Structural Basis for H-NS-mediated Trapping of RNA Polymerase in the Open Initiation Complex at the rrnB P1

Dame, Remus T.; Wyman, Claire; Wurm, Reinhild; Wagner, Rolf; Goosen, Nora

doi:10.1074/jbc.c100603200

Cited by 164 publications

(146 citation statements)

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“…3 A, B). The structure and proposed mode of interaction with DNA provides a rationale for data on the nucleation (28,29) and bridging (24, 30) models of gene repression by H-NS and is consistent with biophysical studies (31) as well as imaging of H-NS: DNA nucleoprotein complexes by atomic force microscopy and electron microscopy (23,32,33). Small angle X-ray scattering (SAXS) analysis showed that at 10°C and 0.3-0.4 mM H-NS 1-83 adopts a conformation in solution that is comparable to the oligomer present in the crystal; under these conditions extending to an average of eight monomers or four dimeric units (Fig.…”

Section: Resultsmentioning

confidence: 83%

H-NS forms a superhelical protein scaffold for DNA condensation

Arold

Leonard²,

Parkinson

et al. 2010

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

179

251

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The histone-like nucleoid structuring (H-NS) protein plays a fundamental role in DNA condensation and is a key regulator of enterobacterial gene expression in response to changes in osmolarity, pH, and temperature. The protein is capable of high-order self-association via interactions of its oligomerization domain. Using crystallography, we have solved the structure of this complete domain in an oligomerized state. The observed superhelical structure establishes a mechanism for the self-association of H-NS via both an N-terminal antiparallel coiled-coil and a second, hitherto unidentified, helix-turn-helix dimerization interface at the C-terminal end of the oligomerization domain. The helical scaffold suggests the formation of a H-NS:plectonemic DNA nucleoprotein complex that is capable of explaining published biophysical and functional data, and establishes a unifying structural basis for coordinating the DNA packaging and transcription repression functions of H-NS.chromatin | DNA binding | nucleoid | supercoil | transcriptional regulation

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Section: Resultsmentioning

confidence: 83%

H-NS forms a superhelical protein scaffold for DNA condensation

Arold

Leonard²,

Parkinson

et al. 2010

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

179

251

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“…H-NS exists primarily as a dimer at low concentrations but can multimerize into higher order complexes [4,5] that form bridges between adjacent DNA helices [6]. Optical tweezers have been used to demonstrate that H-NS dimers or multimers can simultaneously interact with separate DNA binding sites [7••].…”

Section: H-ns--a Nucleoid Proteinmentioning

confidence: 99%

“…Regulatory effects of supercoiling are linked to metabolic and environmental conditions. Thus, H-NS has been viewed as a nucleoid structuring protein with global effects on gene expression [3].H-NS exists primarily as a dimer at low concentrations but can multimerize into higher order complexes [4,5] that form bridges between adjacent DNA helices [6]. Optical tweezers have been used to demonstrate that H-NS dimers or multimers can simultaneously interact with separate DNA binding sites [7••].…”

mentioning

confidence: 99%

New insights into transcriptional regulation by H-NS

Fang

Rimsky

2008

Current Opinion in Microbiology

188

173

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H-NS, a nucleoid-associated DNA-binding protein of enteric bacteria, was discovered thirty-five years ago and subsequently found to exert widespread and highly pleiotropic effects on gene regulation. H-NS binds to high-affinity sites and spreads along adjacent AT-rich DNA to silence transcription. Preferential binding to sequences with higher AT-content than the resident genome allows H-NS to repress the expression of foreign DNA in a process known as "xenogeneic silencing." Counter-silencing by a variety of mechanisms facilitates the evolutionary acquisition of horizontally transferred genes and their integration into pre-existing regulatory networks. This review will highlight recent insights into the mechanism and biological importance of H-NS-DNA interactions. H-NS--A Nucleoid ProteinH-NS is an abundant DNA-binding protein implicated in the organization of the bacterial chromosome [1]. H-NS and other nucleoid-associated proteins can affect DNA topology at specific loci, thereby modulating gene transcription. Binding by these proteins is proposed to selectively direct supercoiling effects to promoters [2•]. Mutation of hns alters the responsiveness of transcription to changes in DNA superhelicity. Regulatory effects of supercoiling are linked to metabolic and environmental conditions. Thus, H-NS has been viewed as a nucleoid structuring protein with global effects on gene expression [3].H-NS exists primarily as a dimer at low concentrations but can multimerize into higher order complexes [4,5] that form bridges between adjacent DNA helices [6]. Optical tweezers have been used to demonstrate that H-NS dimers or multimers can simultaneously interact with separate DNA binding sites [7••]. H-NS-coated DNA is not self-interactive, suggesting that dimerization or oligomerization must precede DNA binding for bridging to occur. Force measurements suggest that transcription barriers created by H-NS binding are weak (∼7 pN) and readily overcome, so that H-NS oligomers pose only a relative barrier to translocating RNA polymerase. DNA bridging is a conserved feature of H-NS homologs found in most gram-negative bacteria [8] that appears to constrain large DNA loops [9••] and helps to account for the effects of H-NS on transcription. However, it must be noted that the relationship between bridging as a general effect and the silencing of specific promoters is not yet clear.H-NS is more appropriately viewed as a determinant of chromosomal architecture rather than as a general structural component. The analysis of nucleoids treated with urea suggests that *Corresponding Author : Tel 206-275-0966, Fax 206-616-1575, e-mail : fcfang@u.washington.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production proce...

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“…In addition to RNAP, three transcription factors have been reported to bind site-specifically to the E. coli rRNA promoter region, Fis, Lrp, and H-NS (Ross et al 1990;Hirvonen et al 2001;Dame et al 2002;Pul et al 2007). Each has been reported to influence chromosome structure (Skoko et al 2006;Bouffartigues et al 2007;Hadizadeh et al 2012), making these factors candidates for contributors to rRNA operon colocalization.…”

Section: (C) Oric Rrnc (Rlg11999) (D) Rrnb Oric (Rlg7440) (E) λAtmentioning

confidence: 99%

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

et al. 2016

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The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180°on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.

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Structural Basis for H-NS-mediated Trapping of RNA Polymerase in the Open Initiation Complex at the rrnB P1

Cited by 164 publications

References 50 publications

H-NS forms a superhelical protein scaffold for DNA condensation

H-NS forms a superhelical protein scaffold for DNA condensation

New insights into transcriptional regulation by H-NS

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

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