Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments

Shen, Beth A.; Hustmyer, Christine M.; Roston, Daniel; Wolfe, Michael B.; Landick, Robert

doi:10.1016/j.isci.2022.104429

Cited by 14 publications

(18 citation statements)

References 79 publications

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“…This forms a ‘nucleation point’ from which H‐NS dimers multimerise laterally over the DNA via dimer‐dimer interaction domains (amino acids 52‐84) forming an H‐NS:DNA filament (Figure 1a). The H‐NS DNA‐binding domains in a filament contact the DNA in the minor groove every 8‐17 base pairs at an average of one contact per 10 base pairs (Shen et al, 2022). The contact site is confined to a locus that can be physically accessed by the DNA‐binding domain and is distinguished by its narrower minor groove width, lower electrostatic potential and TA step (Shen et al, 2022).…”

Section: The Coupled Sensor‐effector System Of H‐nsmentioning

confidence: 99%

“…The H‐NS DNA‐binding domains in a filament contact the DNA in the minor groove every 8‐17 base pairs at an average of one contact per 10 base pairs (Shen et al, 2022). The contact site is confined to a locus that can be physically accessed by the DNA‐binding domain and is distinguished by its narrower minor groove width, lower electrostatic potential and TA step (Shen et al, 2022). H‐NS multimerization is co‐operative and allows the filament to extend towards lower affinity regions (Arold et al, 2010; Leonard et al, 2009).…”

Section: The Coupled Sensor‐effector System Of H‐nsmentioning

confidence: 99%

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Three‐dimensional chromosome re‐modelling: The integral mechanism of transcription regulation in bacteria

Rashid

Dame

2023

Molecular Microbiology

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The bacterial chromosome is compacted and organised in the nucleoid of bacterial cells in a manner that allows every gene to be accessible on demand. The organisation is mediated by DNA-binding architectural proteins, commonly referred to as nucleoid-associated proteins, or NAPs, that exert their role by folding, bridging and twisting the chromosome, locally, at the scale of individual operons or regulatory elements, and over longer ranges resulting in compaction of macrodomains and the formation of inter-arm interactions. The chromosome is also compacted by DNA supercoiling that is maintained by DNA topoisomerases and gyrases. Actively transcribed genes and some NAPs behave as supercoil diffusion barriers, restricting supercoiling density to smaller chromosome segments (reviewed in Dame et al. (2020)). The steric effects of chromosome compaction limit the accessibility of open reading frames and regulatory elements, making chromatin structure a direct regulator of transcription. Being the architects of bacterial chromosomes, NAPs inherently play a dual role in the cell, functioning as chromosome structuring proteins and as transcription factors. The biochemical properties of proteins are affected by fluctuations in temperature, pH and osmolarity. This can result in, among others, the loss or gain of functionality, a change in multimeric state and a change in protein stability. Often, in NAPs, susceptibility to

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Section: The Coupled Sensor‐effector System Of H‐nsmentioning

confidence: 99%

Section: The Coupled Sensor‐effector System Of H‐nsmentioning

confidence: 99%

Three‐dimensional chromosome re‐modelling: The integral mechanism of transcription regulation in bacteria

Rashid

Dame

2023

Molecular Microbiology

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“…To test this, we scored CFT073 genes for DNA sequence and shape features associated with high affinity H-NS binding ( 77 ). High A/T content, TA steps, narrow minor-groove width, and lower electrostatic potential favor H-NS binding, and all were enriched in CFT073 genes bound by H-NS–StpA ( Fig.…”

Section: Resultsmentioning

confidence: 99%

RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS–StpA Nucleoprotein Filaments in Pathogenic Escherichiacoli

Hustmyer

Wolfe

Welch

et al. 2022

mBio

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“…Additionally, Hha, another E. coli NAP, was shown to support H-NS/DNA bridged filaments despite Hha lacking a predicted DNA-binding domain [23]. While the role that NAPs play in the transcriptional regulatory landscape of E. coli is well established (although ongoing discoveries continue to be made on the regulatory mechanisms of NAPs in that system and other enterobacteria [23,24,27,[29][30][31][32]), less is known about the mechanisms and effects of xenogeneic silencers and other NAPs in other organisms, such as V. cholerae.…”

Section: Introductionmentioning

confidence: 99%

Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate ofVibrio cholerae

Rakibova,

Dunham,

Seed

et al. 2024

Preprint

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Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches it occupies. H-NS, the histone-like nucleoid structuring protein, is the best studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified a few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs.

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Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments

Cited by 14 publications

References 79 publications

Three‐dimensional chromosome re‐modelling: The integral mechanism of transcription regulation in bacteria

Three‐dimensional chromosome re‐modelling: The integral mechanism of transcription regulation in bacteria

RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS–StpA Nucleoprotein Filaments in Pathogenic Escherichiacoli

Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate ofVibrio cholerae

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