Histone-like nucleoid structuring (H-NS) protein silences the beta-glucoside (bgl) utilization operon in Escherichia coli by forming a DNA loop

Lam, Katie Jing Kay; Zhang, Zhongge; Saier, Milton H.

doi:10.1016/j.csbj.2022.11.027

Cited by 5 publications

(9 citation statements)

References 74 publications

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“…Direct demonstration of such environment‐dependent, structure‐regulated transcription in the context of the bacterial chromosome is still elusive. A recent study of the role of H‐NS‐mediated bridging in regulating the expression of the bgl operon also does not yet provide explicit proof for transcription regulation by local chromatin re‐organisation (Lam et al, 2022).…”

Section: The Elusive Chromosomementioning

confidence: 99%

“…silico molecular dynamics simulations(van der Valk et al, 2017).Direct demonstration of such environment-dependent, structureregulated transcription in the context of the bacterial chromosome is still elusive. A recent study of the role of H-NS-mediated bridging in regulating the expression of the bgl operon also does not yet provide explicit proof for transcription regulation by local chromatin re-organisation(Lam et al, 2022).Chromosome conformation capture (3C)-based assays can provide direct evidence. 3C-based assays reveal in vivo threedimensional chromosome architecture with sequence information.The variety of these assays enable studies of chromosome organisation from the scale of individual genes and operons to whole genomes.…”

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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 Elusive Chromosomementioning

confidence: 99%

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confidence: 99%

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

Rashid

Dame

2023

Molecular Microbiology

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“…Data published by other groups indicate that the upstream and downstream H-NS binding sites exhibit synergy with each other ( Nagarajavel et al, 2007 ). Building upon this discovery, recent data from our group suggest the formation of a repression loop structure that blocks access of RNA polymerase to the bgl promoter ( Lam et al, 2022 ; Tran et al, 2022 ).…”

Section: Introductionmentioning

confidence: 92%

“…5.4 β-glucosidase (BglB) assay β-glucosidase assay was performed as described in our previous study (Lam et al, 2022). Briefly, 20 μL of LB culture was transferred to M63 minimal medium with 0.66% casamino acids (CAA).…”

Section: β-Galactosidase (Lacz) Assaysmentioning

confidence: 99%

“…Both the pathogenic and non-pathogenic forms of E. coli contain this operon, and to our knowledge it is never expressed in WT. Binding of the global histone-like nucleoid structuring (H-NS) protein at two sites on either side of the otherwise active bgl promoter is the most important factor in silencing transcription of the bgl operon by a strong repression mechanism ( Schnetz, 1995 ; Dole et al, 2004 ; Lam et al, 2022 ). Data published by other groups indicate that the upstream and downstream H-NS binding sites exhibit synergy with each other ( Nagarajavel et al, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

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The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli

Kopkowski,

Zhang,

Saier

2024

Front. Microbiol.

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The bglGFB operon in Escherichia coli K-12 strain BW25113, encoding the proteins necessary for the uptake and metabolism of β-glucosides, is normally not expressed. Insertion of either IS1 or IS5 upstream of the bgl promoter activates expression of the operon only when the cell is starving in the presence of a β-glucoside, drastically increasing transcription and allowing the cell to survive and grow using this carbon source. Details surrounding the exact mechanism and regulation of the IS insertional event remain unclear. In this work, the role of several DNA-binding proteins in how they affect the rate of insertion upstream of bgl are examined via mutation assays and protocols measuring transcription. Both Crp and IHF exert a positive effect on insertional Bgl+ mutations when present, active, and functional in the cell. Our results characterize IHF’s effect in conjunction with other mutations, show that IHF’s effect on IS insertion into bgl also affects other operons, and indicate that it may exert its effect by binding to and altering the DNA conformation of IS1 and IS5 in their native locations, rather than by directly influencing transposase gene expression. In contrast, the cAMP-CRP complex acts directly upon the bgl operon by binding upstream of the promoter, presumably altering local DNA into a conformation that enhances IS insertion.

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The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli

Rashid,

Crémazy,

Hofmann

et al. 2023

Nat Commun

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Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.

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Histone-like nucleoid structuring (H-NS) protein silences the beta-glucoside (bgl) utilization operon in Escherichia coli by forming a DNA loop

Cited by 5 publications

References 74 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

The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli

The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli

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