{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:19:25Z","timestamp":1785406765514,"version":"3.56.0"},"posted":{"date-parts":[[2025,12,23]]},"group-title":"Biophysics","reference-count":61,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R01 GM143182"],"award-info":[{"award-number":["R01 GM143182"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01GM141242"],"award-info":[{"award-number":["R01GM141242"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01AI172822"],"award-info":[{"award-number":["R01AI172822"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01GM144731"],"award-info":[{"award-number":["R01GM144731"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"U.S. National Science Foundation","doi-asserted-by":"crossref","award":["2022049"],"award-info":[{"award-number":["2022049"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The bacterial nucleoid undergoes extensive structural reorganization during growth, influenced by nucleoid-associated proteins (NAPs) whose interactions and effects on nucleoid organization remain unclear. We investigated these interactions by tracking single molecules of the NAP HU\u03b1-PAmCherry in living\n                  <jats:italic>Escherichia coli<\/jats:italic>\n                  cells in different growth phases, and we further examined how two NAPs, Dps and H-NS, impact HU\u03b1 dynamics. HU\u03b1 mobility varies with growth phase: In exponential phase, HU\u03b1 has two distinct mobility states: a fast-diffusing state and a slower, interacting state. In stationary phase, we observed a third population of very slow molecules, suggesting stable HU\u03b1 binding or confinement within compacted DNA. Deleting\n                  <jats:italic>dps<\/jats:italic>\n                  increases HU\u03b1 mobility in stationary phase, consistent with findings that Dps promotes short-range DNA contacts and nucleoid compaction in deep stationary phase. We measured in exponential phase that\n                  <jats:italic>hns<\/jats:italic>\n                  deletion leads to nucleoid compaction, faster HU\u03b1 diffusion, and a third population of very slow HU\u03b1 molecules in these cells. In stationary phase, deleting\n                  <jats:italic>hns<\/jats:italic>\n                  increases these stably bound HU\u03b1 molecules. Our results show that growth-phase-dependent nucleoid reorganization by Dps and H-NS influences the behavior and function of other NAPs.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Graphical Abstract<\/jats:title>\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"695591v2_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                  <jats:p>The nucleoid-associated proteins Dps, H-NS, and HU shape the bacterial chromosome in the deep stationary phase through their interactions with the nucleoid.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2025.12.19.695591","type":"posted-content","created":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T11:05:28Z","timestamp":1766487928000},"source":"Crossref","is-referenced-by-count":0,"title":["Characterizing the Impact of Nucleoid-Associated Proteins on HU-DNA Interactions by Live-Cell Single-Molecule Tracking"],"prefix":"10.64898","author":[{"given":"D. E. H.","family":"Fuller","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6190-392X","authenticated-orcid":false,"given":"X.","family":"Dai","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9646-5333","authenticated-orcid":false,"given":"L. A.","family":"McCarthy","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1491-2305","authenticated-orcid":false,"given":"L. E.","family":"Way","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University, Bloomington, IN, 47405, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6458-180X","authenticated-orcid":false,"given":"X.","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biology, Indiana University, Bloomington, IN, 47405, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2038-6484","authenticated-orcid":false,"given":"J. S.","family":"Biteen","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026030701552095000_2025.12.19.695591v2.1","doi-asserted-by":"publisher","DOI":"10.1002\/jcb.20519"},{"key":"2026030701552095000_2025.12.19.695591v2.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biochi.2010.06.024"},{"key":"2026030701552095000_2025.12.19.695591v2.3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1139"},{"key":"2026030701552095000_2025.12.19.695591v2.4","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.275.11.8103"},{"key":"2026030701552095000_2025.12.19.695591v2.5","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2261"},{"key":"2026030701552095000_2025.12.19.695591v2.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2023.104861"},{"key":"2026030701552095000_2025.12.19.695591v2.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2020.09.023"},{"key":"2026030701552095000_2025.12.19.695591v2.8","doi-asserted-by":"crossref","unstructured":"Ho\u0142\u00f3wka, J. & Zakrzewska-Czerwi\u0144ska, J . Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress. Front. Microbiol. 11, 590 (2020).","DOI":"10.3389\/fmicb.2020.00590"},{"key":"2026030701552095000_2025.12.19.695591v2.9","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.115.178970"},{"key":"2026030701552095000_2025.12.19.695591v2.10","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.13.4192-4198.2004"},{"key":"2026030701552095000_2025.12.19.695591v2.11","doi-asserted-by":"publisher","DOI":"10.1101\/gad.6.12b.2646"},{"key":"2026030701552095000_2025.12.19.695591v2.12","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0498-294"},{"key":"2026030701552095000_2025.12.19.695591v2.13","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00036-22"},{"key":"2026030701552095000_2025.12.19.695591v2.14","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00475-15"},{"key":"2026030701552095000_2025.12.19.695591v2.15","first-page":"e00114","article-title":"Dps Protects Enterohemorrhagic Escherichia coli against Acid-Induced Antimicrobial Peptide Killing","volume":"202","year":"2020","journal-title":"J. Bacteriol"},{"key":"2026030701552095000_2025.12.19.695591v2.16","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02000"},{"key":"2026030701552095000_2025.12.19.695591v2.17","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.mi.47.100193.004231"},{"key":"2026030701552095000_2025.12.19.695591v2.18","first-page":"e00542","article-title":"Controlled burn: interconnections between energy-spilling pathways and metabolic signaling in bacteria","volume":"207","year":"2025","journal-title":"J. Bacteriol"},{"key":"2026030701552095000_2025.12.19.695591v2.19","doi-asserted-by":"publisher","DOI":"10.1128\/JB.181.20.6361-6370.1999"},{"key":"2026030701552095000_2025.12.19.695591v2.20","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03855.x"},{"key":"2026030701552095000_2025.12.19.695591v2.21","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M206186200"},{"key":"2026030701552095000_2025.12.19.695591v2.22","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1016\/j.bbagen.2010.01.013","article-title":"The multifaceted capacity of Dps proteins to combat bacterial stress conditions: Detoxification of iron and hydrogen peroxide and DNA binding","volume":"1800","year":"2010","journal-title":"Biochim. Biophys. Acta BBA - Gen. Subj"},{"key":"2026030701552095000_2025.12.19.695591v2.23","doi-asserted-by":"publisher","DOI":"10.1038\/21918"},{"key":"2026030701552095000_2025.12.19.695591v2.24","doi-asserted-by":"crossref","unstructured":"McCarthy, L. A. et al. Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics, and organization. Nucleic Acids Res. 54, (2026).","DOI":"10.1093\/nar\/gkaf1463"},{"key":"2026030701552095000_2025.12.19.695591v2.25","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/BF00334684","article-title":"Identification, cloning, nucleotide sequence and chromosomal map location of hns, the structural gene for Escherichia coli DNA-binding protein H-NS","volume":"212","year":"1988","journal-title":"Mol. Gen. Genet. MGG"},{"key":"2026030701552095000_2025.12.19.695591v2.26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky826"},{"key":"2026030701552095000_2025.12.19.695591v2.27","doi-asserted-by":"publisher","DOI":"10.1038\/nature05283"},{"key":"2026030701552095000_2025.12.19.695591v2.28","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1534\/g3.114.016139","article-title":"Gene Regulation by H-NS as a Function of Growth Conditions Depends on Chromosomal Position in Escherichia coli","volume":"5","year":"2015","journal-title":"G3 GenesGenomesGenetics"},{"key":"2026030701552095000_2025.12.19.695591v2.29","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro883"},{"key":"2026030701552095000_2025.12.19.695591v2.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2019.07.013"},{"key":"2026030701552095000_2025.12.19.695591v2.31","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2001.02358.x"},{"key":"2026030701552095000_2025.12.19.695591v2.32","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)01141-5"},{"key":"2026030701552095000_2025.12.19.695591v2.33","doi-asserted-by":"publisher","DOI":"10.1042\/BST20160190"},{"key":"2026030701552095000_2025.12.19.695591v2.34","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/s41586-025-09396-y","article-title":"Elementary 3D organization of active and silenced E. coli genome","volume":"645","year":"2025","journal-title":"Nature"},{"key":"2026030701552095000_2025.12.19.695591v2.35","doi-asserted-by":"publisher","DOI":"10.1101\/2025.10.14.682352"},{"key":"2026030701552095000_2025.12.19.695591v2.36","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1406593111"},{"key":"2026030701552095000_2025.12.19.695591v2.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2020.03.008"},{"key":"2026030701552095000_2025.12.19.695591v2.38","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.14572"},{"key":"2026030701552095000_2025.12.19.695591v2.39","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.36.4.525-557.1972"},{"key":"2026030701552095000_2025.12.19.695591v2.40","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01639-4"},{"key":"2026030701552095000_2025.12.19.695591v2.41","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2019.02.006"},{"key":"2026030701552095000_2025.12.19.695591v2.42","doi-asserted-by":"publisher","DOI":"10.1137\/0105003"},{"key":"2026030701552095000_2025.12.19.695591v2.43","doi-asserted-by":"publisher","DOI":"10.1126\/science.1127344"},{"key":"2026030701552095000_2025.12.19.695591v2.44","first-page":"e01919","article-title":"Nucleoid compaction influences carboxysome localization and dynamics in Synechococcus elongatus PCC 7942","volume":"16","year":"2025","journal-title":"mBio"},{"key":"2026030701552095000_2025.12.19.695591v2.45","doi-asserted-by":"publisher","DOI":"10.1006\/meth.2001.1262"},{"key":"2026030701552095000_2025.12.19.695591v2.46","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.15033"},{"key":"2026030701552095000_2025.12.19.695591v2.47","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00840-12"},{"key":"2026030701552095000_2025.12.19.695591v2.48","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(92)90354-F"},{"key":"2026030701552095000_2025.12.19.695591v2.49","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1994.tb06256.x"},{"key":"2026030701552095000_2025.12.19.695591v2.50","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1997.tb12724.x"},{"key":"2026030701552095000_2025.12.19.695591v2.51","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0020081"},{"key":"2026030701552095000_2025.12.19.695591v2.52","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2008.06253.x"},{"key":"2026030701552095000_2025.12.19.695591v2.53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0093031"},{"key":"2026030701552095000_2025.12.19.695591v2.54","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03644.x"},{"key":"2026030701552095000_2025.12.19.695591v2.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.06.049"},{"key":"2026030701552095000_2025.12.19.695591v2.56","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh915"},{"key":"2026030701552095000_2025.12.19.695591v2.57","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.00143-20"},{"key":"2026030701552095000_2025.12.19.695591v2.58","doi-asserted-by":"publisher","DOI":"10.1016\/j.jsb.2006.03.022"},{"key":"2026030701552095000_2025.12.19.695591v2.59","doi-asserted-by":"publisher","DOI":"10.1128\/jb.177.12.3455-3464.1995"},{"key":"2026030701552095000_2025.12.19.695591v2.60","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00919-15"},{"key":"2026030701552095000_2025.12.19.695591v2.61","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku566"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2025.12.19.695591","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:16:17Z","timestamp":1782278177000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2025.12.19.695591"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,23]]},"references-count":61,"URL":"https:\/\/doi.org\/10.64898\/2025.12.19.695591","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1002\/cphc.202500916","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,12,23]]},"subtype":"preprint"}}