biostudies-literatureErkelens AMChina Scholarship CouncilDutch Research Council (NWO)Ministry of Science and Innovation of the Spanish GovernmentSpanish Ministry of Universities and Autonomous University of Madrid12166-12185https://www.ebi.ac.uk/biostudies/studies/S-EPMC9757077biostudies-literatureUnknown50(21)Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA briNucleic acids researchThe B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues.PMC9757077PID2019_108778GB_C21201506880001016.160.613VICI 016.160.613/533OCENW.GROOT.2019.012Erkelens AMKeek HGJDame RTMiguel-Arribas AQin LMarkus DMeijer WJJAbia DCajili MKMvan Erp BSchwab SfalseThe B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues.Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bri2022-01-01T00:00:00Z2022 Nov2026-06-22T03:14:08.671Z2024-11-06T22:12:52.066ZS-EPMC97570773640891010.1093/nar/gkac1064