In vivo non‐specific binding of λ CI and Cro repressors is significant

Bakk, Audun; Metzler, Ralf

doi:10.1016/s0014-5793(04)00249-2

Cited by 42 publications

(48 citation statements)

References 28 publications

(53 reference statements)

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“…Recent expression measurements for the P RM promoter have suggested that this is the case for CI (7,8,14) (see also Fig. S2).…”

Section: Dna Looping Allows the Switch To Function Despite CI Depletionmentioning

confidence: 79%

“…We model nonspecific DNA binding (8,14) by including in our reaction set association and dissociation of CI and Cro dimers to 10 7 genomic DNA sites, corresponding to 2-3 copies of the bacterial genome. The association rate k a is assumed to be diffusion-limited, and we assume identical nonspecific binding affinities for CI and Cro.…”

Section: The Modelmentioning

confidence: 99%

“…Stochastic fluctuations in gene regulation (''noise'') might be expected to cause spontaneous transitions from the lysogenic to lytic states, even in lysogens lacking RecA; yet the rate of these transitions is so low that it is almost unmeasurable. Second, recent measurements of P RM and P R promoter activity suggest that only a small fraction of the total CI in the cell is available for binding to O R (7,8,(12)(13)(14), whereas other measurements show that the total concentration of CI in the lysogen varies dramatically from cell to cell (15). Taken together, these results suggest that the stability of the lysogen is rather insensitive to the number of free intracellular CI molecules.…”

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confidence: 99%

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DNA looping provides stability and robustness to the bacteriophage λ switch

Morelli

Wolde

Allen

2009

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

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The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage λ presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of the extreme stability of the lysogenic state remains unclear. We have constructed a stochastic model for this switch. Using Forward Flux Sampling simulations, we show that this model predicts an extremely low rate of spontaneous prophage induction in a recA mutant, in agreement with experimental observations. In our model, the DNA loop formed by octamerization of CI bound to the O L and O R operator regions is crucial for stability, allowing the lysogenic state to remain stable even when a large fraction of the total CI is depleted by nonspecific binding to genomic DNA. DNA looping also ensures that the switch is robust to mutations in the order of the O R binding sites. Our results suggest that DNA looping can provide a mechanism to maintain a stable lysogenic state in the face of a range of challenges including noisy gene expression, nonspecific DNA binding, and operator site mutations.

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“…Recent expression measurements for the P RM promoter have suggested that this is the case for CI (7,8,14) (see also Fig. S2).…”

Section: Dna Looping Allows the Switch To Function Despite CI Depletionmentioning

confidence: 79%

Section: The Modelmentioning

confidence: 99%

mentioning

confidence: 99%

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DNA looping provides stability and robustness to the bacteriophage λ switch

Morelli

Wolde

Allen

2009

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

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“…For the purposes of this review, we make the simplified assumption that the key molecular players (RNAP and TFs) are bound to the DNA either specifically or non-specifically. This question has been addressed in the context of the λ switch [27], for the lac repressor [21,28] and for RNAP [29]. Stated differently, as a simplification, we will ignore the contribution of 'free' polymerase in the cytoplasm, in addition to those RNAP molecules that are engaged in transcription on other promoters.…”

Section: Thermodynamic Models Of Gene Regulation: the Regulation Factormentioning

confidence: 99%

Transcriptional regulation by the numbers: models

Bintu

Buchler

García

et al. 2005

Current Opinion in Genetics & Development

725

884

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The expression of genes is regularly characterized with respect to how much, how fast, when and where. Such quantitative data demands quantitative models. Thermodynamic models are based on the assumption that the level of gene expression is proportional to the equilibrium probability that RNA polymerase (RNAP) is bound to the promoter of interest. Statistical mechanics provides a framework for computing these probabilities. Within this framework, interactions of activators, repressors, helper molecules and RNAP are described by a single function, the 'regulation factor'. This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell.

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“…According to the Bergvon Hippel-facilitated diffusion model (5) DNA-binding proteins combine 3-dimensional diffusion in the bulk and 1-dimensional diffusion along the DNA chain (6)(7)(8)(9). This linear diffusion is mediated by nonspecific binding, the protein's binding affinity to noncognate DNA made possible by the heteropolymeric nature of DNA (10)(11)(12). An additional search mechanism already proposed in the works of Berg and von Hippel are intersegmental transfers: some proteins with two DNA-binding sites can intermittently bind nonspecifically to 2 DNA-segments that are far apart along the DNA contour but are brought in close contact in the embedding (real) space by DNA looping.…”

mentioning

confidence: 99%

Facilitated diffusion with DNA coiling

Lomholt

Broek

Kalisch

et al. 2009

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

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187

188

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When DNA-binding proteins search for their specific binding site on a DNA molecule they alternate between linear 1-dimensional diffusion along the DNA molecule, mediated by nonspecific binding, and 3-dimensional volume excursion events between successive dissociation from and rebinding to DNA. If the DNA molecule is kept in a straight configuration, for instance, by optical tweezers, these 3-dimensional excursions may be divided into long volume excursions and short hops along the DNA. These short hops correspond to immediate rebindings after dissociation such that a rebinding event to the DNA occurs at a site that is close to the site of the preceding dissociation. When the DNA molecule is allowed to coil up, immediate rebinding may also lead to so-called intersegmental jumps, i.e., immediate rebindings to a DNA segment that is far away from the unbinding site when measured in the chemical distance along the DNA, but close by in the embedding 3-dimensional space. This effect is made possible by DNA looping. The significance of intersegmental jumps was recently demonstrated in a single DNA optical tweezers setup. Here we present a theoretical approach in which we explicitly take the effect of DNA coiling into account. By including the spatial correlations of the short hops we demonstrate how the facilitated diffusion model can be extended to account for intersegmental jumping at varying DNA densities. It is also shown that our approach provides a quantitative interpretation of the experimentally measured enhancement of the target location by DNA-binding proteins.gene regulation | search processes | random processes | intersegmental jumps | single-molecule biophysics A t any given instant of time a biological cell only uses part of its genes for production of other molecules (RNA, proteins). During the development of the cell, or the organism the cell belongs to, different genes may be turned on. A classical example is the lactose metabolism of bacteria: in absence of lactose the Lac repressor is specifically bound at the lacZ gene and prevents unnecessary production of the lactose enzyme used to digest the milk sugar; when only lactose and no glucose is present the lacZ gene is activated and lactose-digesting enzymes are produced. Equally famed is the λ switch in Escherichia coli bacteria that are infected by bacteriophage λ. There, the λ switch decides between the dormant lysogenic state or the state of lysis that leads to the production of new phages and ultimate death of the E.coli host cell. Molecularly, the regulation of a gene relies on the presence of certain DNA-binding proteins, so-called transcription factors, that bind to a specific binding site close to the starting sequence of the related gene. The transcription factor then promotes or inhibits binding of RNA polymerase and thus regulates the transcription of this gene. This strategy allows eukaryotic and prokaryotic cells as well as viruses to respond to different internal or external signals (1, 2).The binding of the protein to its specific bindin...

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In vivo non‐specific binding of λ CI and Cro repressors is significant

Cited by 42 publications

References 28 publications

DNA looping provides stability and robustness to the bacteriophage λ switch

DNA looping provides stability and robustness to the bacteriophage λ switch

Transcriptional regulation by the numbers: models

Facilitated diffusion with DNA coiling

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