The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues

• Published in: Nucleic acids research 2022-11, Vol.50 (21), p.12166-12185
• Main Authors: Erkelens, Amanda M, Qin, Liang, van Erp, Bert, Miguel-Arribas, Andrés, Abia, David, Keek, Helena G J, Markus, Dorijn, Cajili, Marc K M, Schwab, Samuel, Meijer, Wilfried J J, Dame, Remus T
• Format: Article
• Language: English
• Subjects: Bacillus subtilis - metabolism; Bacterial Proteins - metabolism; DNA - metabolism; DNA-Binding Proteins - metabolism; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression Regulation, Bacterial; Gene regulation, Chromatin and Epigenetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkac1064

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 bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family.