DNA supercoiling and nucleoid architecture

nucleoid compactionDNA supercoiling by gyrase is linked to nucleoid compaction

Rogier Stuger, Conrad L. Woldringh, Coen C. van der Weijden, Norbert O.E. Vischer, Barbara M. Bakker, Rob J.M. van Spanning, Jacky L. Snoep, Hans V. Westerhoff

Mol Biol Rep 29 (2002) 79-82

erratum in Mol Biol Rep 30 (2003) 133

Molecular Cell Physiology, Free University, Amsterdam, The Netherlands.

The genes of E. coli are located on a circular chromosome of 4.6 million basepairs. This 1.6 mm long molecule is compressed into a nucleoid to fit inside the 1-2 μm cell in a functional format. To examine the role of DNA supercoiling as nucleoid compaction force we modulated the activity of DNA gyrase by electronic, genetic, and chemical means. A model based on physical properties of DNA and other cell components predicts that relaxation of supercoiling expands the nucleoid. Nucleoid size did not increase after reduction of DNA gyrase levels by genetic or chemical means, but nucleoids expanded upon chemical inhibition of gyrase in chloramphenicol-treated cells, indicating that supercoiling may help to compress the genome.  [full-text pdf]  [erratum pdf]

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some papers on DNA supercoiling and nucleoid compaction

B Peter, A Breier, A Khodursky, J Arsuaga, P Brown, N Cozzarelli. DNA-microarray-based identification of supercoiling-sensitive transcription and responses to topoisomerase inhibition in E. coli. in preparation

R Stuger, CL Woldringh, CC van der Weijden, NOE Vischer, BM Bakker, RJM van Spanning, JL Snoep, HV Westerhoff. DNA supercoiling by gyrase is linked to nucleoid compaction. Mol Biol Rep 29 (2002) 79-82  [abstract]  [full-text pdf]  [erratum pdf]

JL Snoep, CC van der Weijden, HW Andersen, HV Westerhoff, PR Jensen. DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. Eur J Biochem 269 (2002) 1662-1669  [abstract]  [full-text pdf]

S Cunha, CL Woldringh, T Odijk. Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids. J Struct Biol 136 (2001) 53-66  [abstract]  [full-text pdf]

EL Zechiedrich, AB Khodursky, S Bachellier, R Schneider, D Chen, DM Lilley, NR Cozzarelli. Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J Biol Chem 275 (2000) 8103-8113  [abstract]  [full-text pdf]

PR Jensen, CC van der Weijden, LB Jensen, HV Westerhoff, JL Snoep. Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli. Eur J Biochem 266 (1999) 865-877  [abstract]  [full-text pdf]

T Odijk. Osmotic compaction of supercoiled DNA into a bacterial nucleoid. Biophys Chem 73 (1998) 23-29  [abstract]  [full text @ ScienceDirect]

CL Woldringh, PR Jensen, HV Westerhoff. Structure and partitioning of bacterial DNA: determined by a balance of compaction and expansion forces? (review) FEMS Microbiol Lett 131 (1995) 235-242  [abstract]

more sites

Conrad Woldringh (U of Amsterdam) makes nucleoids glow in the dark
Steve Kowalczykowski (Davis, CA) unzips DNA
John Marko (Chicago) pulls plasmids & chromosomes
Dave Sherratt (Oxford) pulls chromosomes apart and recombines 'em

Wikipedia on DNA supercoiling and nucleoids

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