Repression oflacPromoter as a Function of Distance, Phase and Quality of an AuxiliarylacOperator

Müller, Johannes; Oehler, Stefan; Müller‐Hill, Benno

doi:10.1006/jmbi.1996.0143

Cited by 236 publications

(323 citation statements)

References 48 publications

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“…The experiments of Becker et al differ from those of Muller et al (7) mainly in quantitative details. Becker et al (21) used a weaker main operator, a lower number of repressors per cell, and measured the repression levels for fewer loop lengths.…”

Section: Appendix Ii: Corroboration Of the Main Resultsmentioning

confidence: 62%

“…3b). This mathematical transformation reveals a wealth of details that were not evident in the repression level curves (7,9). As expected, the free energy oscillates with the helical periodicity of DNA (7, 9-11) because the operators must have the right phase to bind simultaneously to the repressor.…”

Section: Resultsmentioning

confidence: 99%

“…To avoid the formation of multiple loops, experiments are typically performed with just the main and one auxiliary operator, as in the case of Muller et al (7). In such a case, there is transcription when the system is in a state in which (i) none of the operators is occupied, or (ii) a repressor is bound to just the auxiliary operator; and there is no transcription when (iii) a repressor is bound to just the main operator, (iv) a repressor is bound to both the main and the auxiliary operators by looping the intervening DNA, or (v) one repressor is bound to the main operator and another repressor to the auxiliary operator.…”

Section: Background and Methodsmentioning

confidence: 99%

“…The distance between operators determines the length of the DNA loop and affects the repression level through the changes in the free energy of looping. For interoperator distances from 57.5 to 98.5 bp, Muller et al (7) systematically varied the distance between two operators in increments of 1 bp and measured the in vivo repression levels under conditions similar to wild type. These physiological measurements of enzyme production in Escherichia coli cell populations allowed us to infer here the in vivo looping properties of DNA with unprecedented accuracy.…”

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confidence: 99%

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Inferring the in vivo looping properties of DNA

Saiz

Rubı́

Vilar

2005

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

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The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computationalexperimental approach for different lengths of the loop and found that, in addition to the intrinsic periodicity of the DNA double helix, the free energy has an oscillatory component of about half the helical period. Moreover, the oscillations have such an amplitude that the effects of regulatory molecules become strongly dependent on their precise DNA positioning and yet easily tunable by their cooperative interactions. These unexpected results can confer to the physical properties of DNA a more prominent role at shaping the properties of gene regulation than previously thought.computational modeling ͉ DNA looping ͉ gene expression ͉ lac operon ͉ regulation T he cell is a densely packed dynamic structure made of thousands of different molecular species that orchestrate their interactions to form a functional unit. Such complexity poses a strong barrier for experimentally characterizing the cellular components: not only the properties of the components can change when studied in vitro outside the cell, but also the in vivo probing of the cell can perturb the process under study (1). Here we use computational modeling to obtain the properties of the in vivo unperturbed components at the molecular level from physiological measurements at the cellular level. Explicitly, we infer the in vivo free energies of DNA looping from enzyme production in the lac operon (2).The formation of DNA loops by the binding of proteins at distal DNA sites plays a fundamental role in many cellular processes, such as transcription, recombination, and replication (3-5). In gene regulation, proteins bound far away from the genes they regulate can be brought to the initiation of transcription region by looping the intervening DNA. The free energy cost of this process determines how easily DNA can loop and therefore the extent to which distal DNA sites can affect each other (5).In the lac operon, there is a repressor molecule that regulates transcription by binding specifically to DNA sites known as operators and preventing the RNA polymerase from transcribing the genes. DNA looping allows the repressor to bind to two operators simultaneously, leading to an increase in repression of transcription. This increase, characterized by the repression level, can be connected to the free energy of looping DNA by a recent model for transcription regulation by the lac repressor (6). The distance between operators determines the length of the DNA loop and affects the repression level through the changes in the free energy of looping. For interoperator distances from 57.5 to 98.5 bp, Muller et al. (7) systematically varied the distance between two operators in increments of 1 bp and measured the in vivo repression levels under conditions similar to wild type. These physiological measurements of enzyme production in Escherichia coli cell populations allowed us to ...

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Section: Appendix Ii: Corroboration Of the Main Resultsmentioning

confidence: 62%

Section: Resultsmentioning

confidence: 99%

Section: Background and Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Inferring the in vivo looping properties of DNA

Saiz

Rubı́

Vilar

2005

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

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“…We will focus on data in which the mechanical properties of DNA are used as an adjustable dial to tune a desired biological outcome during transcriptional regulation. In particular, we will address in vivo experiments like those performed by Müller et al, 101 Law et al, 102 and Becker et al, 103 where the level of repression is systematically measured as a function of the distance between two binding sites for Lac repressor ( Figure 7A inset). For reviews on Lac repressor refer to Matthews and Nichols 105 and to Lewis.…”

Section: Tightly Bent Dna In Transcriptional Regulationmentioning

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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Lac Operon

M��ller-hill¹

2002

Encyclopedia of Molecular Biology

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Repression oflacPromoter as a Function of Distance, Phase and Quality of an AuxiliarylacOperator

Cited by 236 publications

References 48 publications

Inferring the in vivo looping properties of DNA

Inferring the in vivo looping properties of DNA

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

Lac Operon

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