{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:43:01Z","timestamp":1772170981508,"version":"3.50.1"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2008,1,18]],"date-time":"2008-01-18T00:00:00Z","timestamp":1200614400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.0040017","type":"journal-article","created":{"date-parts":[[2008,1,15]],"date-time":"2008-01-15T10:47:22Z","timestamp":1200394042000},"page":"e17","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":25,"title":["Superhelical Destabilization in Regulatory Regions of Stress Response Genes"],"prefix":"10.1371","volume":"4","author":[{"given":"Huiquan","family":"Wang","sequence":"first","affiliation":[]},{"given":"Craig J","family":"Benham","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,1,18]]},"reference":[{"key":"pcbi-0040017-b001","article-title":"Susceptibility to superhelically driven DNA duplex destabilization: A highly conserved property of yeast replication origins.","volume":"1","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"pcbi-0040017-b002","doi-asserted-by":"crossref","first-page":"9464","DOI":"10.1073\/pnas.85.24.9464","article-title":"Stable DNA unwinding, not \u201cbreathing\u201d, accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences.","volume":"85","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040017-b003","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1006\/jmbi.1996.0035","article-title":"Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions.","volume":"255","year":"1996","journal-title":"J Mol Biol"},{"key":"pcbi-0040017-b004","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1146\/annurev.genet.36.032902.111815","article-title":"DNA topology-mediated control of global gene expression in Escherichia coli.","volume":"36","year":"2002","journal-title":"Annu Rev Genet"},{"key":"pcbi-0040017-b005","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/BF00925689","article-title":"Altered topoisomerase activities may be involved in the regualtion of DNA supercoiling in aerobic-anaerovic transitions in Escherichia coli.","volume":"126","year":"1993","journal-title":"Mol Cell Biochem"},{"key":"pcbi-0040017-b006","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/0966-842X(96)30015-2","article-title":"Flexible response: DNA supercoiling, transcription and bacterial adaptation to environmental stress.","volume":"4","year":"1996","journal-title":"Trends Microbiol"},{"key":"pcbi-0040017-b007","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1016\/0092-8674(88)90470-9","article-title":"A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli.","volume":"52","year":"1988","journal-title":"Cell"},{"key":"pcbi-0040017-b008","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1046\/j.1365-2958.2002.03001.x","article-title":"Gene expression profiling of Escherichia coli growth transitions: An expanded stringent response model.","volume":"45","year":"2002","journal-title":"Mol Microbiol"},{"key":"pcbi-0040017-b009","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1101\/gr.401003","article-title":"A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli.","volume":"13","year":"2003","journal-title":"Genome Res"},{"key":"pcbi-0040017-b010","doi-asserted-by":"crossref","first-page":"29837","DOI":"10.1074\/jbc.M213060200","article-title":"Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.","volume":"278","year":"2003","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b011","doi-asserted-by":"crossref","first-page":"7024","DOI":"10.1073\/pnas.84.20.7024","article-title":"Supercoiling of the DNA template during transcription.","volume":"84","year":"1987","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040017-b012","doi-asserted-by":"crossref","first-page":"1092","DOI":"10.1038\/nsmb848","article-title":"The dynamic response of upstream DNA to transcription-generated torsional stress.","volume":"11","year":"2004","journal-title":"Nat Struct Mol Biol"},{"key":"pcbi-0040017-b013","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/0092-8674(89)90574-6","article-title":"DNA supercoiling and prokaryotic transcription.","volume":"56","year":"1989","journal-title":"Cell"},{"key":"pcbi-0040017-b014","doi-asserted-by":"crossref","first-page":"10718","DOI":"10.1021\/bi030110t","article-title":"Effect of varying the supercoiling of DNA on transcription and its regulation.","volume":"42","year":"2003","journal-title":"Biochemistry"},{"key":"pcbi-0040017-b015","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/S1369-5274(99)80022-8","article-title":"DNA structure and transcription.","volume":"2","year":"1999","journal-title":"Curr Opin Microbiol"},{"key":"pcbi-0040017-b016","doi-asserted-by":"crossref","first-page":"10055","DOI":"10.1016\/S0021-9258(19)38778-2","article-title":"Characterization of the integration host factor binding site in the ilvPG1 promoter region in the ilvGMEDA operon of Escherichia coli.","volume":"265","year":"1990","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b017","doi-asserted-by":"crossref","first-page":"21298","DOI":"10.1074\/jbc.273.33.21298","article-title":"Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence.","volume":"273","year":"1998","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b018","doi-asserted-by":"crossref","first-page":"8169","DOI":"10.1074\/jbc.274.12.8169","article-title":"Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition.","volume":"274","year":"1999","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b019","doi-asserted-by":"crossref","unstructured":"WangJCLynchAS 1996 Effects of DNA supercoiling on gene expression. In: LinECCLynchAS Regulation of gene expression in Escherichia coli New York Chapman & Hall 127 147","DOI":"10.1007\/978-1-4684-8601-8_7"},{"key":"pcbi-0040017-b020","doi-asserted-by":"crossref","first-page":"3870","DOI":"10.1073\/pnas.76.8.3870","article-title":"Torsional stress and local denaturation in supercoiled DNA.","volume":"76","year":"1979","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040017-b021","doi-asserted-by":"crossref","first-page":"2999","DOI":"10.1073\/pnas.90.7.2999","article-title":"Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci.","volume":"90","year":"1993","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040017-b022","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1089\/cmb.2004.11.519","article-title":"The analysis of stress-induced DNA duplex destabilization in long genomic DNA sequences.","volume":"11","year":"2004","journal-title":"J Comput Biol"},{"key":"pcbi-0040017-b023","doi-asserted-by":"crossref","first-page":"1477","DOI":"10.1093\/bioinformatics\/bth304","article-title":"WebSIDD: Server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA.","volume":"20","year":"2004","journal-title":"Bioinformatics"},{"key":"pcbi-0040017-b024","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1002\/(SICI)1097-0061(19970330)13:4<313::AID-YEA93>3.0.CO;2-8","article-title":"Analysis of the struture of a natural alterating d(TA)n sequence in yeast chromatin.","volume":"13","year":"1997","journal-title":"Yeast"},{"key":"pcbi-0040017-b025","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1006\/jmbi.1997.1385","article-title":"Stress-induced duplex DNA destabilization in scaffold\/matrix attachment regions.","volume":"274","year":"1997","journal-title":"J Mol Biol"},{"key":"pcbi-0040017-b026","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/0022-2836(92)90404-8","article-title":"Energetics of the strand separation transition in superhelical DNA.","volume":"225","year":"1992","journal-title":"J Mol Biol"},{"key":"pcbi-0040017-b027","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/j.virol.2004.07.023","article-title":"Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function.","volume":"328","year":"2004","journal-title":"Virology"},{"key":"pcbi-0040017-b028","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1101\/gr.2080004","article-title":"Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters.","volume":"14","year":"2004","journal-title":"Genome Res"},{"key":"pcbi-0040017-b029","doi-asserted-by":"crossref","first-page":"10745","DOI":"10.1073\/pnas.200365097","article-title":"An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled.","volume":"97","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040017-b030","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1093\/emboj\/19.5.1034","article-title":"Loss of FBP function arrests cellular proliferation and extinguishes c-myc expression.","volume":"19","year":"2000","journal-title":"EMBO J"},{"key":"pcbi-0040017-b031","doi-asserted-by":"crossref","first-page":"4521","DOI":"10.1002\/j.1460-2075.1993.tb06141.x","article-title":"A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome.","volume":"12","year":"1993","journal-title":"EMBO J"},{"key":"pcbi-0040017-b032","doi-asserted-by":"crossref","first-page":"4335","DOI":"10.1002\/j.1460-2075.1989.tb08620.x","article-title":"The DNA unwinding element: A novel, cis-acting component that facilitates opening of the Escherichia coli replication origin.","volume":"8","year":"1989","journal-title":"EMBO J"},{"key":"pcbi-0040017-b033","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/j.jmb.2005.11.073","article-title":"Correlations between scaffold\/matrix attachment region (S\/MAR) binding activity and DNA duplex destabilization energy.","volume":"358","year":"2006","journal-title":"J Mol Biol"},{"key":"pcbi-0040017-b034","doi-asserted-by":"crossref","first-page":"D373","DOI":"10.1093\/nar\/gkj007","article-title":"SIDDBASE: A database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes.","volume":"34","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040017-b035","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1186\/1471-2105-7-248","article-title":"Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress.","volume":"7","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"pcbi-0040017-b036","doi-asserted-by":"crossref","first-page":"D300","DOI":"10.1093\/nar\/gkh087","article-title":"GenProtEC: An updated and improved analysis of functions of Escherichia coli K-12 proteins.","volume":"32","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040017-b037","unstructured":"FellerW 1968 An introduction to probability theory and its applications New York John Wiley & Sons 626"},{"key":"pcbi-0040017-b038","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families.","volume":"278","year":"1997","journal-title":"Science"},{"key":"pcbi-0040017-b039","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/S1369-5274(99)80026-5","article-title":"Interplay of global regulators and cell physiology in the general stress response of Escherichia coli.","volume":"2","year":"1999","journal-title":"Curr Opin Microbiol"},{"key":"pcbi-0040017-b040","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1111\/j.1365-2958.1992.tb01486.x","article-title":"Control of bacterial DNA supercoiling.","volume":"6","year":"1992","journal-title":"Mol Microbiol"},{"key":"pcbi-0040017-b041","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/S0014-5793(02)03363-X","article-title":"HU: Promoting or counteracting DNA compaction?","volume":"529","year":"2002","journal-title":"FEBS Lett"},{"key":"pcbi-0040017-b042","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1111\/j.1574-6968.1997.tb12724.x","article-title":"Molecular aspects of the E. coli nucleoid protein, H-NS: A central controller of gene regulatory networks.","volume":"156","year":"1997","journal-title":"FEMS Microbiol Lett"},{"key":"pcbi-0040017-b043","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/S0168-6445(03)00066-4","article-title":"Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: Exploiting the metabolic spectrum by controlling alternative gene programs.","volume":"27","year":"2003","journal-title":"FEMS Microbiol Rev"},{"key":"pcbi-0040017-b044","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1128\/JB.131.2.623-630.1977","article-title":"Influence of osmolarity of the growth medium on the outer membrane protein pattern of Escherichia coli.","volume":"131","year":"1977","journal-title":"J Bacteriol"},{"key":"pcbi-0040017-b045","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1111\/j.1365-2958.1989.tb00253.x","article-title":"Molecular characterization of the proU loci of Salmonella typhimurium and Escherichia coli encoding osmoregulated glycine betaine transport systems.","volume":"3","year":"1989","journal-title":"Mol Microbiol"},{"key":"pcbi-0040017-b046","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1111\/j.1365-2958.2003.03965.x","article-title":"Mode of action of the TyrR protein: Repression and activation of the tyrP promoter of Escherichia coli.","volume":"52","year":"2004","journal-title":"Mol Microbiol"},{"key":"pcbi-0040017-b047","doi-asserted-by":"crossref","first-page":"49563","DOI":"10.1074\/jbc.R400026200","article-title":"Bacterial long chain fatty acid transport: Gateway to a fatty acid-responsive signaling system.","volume":"279","year":"2004","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b048","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.gde.2005.09.013","article-title":"For better or worse: Genomic consequences of intracellular mutualism and parasitism.","volume":"15","year":"2005","journal-title":"Curr Opin Genet Dev"},{"key":"pcbi-0040017-b049","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1146\/annurev.mi.47.100193.003121","article-title":"Molecular biology of the LysR family of transcriptional regulators.","volume":"47","year":"1993","journal-title":"Annu Rev Microbiol"},{"key":"pcbi-0040017-b050","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1093\/dnares\/4.2.161","article-title":"Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli.","volume":"4","year":"1997","journal-title":"DNA Res"},{"key":"pcbi-0040017-b051","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/S0966-842X(03)00176-8","article-title":"Making informed decisions: Regulatory interactions between two-component systems.","volume":"11","year":"2003","journal-title":"Trends Microbiol"},{"key":"pcbi-0040017-b052","doi-asserted-by":"crossref","first-page":"11257","DOI":"10.1074\/jbc.273.18.11257","article-title":"Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex.","volume":"273","year":"1998","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b053","doi-asserted-by":"crossref","first-page":"14294","DOI":"10.1073\/pnas.96.25.14294","article-title":"Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli.","volume":"96","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0040017-b054","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s002030100298","article-title":"Sulfonate-sulfur metabolism and its regulation in Escherichia coli.","volume":"176","year":"2001","journal-title":"Arch Microbiol"},{"key":"pcbi-0040017-b055","doi-asserted-by":"crossref","unstructured":"DarwinAJStewartV 1996 Nitrate and nitrite regulation of anaerobic gene expression. In: LinECCLynchAS Regulation of gene expression in Escherichia coli New York Chapman & Hall 343 354","DOI":"10.1007\/978-1-4684-8601-8_17"},{"key":"pcbi-0040017-b056","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes.","volume":"28","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0040017-b057","doi-asserted-by":"crossref","first-page":"R87","DOI":"10.1186\/gb-2004-5-11-r87","article-title":"Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli.","volume":"5","year":"2004","journal-title":"Genome Biol"},{"key":"pcbi-0040017-b058","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1111\/j.1365-2958.2004.04147.x","article-title":"Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism.","volume":"53","year":"2004","journal-title":"Mol Microbiol"},{"key":"pcbi-0040017-b059","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/j.mib.2006.08.007","article-title":"Transcriptional regulatory networks in bacteria: From input signals to output responses.","volume":"9","year":"2006","journal-title":"Curr Opin Microbiol"},{"key":"pcbi-0040017-b060","doi-asserted-by":"crossref","first-page":"15084","DOI":"10.1074\/jbc.M414030200","article-title":"Global gene expression profiling in Escherichia coli K12: Effects of oxygen availability and ArcA.","volume":"280","year":"2005","journal-title":"J Biol Chem"},{"key":"pcbi-0040017-b061","first-page":"21","article-title":"DNA supercoiling and its effects on the structure of DNA.","volume":"1","year":"1984","journal-title":"J Cell Sci Suppl"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040017","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T16:19:58Z","timestamp":1630513198000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0040017"}},"subtitle":[],"editor":[{"given":"J\u00fcrgen","family":"Bode","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,1,18]]},"references-count":61,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2008,1,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0040017","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1099226.555444","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,18]]}}}