Fis protein forms DNA topological barriers to confine transcription‐coupled DNA supercoiling in Escherichia coli

Abstract

Previously, we demonstrated that transcription‐coupled DNA supercoiling (TCDS) potently activated or inhibited nearby promoters in Escherichia coli even in the presence of all four DNA topoisomerases, suggesting that DNA topoisomerases are not the only factors regulating TCDS. A different mechanism exists to confine this localized DNA supercoiling. Using an in vivo system containing the TCDS‐activated leu‐500 promoter (Pleu‐500), we find that the nucleoid‐associated Fis protein potently inhibits the TCDS‐mediated activation of Pleu‐500. We also find that deletion of the fis gene significantly enhances TCDS‐mediated inhibition of transcription of three genes purH, yieP, and yrdA divergently coupled to different rrn operons in the early log phase. These results suggest that Fis protein forms DNA topological barriers upon binding to its recognition sites, blocks TCDS diffusion, and potently inhibits the TCDS‐activated Pleu‐500.

High-Throughput Screening of a Promoter Library Reveals New Persister Mechanisms in Escherichia Coli

“…2D and F ), as reported elsewhere ( 35 , 36 ). Fis forms topological barriers that block supercoiling ( 37 ), which can rescue the cells from the damage caused by fluoroquinolone-bound gyrases ( 14 ). Although the persistence mechanism of Fis protein is well characterized ( 14 ), the ability of ofloxacin to induce fis expression (Fig.…”

DNA sequence-directed cooperation between nucleoid-associated proteins

“…NAPs bind DNA with varying affinities from nanomolar to micromolar concentrations and affect the gene expression by acting as bona fide transcription factors as well as so-called “topological homeostats” ( Muskhelishvili and Travers, 2003 ; Travers et al., 2001 ). The regulation of genomic transcription by NAPs is closely coupled with their propensity to modulate the availability of free or “unconstrained” DNA superhelicity, as NAPs constrain the DNA acting both as supercoil repositories and topological barriers to supercoil diffusion ( Berger et al., 2016 ; Dages et al., 2020 ; Hardy and Cozzarelli, 2005 ; Hatfield and Benham, 2002 ; Muskhelishvili and Travers, 2003 ).…”

Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome

“…6). There is experimental evidence that certain wrapping proteins, like GalR ( 15 ), the λ O protein ( 15 ), and Fis ( 62 ), are able to form topological barriers by blocking the diffusion of twist. However, we checked that the torsional stress equilibrates rapidly in the two moieties of the DNA chain when simulations are performed with = 10 nm instead of 4 nm because equilibration of twist and writhe is mediated in this case by the DNA chain passing repeatedly between beads α and β .…”