E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA

Rouvière‐Yaniv, Josette; Yaniv, Moshe; Germond, Jacques‐Edouard

doi:10.1016/0092-8674(79)90152-1

Cited by 443 publications

(265 citation statements)

References 37 publications

Supporting

Mentioning

252

Contrasting

Order By: Relevance

“…Binding isotherms were cvaluated using the model of Schwarz and Watanabe (1983) (Watanabe et al, 1984). Unexpectedly, binding does not appear to involve cooperativity as indicated by a variety of experiments for HBgl protein (Watanabe et al, 1984;Imber et ai., 1982Imber et ai., , 1987 and for E. coli HU protein (Rouviere-Yaniv et al, 1979). Recent experiments on HU protein, however, have also cast doubt on the cooperativity of its DNA-binding process (Bonnefoy and Rouviere-Yaniv, 1991).…”

Section: Discussionmentioning

confidence: 99%

“…They are small (approximately 10 kDa), basic, abundant proteins capable of wrapping DNA. Escherichia coli HU protein has been shown to introduce negative supercoils into relaxed circular DNA in the presence of topoisomerase I (Rouviere-Yaniv et al, 1979;Broyles and Pettijohn, 1986). This protein can also facilitate DNA recognition by different control proteins through promoting changes in DNA structure (Flashner and Gralla, 1988).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Determination of DNA‐binding parameters for the Bacillus subtilis histone‐like HBsu protein through introduction of fluorophores by site‐directed mutagenesis of a synthetic gene

Groch

Schindelin

Scholtz

et al. 1992

European Journal of Biochemistry

View full text Add to dashboard Cite

A synthetic gene encoding the histone‐like DNA‐binding protein HBsu from Bacillus subtilis has been expressed in Escherichia coli. Yields of the purified protein are at least 20mg/l culture medium. The recombinant HBsu protein is chromatographically, immunologically and functionally identical with the authentic wild‐type protein. N‐terminal sequencing of the purified protein confirms the fidelity of expression of the synthetic gene in E. coli.. Site‐directed mutagenesis of the synthetic gene was employed to replace several amino acid residues of HBsu protein with tryptophan to facilitate the determination of DNA‐binding parameters by fluorescence spectroscopy. According to gel‐retardation experiments, the mutant protein [Phe47 → Trp]HBsu shows identical DNA binding to wild‐type HBsu protein. Analysis of fluorescence binding data reveals that [Phe47 → Trp]HBsu binds double‐stranded DNA with a dissociation constant in the micromolar range. Computer‐assisted fit of binding models to the experimental data renders positive cooperativity of binding unlikely. A dimer of [Phe47 → Trp]HBsu appears to contact three or four base pairs of DNA. These results are in pritial disagreement with earlier measurements on closely homologous proteins which tended to show cooperative binding and a longer DNA contact region.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Determination of DNA‐binding parameters for the Bacillus subtilis histone‐like HBsu protein through introduction of fluorophores by site‐directed mutagenesis of a synthetic gene

Groch

Schindelin

Scholtz

et al. 1992

European Journal of Biochemistry

View full text Add to dashboard Cite

show abstract

“…In bacteria, HU may play, in part, a similar role to the HMG domains. However, unlike HMGB proteins, there is evidence that HU can also compact DNA into a fiber (Rouvière-Yaniv et al 1979) in which the DNA is wrapped in a left-handed sense (Guo and Adhya 2007). Although negative superhelicity can promote transient strand separation in particular sequences , it is only one of several mechanisms that may potentially create short stretches of DNA lacking continuous base pairing.…”

Section: Gradients Of Superhelicity and Protein Bindingmentioning

confidence: 99%

“…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

View full text Add to dashboard Cite

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 ...

show abstract

“…In E. coli, the four most abundant nucleoid-associated proteins are factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) [19][20][21][22][23][24][25]. However, at present, a clear picture of how the E. coli nucleoid is organized is far from being complete.…”

mentioning

confidence: 99%

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

Talukder

Ishihama

2015

Sci. China Life Sci.

View full text Add to dashboard Cite

The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase. In addition to factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Q Hfq) and suppressor of td  phenotype A (StpA). Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, StpA and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli. growth phase, sucrose gradient, bacterial nucleoid, DNA binding protein, DNA compaction Citation:Talukder AA, Ishihama A. Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli. Sci China Life Sci, 2015, 58: 902 -911,

show abstract

E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA

Cited by 443 publications

References 37 publications

Determination of DNA‐binding parameters for the Bacillus subtilis histone‐like HBsu protein through introduction of fluorophores by site‐directed mutagenesis of a synthetic gene

Determination of DNA‐binding parameters for the Bacillus subtilis histone‐like HBsu protein through introduction of fluorophores by site‐directed mutagenesis of a synthetic gene

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

Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli

Contact Info

Product

Resources

About