 2003;100:8654-9 pubmed..Single-enzyme braid relaxation experiments also provide a direct measure of the processivity of the enzyme and offer insight into its mechanochemical cycle. ..
- Richmond T, Davey C. The structure of DNA in the nucleosome core. Nature. 2003;423:145-50 pubmed
- Hardy C, Cozzarelli N. Alteration of Escherichia coli topoisomerase IV to novobiocin resistance. Antimicrob Agents Chemother. 2003;47:941-7 pubmed..We conclude that topo IV is a secondary target of novobiocin and that it is very likely to be inhibited by the same mechanism as DNA gyrase. ..