Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping

Lia, Giuseppe; Bensimon, David; Croquette, Vincent; Allemand, Jean-François; Dunlap, David; Lewis, Dale E.A.; Adhya, Sankar; Finzi, Laura

doi:10.1073/pnas.2034851100

Cited by 105 publications

(97 citation statements)

References 31 publications

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“…Both AraC and the lac repressor act as bivalent DNA-binding proteins and stabilize a supercoiled loop (Lee and Schleif 1989;Bellomy et al 1988). Similarly, the dimeric GalR protein, which wraps DNA, specifically binds to the O E and O I operators of the E. coli galactose operon to form a short loop in the presence of HU protein (Lia et al 2003). For short loops of this type, the two DNA binding sites are normally on the same face of the double helix such that the distance between them can only be varied by an integral number of double helical turns.…”

Section: H-ns Nucleoprotein Complexesmentioning

confidence: 99%

“…For short loops of this type, the two DNA binding sites are normally on the same face of the double helix such that the distance between them can only be varied by an integral number of double helical turns. The formation of the GalR loop requires both negatively supercoiled DNA and HU (Lia et al 2003). Simulations of the binding of HU to the GalR and LacR loops indicate that DNA superhelicity can direct the binding of HU to a specific site within the loop and confer an optimal trajectory on the looped DNA for loop closure by the repressor protein (Wei et al 2014).…”

Section: H-ns Nucleoprotein Complexesmentioning

confidence: 99%

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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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Section: H-ns Nucleoprotein Complexesmentioning

confidence: 99%

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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“…A more sophisticated technique which has been successfully applied to Gal repressor is the magnetic tweezer assay. 153 In this case, the tether can be stretched and twisted as the dynamics of looping and unlooping are followed leading to measurements of the underlying kinetics, thermodynamics, and supercoiling dependence.…”

mentioning

confidence: 99%

“…153 HU has been proven to alter the effective flexibility of DNA. 154 However, this issue has not been studied systematically in the context of DNA looping or in the presence of other nonspecific binding proteins such as H-NS and IHF.…”

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confidence: 99%

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

et al. 2006

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The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence length. Similarly, eukaryotic DNA is packed in DNA-protein complexes (nucleosomes) in which DNA is tightly bent around protein spools. DNA is also tightly bent by many proteins that regulate transcription, resulting in a variation in gene expression that is amenable to quantitative analysis. In these cases, DNA loops are formed with lengths that are comparable to or smaller than the DNA persistence length. The aim of this review is to describe the physical forces associated with tightly bent DNA in all of these settings and to explore the biological consequences of such bending, as increasingly accessible by single-molecule techniques.

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“…Thus, magnetic tweezers were used to test the looping hypothesis and the roles of HU protein and DNA supercoiling (Lia et al 2003). GalR was added to single DNA tethers that were unwound by different amounts.…”

Section: Dna Unwinding (Negative Supercoiling) Is a Key Regulator Of mentioning

confidence: 99%

Supercoiling biases the formation of loops involved in gene regulation

Finzi

Dunlap

2016

Biophys Rev

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The function of DNA as a repository of genetic information is well-known. The post-genomic effort is to understand how this information-containing filament is chaperoned to manage its compaction and topological states. Indeed, the activities of enzymes that transcribe, replicate, or repair DNA are regulated to a large degree by access. Proteins that act at a distance along the filament by binding at one site and contacting another site, perhaps as part of a bigger complex, create loops that constitute topological domains and influence regulation. DNA loops and plectonemes are not necessarily spontaneous, especially large loops under tension for which high energy is required to bring their ends together, or small loops that require accessory proteins to facilitate DNA bending. However, the torsion in stiff filaments such as DNA dramatically modulates the topology, driving it from extended and genetically accessible to more looped and compact, genetically secured forms. Furthermore, there are accessory factors that bias the response of the DNA filament to supercoiling. For example, small molecules like polyamines, which neutralize the negative charge repulsions along the phosphate backbone, enhance flexibility and promote writhe over twist in response to torsion. Such increased flexibility likely pushes the topological equilibrium from twist toward writhe at tensions thought to exist in vivo. A predictable corollary is that stiffening DNA antagonizes looping and bending. Certain sequences are known to be more or less flexible or to exhibit curvature, and this may affect interactions with binding proteins. In vivo all of these factors operate simultaneously on DNA that is generally negatively supercoiled to some degree. Therefore, in order to better understand gene regulation that involves protein-mediated DNA loops, it is critical to understand the thermodynamics and kinetics of looping in DNA that is under tension, negatively supercoiled, and perhaps exposed to molecules that alter elasticity. Recent experiments quantitatively reveal how much negatively supercoiling DNA lowers the free energy of looping, possibly biasing the operation of genetic switches.

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Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping

Cited by 105 publications

References 31 publications

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

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

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

Supercoiling biases the formation of loops involved in gene regulation

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