FIS modulates growth phase‐dependent topological transitions of DNA in <i>Escherichia coli</i>

Schneider, Robert; Travers, Andrew; Muskhelishvili, Georgi

doi:10.1046/j.1365-2958.1997.5951971.x

Cited by 115 publications

(111 citation statements)

References 76 publications

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“…Johnson and colleagues also did not observe altered levels of supercoiling in strains lacking fis (28; R. Johnson, personal communication). These results conflict with results in a previous report in which it was concluded that plasmids are hypersupercoiled in ⌬fis strains (38). We do not know the basis for this discrepancy.…”

Section: Vol 185 2003 Intp and Ppgpp In Feedback Control Of Rrna Sycontrasting

confidence: 57%

Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis

Schneider

Gourse

2003

J Bacteriol

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rRNA synthesis is the rate-limiting step in ribosome synthesis in Escherichia coli. Its regulation has been described in terms of a negative-feedback control loop in which rRNA promoter activity responds to the amount of translation. The feedback nature of this control system was demonstrated previously by artificially changing ribosome synthesis rates and observing responses of rRNA promoters. However, it has not been demonstrated previously that the initiating nucleoside triphosphate (iNTP) and guanosine 5-diphosphate 3-diphosphate (ppGpp), the molecular effectors responsible for controlling rRNA promoters in response to changes in the nutritional environment, are responsible for altering rRNA promoter activities under these feedback conditions. Here, we show that most feedback situations result in changes in the concentrations of both the iNTP and ppGpp and that the directions of these changes are consistent with a role for these two small-molecule regulators in feedback control of rRNA synthesis. In contrast, we observed no change in the level of DNA supercoiling under the feedback conditions examined.In all cells examined, from prokaryotes to humans, expression of the products that make up the translation apparatus (rRNA, tRNA, ribosomal proteins, and associated factors) is tightly regulated. In Escherichia coli, several potentially overlapping regulatory systems have been identified as contributors to the control of rRNA and tRNA expression. Together, these regulatory systems match the protein synthetic potential to the demand for protein synthesis, no matter how the demand is altered (e.g., by nutritional shifts or starvations, by changes in growth phase, or by inhibitors of translation). Dissecting the roles of individual regulatory factors in this complex network has long posed a major experimental challenge (17,25,37).E. coli has seven rRNA operons (rrn), each of which contains two promoters, rrn P1 and rrn P2. During moderate to rapid growth, the rrn P1 promoters provide the majority of rRNA transcription in the cell. Sequences upstream of the Ϫ35 hexamer of rrn P1 promoters account for much of the strength of these promoters.Fis (factor for inversion stimulation) was originally identified for its role in site-specific inversion (23); however, it was shown subsequently to participate in other cellular processes as well, including activation of rrn P1 promoters (34). Each of the seven rrn P1 promoters has binding sites for Fis upstream of the core promoter element (three to five sites, depending on the operon), and activation by Fis increases promoter activity four-to eightfold (19). Between the Fis sites and the Ϫ35 hexamer of the core promoter is an AϩT-rich sequence called the UP element. The C-terminal domain of the alpha subunit (␣CTD) of RNA polymerase binds specifically to the UP element (33), increasing rrn P1 promoter activity 20-to 50-fold, depending on the operon (19). While these upstream promoter elements are essential for the strength of rrn P1 promoters, promoter constructs that lack the...

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Section: Vol 185 2003 Intp and Ppgpp In Feedback Control Of Rrna Sycontrasting

confidence: 57%

Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis

Schneider

Gourse

2003

J Bacteriol

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“…The existence of local gradients of superhelical density in the vicinity of DNA translocases implies that, as the DNA superhelical density varies over a wide range, the nature of the unconstrained superhelicity-the twist-writhe partition-must also vary, with writhe favored at the lower densities. However, in principle, proteins that constrain negative superhelicity might be expected to bind preferentially to DNA within a narrow range of superhelical density, as has been shown for the FIS protein, which favors a low negative superhelical density (Schneider et al 1997). There is unfortunately little information available for other proteins, but another possible example would be the eukaryotic HMG domain, which, in addition to being the principal component of the small HMGB proteins (Thomas and Travers 2001), is found in certain subunits of chromatin remodeling complexes (Quinn et al 1996) and of transcription elongation complexes (Orphanides et al 1999;Brewster et al 2001;Formosa et al 2001;Mason and Struhl 2003).…”

Section: Gradients Of Superhelicity and Protein Bindingmentioning

confidence: 95%

“…It was shown that FIS preferentially binds the supercoiled DNA from the intermediate fraction and much less so from the extremes of the topological spectrum (Schneider et al 1997). This preference is associated with geometrical constraints imposed by local DNA geometry on the binding of closely spaced helix-turn-helix DNAbinding motifs of FIS (Stella et al 2010), such that the FIS molecule can be conceived as a wedge fixing a particular DNA geometry in which the two adjacent major groves are in close proximity.…”

Section: Fis-rna Polymerase Complexmentioning

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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“…With increasing concentrations, Fis interacts with an increasing number of weaker DNA sites until binding becomes nonspecific (8,67). However, distinctions between specific Fis-DNA interactions of various strengths and truly nonspecific interactions (i.e., interactions at random sites) have seemed vague.…”

Section: Specificity Of Bindingmentioning

confidence: 99%

“…The impact of Fis on cell physiology is widespread. As a nucleoid-associated protein, it is able to interact with a large number of DNA sites to alter DNA topology (66,67). Numerous genes are subject to positive or negative regulation by Fis directly or indirectly (6,10,19,22,30,49,56,61,(73)(74)(75).…”

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confidence: 99%

Common and Variable Contributions of Fis Residues to High-Affinity Binding at Different DNA Sequences

et al. 2006

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Fis is a nucleoid-associated protein that interacts with poorly related DNA sequences with a high degree of specificity. A difference of more than 3 orders of magnitude in apparent K d values was observed between specific (K d , ϳ1 to 4 nM) and nonspecific (K d , ϳ4 M) DNA binding. To examine the contributions of Fis residues to the high-affinity binding at different DNA sequences, 13 alanine substitutions were generated in or near the Fis helix-turn-helix DNA binding motif, and the resulting proteins were purified. In vitro binding assays at three different Fis sites (fis P II, hin distal, and attR) revealed that R85, T87, R89, K90, and K91 played major roles in high-affinity DNA binding and that R85, T87, and K90 were consistently vital for binding to all three sites. Other residues made variable contributions to binding, depending on the binding site. N84 was required only for binding to the attR Fis site, and the role of R89 was dramatically altered by the attR DNA flanking sequence. The effects of Fis mutations on fis P II or hin distal site binding in vitro generally correlated with their abilities to mediate fis P repression or DNA inversion in vivo, demonstrating that the in vitro DNAbinding effects are relevant in vivo. The results suggest that while Fis is able to recognize a minimal common set of DNA sequence determinants at different binding sites, it is also equipped with a number of residues that contribute to the binding strength, some of which play variable roles.Fis (factor for inversion stimulation) is the most abundant nucleoid-associated protein during the logarithmic growth phase in rapidly growing Escherichia coli cells (3, 6). However, during mid-to late-logarithmic growth, the intracellular levels of Fis decrease over 500-fold and become nearly imperceptible during the stationary phase. The impact of Fis on cell physiology is widespread. As a nucleoid-associated protein, it is able to interact with a large number of DNA sites to alter DNA topology (66,67). Numerous genes are subject to positive or negative regulation by Fis directly or indirectly (6,10,19,22,30,49,56,61,(73)(74)(75). In the case of the promoters rrnB P1 and proP P2, Fis binding to sites centered at positions Ϫ71 and Ϫ41, respectively, directly stimulates transcription by contacting the C-terminal domain of the RNA polymerase ␣ subunit (␣-CTD) (9, 43). In the case of the fis promoter (fis P), Fis binding to sites I and II, centered at positions ϩ25 and Ϫ44, respectively, negatively autoregulates the fis operon by hindering RNA polymerase binding (6, 50, 58). As its name suggests, Fis also stimulates site-specific DNA inversion involving the Hin, Gin, and Cin family of recombinases (24,32,35). During Hin-mediated DNA inversion, Fis binds to two high-affinity DNA sites (hin-proximal and -distal sites) in a 60-bp recombinational enhancer region and interacts with two DNA-bound Hin recombinases to form a nucleoprotein complex intermediate required for efficient DNA strand cleavage and inversion (25,33). Bacteriophage DNA excis...

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FIS modulates growth phase‐dependent topological transitions of DNA in Escherichia coli

Cited by 115 publications

References 76 publications

Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis

Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis

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

Common and Variable Contributions of Fis Residues to High-Affinity Binding at Different DNA Sequences

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