H-NS mediated compaction of DNA visualised by atomic force microscopy

Dame, Remus T.; Wyman, Claire; Goosen, Nora

doi:10.1093/nar/28.18.3504

Cited by 266 publications

(257 citation statements)

References 33 publications

(33 reference statements)

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Section: Discussionsupporting

confidence: 92%

“…This conclusion is in good agreement with recent microscopic studies, which showed the formation of filamentous structures when visualizing H-NS⅐DNA complexes (41,42). These filaments are constituted by large tracts with two regions of double-stranded DNA held close together (41). It was proposed, from their observation, that the binding of H-NS to DNA would occur through a nucleation step followed by a zipper-like propagation along the DNA (42).…”

Section: Discussionsupporting

confidence: 90%

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The Degree of Oligomerization of the H-NS Nucleoid Structuring Protein Is Related to Specific Binding to DNA

Badaut

Williams

Arluison

et al. 2002

Journal of Biological Chemistry

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At several E. coli promoters, initiation of transcription is repressed by a tight nucleoprotein complex formed by the assembly of the H-NS protein. In order to characterize the relationship between the structure of H-NS oligomers in solution and on relevant DNA fragments, we have compared wild-type H-NS and several transdominant H-NS mutants using gel shift assays, DNase I footprinting, analytical ultracentrifugation, and reactivity toward a cross-linking reagent. In solution, oligomerization occurs through two protein interfaces, one necessary to construct a dimeric core (and involving residues 1-64) and the other required for subsequent assembly of these dimers. We show that, as well as region 64 -95, residues present in the NH 2 -terminal coiled coil domain also participate in this second interface. Our results support the view that the same interacting interfaces are also involved on the DNA. We propose that the dimeric core recognizes specific motifs, with the second interface being critical for their correct head to tail assembly. The COOH-terminal domain of the protein contains the DNA binding motif essential for the discrimination of this specific functional assembly over competitive nonspecific H-NS polymers.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 90%

The Degree of Oligomerization of the H-NS Nucleoid Structuring Protein Is Related to Specific Binding to DNA

Badaut

Williams

Arluison

et al. 2002

Journal of Biological Chemistry

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“…H-NS is responsible for binding and repressing >400 genes in Salmonella (4, 7) and in Escherichia coli (8,9), many of which are DNA sequences obtained through horizontal gene transfer and involved in adaptive stress responses and virulence (10). Numerous phenotypes associated with hns mutations have been described, and the effects of H-NS on gene expression are largely inhibitory (2,11), which is partially explained by the ability of H-NS to bridge adjacent helices of DNA (12,13), causing either the trapping or the occlusion of RNA polymerase in the promoter regions (2,14). H-NS homologs are widespread in the Gram-negative α-, β-, and γ-proteobacteria but have not been identified in Gram-positive bacteria or in any other groups of bacteria, leaving it unclear as to how these bacterial species regulate the genes that they obtain through genetic exchange.…”

Section: H-ns | Virulencementioning

confidence: 99%

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes inMycobacterium tuberculosis

Gordon

Li²,

Wang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

198

250

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Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 of Mycobacterium tuberculosis is a unique nucleoid-associated protein that binds AT-rich regions of the genome, including genomic islands acquired by horizontal gene transfer and regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM and PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain-swapping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA-binding domain. Nuclear magnetic resonance analysis of the DNA-binding domain of Lsr2 and its interaction with DNA reveals a unique structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve a function similar to the Enterobacteriaceae H-NS, likely coordinating global gene regulation and virulence in this group of medically important bacteria.

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“…H-NS is an abundant bacterial NAP, but, unlike HU, which is believed to constrain a toroidal DNA structure analogous to that in a nucleosome (Rouvière-Yaniv et al 1979;Guo and Adhya 2007), H-NS complexes can bridge two DNA duplexes (Dame et al 2000) and concomitantly stabilize the plectonemic form of negatively supercoiled DNA (Schneider et al 2001). In vivo, two principal functions have been ascribed to H-NS: as a repressor of certain genes and gene clusters located in A/T-rich regions of the genome (Navarre et al 2006;Ouafa et al 2012), and as a domainin, assumed to function by stabilizing barriers between distinct topological domains (Hardy and Cozzarelli 2005).…”

Section: H-ns Nucleoprotein Complexesmentioning

confidence: 99%

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Muskhelishvili

Travers

2016

Biophys Rev

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We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.Keywords DNA supercoiling . DNA translocases . Chromatin organization . Superhelicity gradients . DNA untwisting . DNAwrithing Dynamic changes of DNA supercoiling act as a driving force behind the alterations of genetic activity and DNA compaction both in eukaryotes and prokaryotes. Both these processes involve formation of spatially organized nucleoprotein structures by DNA architectural proteins. Whereas in eukaryotes the paradigmal example is the histone octamer, in prokaryotes a similar function is attributed to a small class of highly abundant nucleoid-associated proteins. We argue that, depending on the primary sequence organization, the changes of superhelicity elicit various alterations of local DNA geometry, while these, in turn, facilitate the assembly of distinct nucleoprotein structures pertinent to genetic function. Genome-wide conversion of the superhelical energy into various three-dimensional DNA structures thus acts as an analogue code coordinating the energy supply with the genetic expression of the chromosome.Recent studies make it increasingly clear that the DNA double helix carries at least two types of encoded information and that these include the well-known genetic code and the structural information determining the form and physical properties of the double helix itself. Since both these information types are inscribed in the same DNA sequence, and yet one is discrete whereas the other is continuous, they have been respectively dubbed the digital and analog DNA codes (Marr et al. 2008;Travers et al. 2012;Muskhelishvili and Travers 2013). The potential of the DNA to adopt distinct configurations is strongly modulated by DNA supercoiling, which is increasingly recognized as one of the major forces coordinating the cellular DNA transactions in both prokaryotes (including Archaea) and eukaryotes.DNA supercoiling can be generated by the simple application of torque to the double helix (Strick et al. 1998) but, importantly, because the DNA molecule itself possesses chirality-it is, after all, a right-handed double helix-the local structures stabilized by changes in superhelical density depend on both the sign and strength of the applied torque. For example, both positive and negative torque (respectively overand underwinding of the double helix) can change the intrinsic coiling of ...

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H-NS mediated compaction of DNA visualised by atomic force microscopy

Cited by 266 publications

References 33 publications

The Degree of Oligomerization of the H-NS Nucleoid Structuring Protein Is Related to Specific Binding to DNA

The Degree of Oligomerization of the H-NS Nucleoid Structuring Protein Is Related to Specific Binding to DNA

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes inMycobacterium tuberculosis

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

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