{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T06:10:25Z","timestamp":1781071825124,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008680","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,17]],"date-time":"2021-02-17T00:00:00Z","timestamp":1613520000000}}],"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T00:00:00Z","timestamp":1612396800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["TRR 174"],"award-info":[{"award-number":["TRR 174"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["TRR 174"],"award-info":[{"award-number":["TRR 174"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Membrane proteins account for about one third of the cellular proteome, but it is still unclear how dynamic they are and how they establish functional contacts with cytoplasmic interaction partners. Here, we consider a membrane-integrated one-component receptor that also acts as a transcriptional activator, and analyze how it kinetically locates its specific binding site on the genome. We focus on the case of CadC, the pH receptor of the acid stress response Cad system in\n                    <jats:italic>E. coli<\/jats:italic>\n                    . CadC is a prime example of a one-component signaling protein that directly binds to its cognate target site on the chromosome to regulate transcription. We combined fluorescence microscopy experiments, mathematical analysis, and kinetic Monte Carlo simulations to probe this target search process. Using fluorescently labeled CadC, we measured the time from activation of the receptor until successful binding to the DNA in single cells, exploiting that stable receptor-DNA complexes are visible as fluorescent spots. Our experimental data indicate that CadC is highly mobile in the membrane and finds its target by a 2D diffusion and capture mechanism. DNA mobility is constrained due to the overall chromosome organization, but a labeled DNA locus in the vicinity of the target site appears sufficiently mobile to randomly come close to the membrane. Relocation of the DNA target site to a distant position on the chromosome had almost no effect on the mean search time, which was between four and five minutes in either case. However, a mutant strain with two binding sites displayed a mean search time that was reduced by about a factor of two. This behavior is consistent with simulations of a coarse-grained lattice model for the coupled dynamics of DNA within a cell volume and proteins on its surface. The model also rationalizes the experimentally determined distribution of search times. Overall our findings reveal that DNA target search does not present a much bigger kinetic challenge for membrane-integrated proteins than for cytoplasmic proteins. More generally, diffusion and capture mechanisms may be sufficient for bacterial membrane proteins to establish functional contacts with cytoplasmic targets.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008680","type":"journal-article","created":{"date-parts":[[2021,2,6]],"date-time":"2021-02-06T13:59:49Z","timestamp":1612619989000},"page":"e1008680","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Dynamics of chromosomal target search by a membrane-integrated one-component receptor"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6641-1369","authenticated-orcid":true,"given":"Linda","family":"Martini","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6779-2343","authenticated-orcid":true,"given":"Sophie","family":"Brameyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7042-2247","authenticated-orcid":true,"given":"Elisabeth","family":"Hoyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0779-6841","authenticated-orcid":true,"given":"Kirsten","family":"Jung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0859-6422","authenticated-orcid":true,"given":"Ulrich","family":"Gerland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,2,4]]},"reference":[{"issue":"2","key":"pcbi.1008680.ref001","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nrmicro821","article-title":"Bacterial biofilms: from the natural environment to infectious diseases","volume":"2","author":"L Hall-Stoodley","year":"2004","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"pcbi.1008680.ref002","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.tim.2004.12.006","article-title":"One-component systems dominate signal transduction in prokaryotes","volume":"13","author":"LE Ulrich","year":"2005","journal-title":"Trends Microbiol"},{"issue":"1","key":"pcbi.1008680.ref003","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev.biochem.69.1.183","article-title":"Two-component signal transduction","volume":"69","author":"AM Stock","year":"2000","journal-title":"Annu Rev Biochem"},{"issue":"3","key":"pcbi.1008680.ref004","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/0022-2836(70)90074-4","article-title":"The lac represser-operator interaction: III. Kinetic studies","volume":"53","author":"AD Riggs","year":"1970","journal-title":"J Mol Biol"},{"key":"pcbi.1008680.ref005","first-page":"198","article-title":"Reduction of dimensionality in biological diffusion processes","volume":"198","author":"G Adam","year":"1968","journal-title":"Struct Chem Mol Biol"},{"issue":"3","key":"pcbi.1008680.ref006","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/0301-4622(74)80050-5","article-title":"Diffusion controlled reaction rates in spheroidal geometry: application to repressor-operator association and membrane bound enzymes","volume":"2","author":"PH Richter","year":"1974","journal-title":"Biophys Chem"},{"issue":"24","key":"pcbi.1008680.ref007","doi-asserted-by":"crossref","first-page":"6929","DOI":"10.1021\/bi00527a028","article-title":"Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory","volume":"20","author":"OG Berg","year":"1981","journal-title":"Biochemistry"},{"issue":"6","key":"pcbi.1008680.ref008","doi-asserted-by":"crossref","first-page":"4021","DOI":"10.1529\/biophysj.104.050765","article-title":"Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential","volume":"87","author":"M Slutsky","year":"2004","journal-title":"Biophys J"},{"issue":"8","key":"pcbi.1008680.ref009","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1529\/biophysj.105.078162","article-title":"How proteins search for their specific sites on DNA: the role of DNA conformation","volume":"90","author":"T Hu","year":"2006","journal-title":"Biophys J"},{"issue":"12","key":"pcbi.1008680.ref010","doi-asserted-by":"crossref","first-page":"4118","DOI":"10.1093\/nar\/gkn376","article-title":"Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA","volume":"36","author":"I Bonnet","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"pcbi.1008680.ref011","doi-asserted-by":"crossref","first-page":"188101","DOI":"10.1103\/PhysRevLett.102.188101","article-title":"Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins","volume":"102","author":"C Loverdo","year":"2009","journal-title":"Phys Rev Lett"},{"issue":"5828","key":"pcbi.1008680.ref012","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1126\/science.1141967","article-title":"Probing transcription factor dynamics at the single-molecule level in a living cell","volume":"316","author":"J Elf","year":"2007","journal-title":"Science"},{"issue":"6088","key":"pcbi.1008680.ref013","doi-asserted-by":"crossref","first-page":"1595","DOI":"10.1126\/science.1221648","article-title":"The lac repressor displays facilitated diffusion in living cells","volume":"336","author":"P Hammar","year":"2012","journal-title":"Science"},{"issue":"41","key":"pcbi.1008680.ref014","doi-asserted-by":"crossref","first-page":"15738","DOI":"10.1073\/pnas.0804248105","article-title":"How DNA coiling enhances target localization by proteins","volume":"105","author":"B van den Broek","year":"2008","journal-title":"Proc Natl Acad Sci"},{"issue":"5","key":"pcbi.1008680.ref015","doi-asserted-by":"crossref","first-page":"051911","DOI":"10.1103\/PhysRevE.84.051911","article-title":"Target search on a dynamic DNA molecule","volume":"84","author":"T Sch\u00f6tz","year":"2011","journal-title":"Phys Rev E"},{"issue":"4","key":"pcbi.1008680.ref016","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nphys1222","article-title":"Effects of macromolecular crowding and DNA looping on gene regulation kinetics","volume":"5","author":"GW Li","year":"2009","journal-title":"Nat Phys"},{"issue":"2","key":"pcbi.1008680.ref017","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/0092-8674(87)90430-2","article-title":"Cholera toxin transcriptional activator ToxR is a transmembrane DNA binding protein","volume":"48","author":"VL Miller","year":"1987","journal-title":"Cell"},{"issue":"5","key":"pcbi.1008680.ref018","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nmeth.2413","article-title":"A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum","volume":"10","author":"NC Shaner","year":"2013","journal-title":"Nat Methods"},{"issue":"3","key":"pcbi.1008680.ref019","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1046\/j.1365-2958.1997.3511719.x","article-title":"Transcriptional regulation of the Yersinia pseudotuberculosis pH 6 antigen adhesin by two envelope-associated components","volume":"24","author":"Y Yang","year":"1997","journal-title":"Mol Microbiol"},{"issue":"15","key":"pcbi.1008680.ref020","doi-asserted-by":"crossref","first-page":"2548","DOI":"10.1016\/j.jmb.2015.05.001","article-title":"Structural and functional analysis of the signal-transducing linker in the pH-responsive one-component system CadC of Escherichia coli","volume":"427","author":"S Buchner","year":"2015","journal-title":"J Mol Biol"},{"issue":"1","key":"pcbi.1008680.ref021","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1046\/j.1365-2958.2002.02993.x","article-title":"The role of co-transcriptional translation and protein translocation (transertion) in bacterial chromosome segregation","volume":"45","author":"CL Woldringh","year":"2002","journal-title":"Mol Microbiol"},{"key":"pcbi.1008680.ref022","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1146\/annurev-genet-112414-054958","article-title":"Chromosome-membrane interactions in bacteria","volume":"49","author":"M Roggiani","year":"2015","journal-title":"Annu Rev Genet"},{"issue":"3","key":"pcbi.1008680.ref023","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1007\/s13213-012-0596-3","article-title":"Biomacromolecular localization in bacterial cells by the diffusion and capture mechanism","volume":"63","author":"MAP Rodriguez","year":"2013","journal-title":"Ann Microbiol"},{"issue":"4","key":"pcbi.1008680.ref024","doi-asserted-by":"crossref","first-page":"180023","DOI":"10.1098\/rsob.180023","article-title":"Bacterial transmembrane signalling systems and their engineering for biosensing","volume":"8","author":"K Jung","year":"2018","journal-title":"Open Biol"},{"issue":"2","key":"pcbi.1008680.ref025","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.jmb.2009.08.037","article-title":"Induction kinetics of a conditional pH stress response system in Escherichia coli","volume":"393","author":"G Fritz","year":"2009","journal-title":"J Mol Biol"},{"issue":"1-2","key":"pcbi.1008680.ref026","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.jmb.2012.08.023","article-title":"Deactivation of the E. coli pH stress sensor CadC by cadaverine","volume":"424","author":"I Haneburger","year":"2012","journal-title":"J Mol Biol"},{"issue":"1","key":"pcbi.1008680.ref027","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/s42003-018-0248-7","article-title":"DNA-binding directs the localization of a membrane-integrated receptor of the ToxR family","volume":"2","author":"S Brameyer","year":"2019","journal-title":"Commun Biol"},{"issue":"8","key":"pcbi.1008680.ref028","doi-asserted-by":"crossref","first-page":"2504","DOI":"10.1093\/nar\/gki549","article-title":"Activity of Lac repressor anchored to the Escherichia coli inner membrane","volume":"33","author":"B G\u00f6rke","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008680.ref029","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511606014","volume-title":"A guide to first-passage processes","author":"S Redner","year":"2001"},{"issue":"1","key":"pcbi.1008680.ref030","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1038\/s41598-017-01031-9","article-title":"Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator","volume":"7","author":"A Schlundt","year":"2017","journal-title":"Sci Rep"},{"issue":"12","key":"pcbi.1008680.ref031","doi-asserted-by":"crossref","first-page":"10681","DOI":"10.1074\/jbc.M110.196923","article-title":"New insights into the signaling mechanism of the pH-responsive, membrane-integrated transcriptional activator CadC of Escherichia coli","volume":"286","author":"I Haneburger","year":"2011","journal-title":"J Biol Chem"},{"issue":"3","key":"pcbi.1008680.ref032","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1111\/j.1365-2958.2007.06070.x","article-title":"The membrane-integrated transcriptional activator CadC of Escherichia coli senses lysine indirectly via the interaction with the lysine permease LysP","volume":"67","author":"L Tetsch","year":"2008","journal-title":"Mol Microbiol"},{"issue":"1","key":"pcbi.1008680.ref033","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.jmb.2013.09.017","article-title":"New insights into the interplay between the lysine transporter LysP and the pH sensor CadC in Escherichia coli","volume":"426","author":"M Rauschmeier","year":"2014","journal-title":"J Mol Biol"},{"issue":"16","key":"pcbi.1008680.ref034","doi-asserted-by":"crossref","first-page":"2942","DOI":"10.1016\/j.jmb.2014.06.006","article-title":"Topology, dimerization, and stability of the single-span membrane protein CadC","volume":"426","author":"E Lindner","year":"2014","journal-title":"J Mol Biol"},{"issue":"6115","key":"pcbi.1008680.ref035","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1126\/science.1228985","article-title":"Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches","volume":"339","author":"S Ude","year":"2013","journal-title":"Science"},{"issue":"D1","key":"pcbi.1008680.ref036","doi-asserted-by":"crossref","first-page":"D613","DOI":"10.1093\/nar\/gks1235","article-title":"EcoGene 3.0","volume":"41","author":"J Zhou","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1008680.ref037","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1101\/gad.231050.113","article-title":"The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer","volume":"28","author":"B Youngren","year":"2014","journal-title":"Genes Dev"},{"issue":"23","key":"pcbi.1008680.ref038","doi-asserted-by":"crossref","first-page":"238102","DOI":"10.1103\/PhysRevLett.104.238102","article-title":"Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm","volume":"104","author":"SC Weber","year":"2010","journal-title":"Phys Rev Lett"},{"issue":"6","key":"pcbi.1008680.ref039","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1111\/j.1365-2958.2008.06239.x","article-title":"DNA dynamics vary according to macrodomain topography in the E. coli chromosome","volume":"68","author":"O Espeli","year":"2008","journal-title":"Mol Microbiol"},{"issue":"7","key":"pcbi.1008680.ref040","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.1063\/1.1699180","article-title":"A theory of the linear viscoelastic properties of dilute solutions of coiling polymers","volume":"21","author":"PE Rouse","year":"1953","journal-title":"J Chem Phys"},{"key":"pcbi.1008680.ref041","doi-asserted-by":"crossref","first-page":"3003","DOI":"10.1038\/ncomms3003","article-title":"Short-time movement of E. coli chromosomal loci depends on coordinate and subcellular localization","volume":"4","author":"A Javer","year":"2013","journal-title":"Nat Commun"},{"issue":"3","key":"pcbi.1008680.ref042","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1007\/s10955-005-8028-4","article-title":"Narrow escape, Part III: Non-smooth domains and Riemann surfaces","volume":"122","author":"A Singer","year":"2006","journal-title":"J Stat Phys"},{"issue":"24","key":"pcbi.1008680.ref043","doi-asserted-by":"crossref","first-page":"244906","DOI":"10.1063\/1.4772403","article-title":"Encounter dynamics of a small target by a polymer diffusing in a confined domain","volume":"137","author":"A Amitai","year":"2012","journal-title":"J Chem Phys"},{"issue":"1","key":"pcbi.1008680.ref044","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1038\/nrmicro1795","article-title":"Getting organized\u2014how bacterial cells move proteins and DNA","volume":"6","author":"M Thanbichler","year":"2008","journal-title":"Nat Rev Microbiol"},{"issue":"13","key":"pcbi.1008680.ref045","doi-asserted-by":"crossref","first-page":"8701","DOI":"10.1073\/pnas.132235899","article-title":"Evidence that subcellular localization of a bacterial membrane protein is achieved by diffusion and capture","volume":"99","author":"DZ Rudner","year":"2002","journal-title":"Proc Natl Acad Sci"},{"issue":"7678","key":"pcbi.1008680.ref046","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature24299","article-title":"A global resource allocation strategy governs growth transition kinetics of Escherichia coli","volume":"551","author":"DW Erickson","year":"2017","journal-title":"Nature"},{"key":"pcbi.1008680.ref047","doi-asserted-by":"crossref","first-page":"7745","DOI":"10.1007\/s00216-016-9871-7","article-title":"Study of the degradation of a multidrug transporter using a non-radioactive pulse chase method","volume":"408","author":"Q Chai","year":"2016","journal-title":"Anal Bioanal Chem"},{"issue":"4","key":"pcbi.1008680.ref048","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1016\/j.bpj.2009.11.002","article-title":"Mobility of cytoplasmic, membrane, and DNA-binding proteins in Escherichia coli","volume":"98","author":"M Kumar","year":"2010","journal-title":"Biophys J"},{"issue":"5","key":"pcbi.1008680.ref049","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1016\/j.bpj.2016.01.010","article-title":"MreB-dependent organization of the E. coli cytoplasmic membrane controls membrane protein diffusion","volume":"110","author":"F Oswald","year":"2016","journal-title":"Biophys J"},{"issue":"1","key":"pcbi.1008680.ref050","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1242\/jcs.138628","article-title":"How do bacteria localize proteins to the cell pole?","volume":"127","author":"G Laloux","year":"2014","journal-title":"J Cell Sci"},{"issue":"7","key":"pcbi.1008680.ref051","doi-asserted-by":"crossref","first-page":"3740","DOI":"10.1128\/JB.171.7.3740-3745.1989","article-title":"Normal growth and division of Escherichia coli with a reduced amount of murein","volume":"171","author":"R Prats","year":"1989","journal-title":"J Bacteriol"},{"issue":"1","key":"pcbi.1008680.ref052","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1007\/s12575-009-9008-x","article-title":"Size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy","volume":"11","author":"HP Erickson","year":"2009","journal-title":"Biol Proced Online"},{"issue":"3","key":"pcbi.1008680.ref053","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/s41564-019-0657-5","article-title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","volume":"5","author":"N Baranova","year":"2020","journal-title":"Nat Microbiol"},{"issue":"4","key":"pcbi.1008680.ref054","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1093\/nar\/gkq932","article-title":"Temperature dependence of DNA persistence length","volume":"39","author":"S Geggier","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"pcbi.1008680.ref055","doi-asserted-by":"crossref","first-page":"2819","DOI":"10.1021\/ma00187a030","article-title":"The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions","volume":"21","author":"I Carmesin","year":"1988","journal-title":"Macromolecules"},{"issue":"6","key":"pcbi.1008680.ref056","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1063\/1.1699114","article-title":"Equation of state calculations by fast computing machines","volume":"21","author":"N Metropolis","year":"1953","journal-title":"J Chem Phys"},{"issue":"2","key":"pcbi.1008680.ref057","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s10820-006-9042-9","article-title":"An overview of spatial microscopic and accelerated kinetic Monte Carlo methods","volume":"14","author":"A Chatterjee","year":"2007","journal-title":"J Comput Aided Mol Des"},{"issue":"5331","key":"pcbi.1008680.ref058","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The complete genome sequence of Escherichia coli K-12","volume":"277","author":"FR Blattner","year":"1997","journal-title":"Science"},{"issue":"25","key":"pcbi.1008680.ref059","doi-asserted-by":"crossref","first-page":"12625","DOI":"10.1039\/C4CP00299G","article-title":"Imaging and quantification of trans-membrane protein diffusion in living bacteria","volume":"16","author":"F Oswald","year":"2014","journal-title":"Phys Chem Chem Phys"},{"issue":"2","key":"pcbi.1008680.ref060","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1128\/JB.108.2.639-644.1971","article-title":"Potassium transport loci in Escherichia coli K-12","volume":"108","author":"W Epstein","year":"1971","journal-title":"J Bacteriol"},{"issue":"5","key":"pcbi.1008680.ref061","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.1318","article-title":"Enzymatic assembly of DNA molecules up to several hundred kilobases","volume":"6","author":"DG Gibson","year":"2009","journal-title":"Nat Methods"},{"issue":"6","key":"pcbi.1008680.ref062","doi-asserted-by":"crossref","first-page":"2575","DOI":"10.1128\/JB.170.6.2575-2583.1988","article-title":"A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR","volume":"170","author":"VL Miller","year":"1988","journal-title":"J Bacteriol"},{"issue":"2","key":"pcbi.1008680.ref063","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1128\/JB.179.2.538-540.1997","article-title":"Maintenance of broad-host-range incompatibility group P and group Q plasmids and transposition of Tn5 in Bartonella henselae following conjugal plasmid transfer from Escherichia coli","volume":"179","author":"C Dehio","year":"1997","journal-title":"J Bacteriol"},{"issue":"1","key":"pcbi.1008680.ref064","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1159\/000090346","article-title":"CadC-mediated activation of the cadBA promoter in Escherichia coli","volume":"10","author":"C K\u00fcper","year":"2005","journal-title":"J Mol Microbiol Biotechnol"},{"issue":"2","key":"pcbi.1008680.ref065","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1111\/j.1365-2958.2006.05346.x","article-title":"The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves","volume":"62","author":"HJ Nielsen","year":"2006","journal-title":"Mol Microbiol"},{"issue":"4","key":"pcbi.1008680.ref066","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1111\/mmi.13264","article-title":"Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis","volume":"99","author":"A Paintdakhi","year":"2016","journal-title":"Mol Microbiol"},{"issue":"3","key":"pcbi.1008680.ref067","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1111\/j.1539-6924.1989.tb01007.x","article-title":"Numerical recipes in C: the art of scientific computing","volume":"9","author":"MC Seiler","year":"1989","journal-title":"Risk Anal"},{"key":"pcbi.1008680.ref068","article-title":"Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes","author":"M Socol","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008680.ref069","volume-title":"The theory of polymer dynamics","author":"M Doi","year":"1988"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008680","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,2,17]],"date-time":"2021-02-17T00:00:00Z","timestamp":1613520000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008680","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,17]],"date-time":"2021-02-17T16:34:08Z","timestamp":1613579648000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008680"}},"subtitle":[],"editor":[{"given":"Tamar","family":"Schlick","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,2,4]]},"references-count":69,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008680","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.06.28.176644","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,4]]}}}