Locus of Enterocyte Effacement-encoded Regulator (Ler) of Pathogenic Escherichia coli Competes Off Histone-like Nucleoid-structuring Protein (H-NS) through Noncooperative DNA Binding

Winardhi, Ricksen S.; Gulvady, Ranjit; Mellies, Jay L.; Yan, Jie

doi:10.1074/jbc.m113.545954

Cited by 41 publications

(43 citation statements)

References 44 publications

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“…Therefore, the above conclusions have wide biological implications because they can be further generalized to understand collective behavior of DNA-stiffening and DNA-wrapping/bending proteins in other cell types, especially taking into account that an increasing number of architectural proteins that can form rigid nucleoprotein filaments have been recently identified as crucial DNA organizing elements and gene transcription factors in different bacteria (31,51,52,(57)(58)(59)(60)(61).…”

Section: Discussionmentioning

confidence: 99%

Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner

Efremov

Maruyama

et al. 2015

Journal of Biological Chemistry

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Background: TrmBL2 and histones maintain the genome functioning in hyperthermophilic euryarchaeal cells. Results: TrmBL2 forms filaments on DNA through cooperative binding and competes with histones in a salt-and DNA supercoiling-dependent manner. Conclusion: TrmBL2-histone collective behavior dynamically controls DNA organization. Significance: The discovered mechanisms provide insights into the regulation of the genome structure and global transcription profile by TrmBL2 and histones.

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Section: Discussionmentioning

confidence: 99%

Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner

Efremov

Maruyama

et al. 2015

Journal of Biological Chemistry

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“…Ler, much like H-NS, can form multimers via its N-terminal dimerization domain [Mellies et al, 2011]. Ler is believed to form rigid filaments along the DNA [Bhat et al, 2014;Mellies et al, 2011;Winardhi et al, 2014]. In addition, it may be capable of forming DNA bridges in vitro on specific sequences [Bhat et al, 2014].…”

Section: 'Partial' Homologues Of H-ns: H-nst and Lermentioning

confidence: 99%

Genomic Looping: A Key Principle of Chromatin Organization

Valk

Vreede²,

Crémazy³

et al. 2014

Microb Physiol

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The effective volume occupied by the genomes of all forms of life far exceeds that of the cells in which they are contained. Therefore, all organisms have developed mechanisms for compactly folding and functionally organizing their genetic material. Through recent advances in fluorescent microscopy and 3C-based technologies, we finally have a first glimpse into the complex mechanisms governing the 3-D folding of genomes. A key feature of genome organization in all domains of life is the formation of DNA loops. Here, we describe the main players in DNA organization with a focus on DNA-bridging proteins. Specifically, we discuss the properties of the bacterial DNA-bridging protein H-NS. Via two different modes of binding to DNA, this protein is a key driver of bacterial genome organization and provides a link between 3-D organization and transcription regulation. Importantly, H-NS function is modulated in response to environmental cues, which are translated into adapted gene expression patterns. We delve into the mechanisms underlying DNA looping and explore the complex and subtle modulation of these diverse, yet difficult-to-study, structures. DNA looping is universal and a conserved mechanism of genome organization throughout all domains of life.

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“…In each case, the anti-silencing mechanism is triggered by an environmental signal, or a set of signals, that characterise the niche in the host where infection occurs [Rhen and Dorman, 2005;Stoebel et al, 2008]. Other NAPs, such as HU, IHF and Fis play more or less well-characterized roles in the modulation of H-NS-mediated silencing in these pathogens, working in concert with conventional transcription factors to switch on virulence gene expression [Cameron et al, 2012;Falconi et al, 2001;Kahramanoglou et al, 2011;Ouafa et al, 2012;Porter and Dorman, 1997;Schechter et al, 2003;Walthers et al, 2011;Winardhi et al, 2014]. Some pathogenic strains of E. coli encode H-NS paralogues such as H-NSB and Hfp that can confer new and subtle phenotypes on the bacterium.…”

Section: H-ns Family Proteins Transcription and Genome Evolutionmentioning

confidence: 99%

“…A similar pattern of silencing and anti-silencing has been described in pathogens such as Shigella flexneri [Beloin and Dorman, 2003;Tran et al, 2011;Turner and Dorman, 2007], Vibrio cholerae [Stonehouse et al, 2011;Yu and DiRita, 2002], Yersinia spp. [Baños et al, 2008;Ellison and Miller, 2006], disease-causing strains of E. coli [Martínez-Santos et al, 2012;Trachman and Yasmin, 2004;Winardhi et al, 2014] and the plant pathogen Dickeya [Reverchon and Nasser, 2013]. In each case, the anti-silencing mechanism is triggered by an environmental signal, or a set of signals, that characterise the niche in the host where infection occurs [Rhen and Dorman, 2005;Stoebel et al, 2008].…”

Section: H-ns Family Proteins Transcription and Genome Evolutionmentioning

confidence: 99%

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Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation

Dorman¹

2014

Microb Physiol

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Nucleoid-associated proteins typically are abundant, low-molecular-mass polypeptides that bind DNA and alter its shape and its ability to participate in transactions such as transcription. Some can bind RNA and influence the gene expression profile of the cell at a posttranscriptional level. They also have the potential to model and remodel the structure of the nucleoid, contributing to chromosome packaging within the cell. Some nucleoid-associated proteins have been implicated in the facilitation of chromosome evolution through their ability to silence transcription, allowing new genes to be integrated into the nucleoid both physically and in a regulatory sense. The dynamic composition of the population of nucleoid-associated proteins in model bacteria such as Escherichia coli and Salmonella enterica links nucleoid structure and the global regulation of gene expression, enhancing microbial competitive fitness and survival in complex environments.

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Locus of Enterocyte Effacement-encoded Regulator (Ler) of Pathogenic Escherichia coli Competes Off Histone-like Nucleoid-structuring Protein (H-NS) through Noncooperative DNA Binding

Cited by 41 publications

References 44 publications

Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner

Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner

Genomic Looping: A Key Principle of Chromatin Organization

Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation

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