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Gene location and DNA density determine transcription factor distributions in Escherichia coli.

Kuhlman TE, Cox EC - Mol. Syst. Biol. (2012)

Bottom Line: Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene.We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid.We propose a model for intranucleoid diffusion that can reconcile these results with previous measurements of LacI diffusion, and we discuss the implications of these findings for gene regulation in bacteria and eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ, USA. tkuhlman@illinois.edu

ABSTRACT
The diffusion coefficient of the transcription factor LacI within living Escherichia coli has been measured directly by in vivo tracking to be D = 0.4 μm(2)/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell. Here, we test this expectation of spatial homogeneity by single-molecule visualization of LacI molecules non-specifically bound to DNA in fixed cells. Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene. We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid. Finally, we show that LacI inhomogeneity increases the strength with which targets located proximally to the LacI gene are regulated. We propose a model for intranucleoid diffusion that can reconcile these results with previous measurements of LacI diffusion, and we discuss the implications of these findings for gene regulation in bacteria and eukaryotes.

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A model of intranucleoid diffusion. TFs are produced at the site of the source gene within the nucleoid. TFs are initially confined to the nucleoid and diffuse via 1D sliding along the chromosome combined with short 3D hops between domains, which we coarse grain together as effective 1D diffusion along the entire nucleoid. TFs are excluded from the nucleoid with rate constant k1, where they quickly homogenize via rapid 3D diffusion to form a background pool of repressor. TFs can be recaptured into the nucleoid rate constant k2, and are diluted with rate constant β.
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f7: A model of intranucleoid diffusion. TFs are produced at the site of the source gene within the nucleoid. TFs are initially confined to the nucleoid and diffuse via 1D sliding along the chromosome combined with short 3D hops between domains, which we coarse grain together as effective 1D diffusion along the entire nucleoid. TFs are excluded from the nucleoid with rate constant k1, where they quickly homogenize via rapid 3D diffusion to form a background pool of repressor. TFs can be recaptured into the nucleoid rate constant k2, and are diluted with rate constant β.

Mentions: where α is the rate of TF production, β is the rate constant for degradation or dilution, D1 and D3 are the intranucleoid and extranucleoid diffusion coefficients, respectively, k1 and k2 are nucleoid exclusion and capture rate constants, respectively, and f is the fraction of TFs initially confined to the nucleoid after translation. We postulate that hops through 3D space of short duration within the nucleoid can be coarse grained along with true 1D sliding along DNA into effective 1D diffusion along the nucleoid. Only when TFs escape into the cytoplasm for an extended 3D excursion they are considered to be undergoing true 3D diffusion, and this escape is assumed to occur with linear rate constant k1 as a result of nucleoid exclusion forces. In this view, the escape rate constant k1 serves as the degradation rate constant of the nucleoid-confined sub-population. After escape, TFs diffusing in 3D rapidly form a homogeneous background pool and can be recaptured by the nucleoid with linear rate constant k2. A cartoon illustrating this argument is shown in Figure 7. The steady-state solution of a simplified 1D version of this model yields an enhancement of TF concentration around the encoding gene located at a position x0 (Kuhlman and Cox, in preparation):


Gene location and DNA density determine transcription factor distributions in Escherichia coli.

Kuhlman TE, Cox EC - Mol. Syst. Biol. (2012)

A model of intranucleoid diffusion. TFs are produced at the site of the source gene within the nucleoid. TFs are initially confined to the nucleoid and diffuse via 1D sliding along the chromosome combined with short 3D hops between domains, which we coarse grain together as effective 1D diffusion along the entire nucleoid. TFs are excluded from the nucleoid with rate constant k1, where they quickly homogenize via rapid 3D diffusion to form a background pool of repressor. TFs can be recaptured into the nucleoid rate constant k2, and are diluted with rate constant β.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472691&req=5

f7: A model of intranucleoid diffusion. TFs are produced at the site of the source gene within the nucleoid. TFs are initially confined to the nucleoid and diffuse via 1D sliding along the chromosome combined with short 3D hops between domains, which we coarse grain together as effective 1D diffusion along the entire nucleoid. TFs are excluded from the nucleoid with rate constant k1, where they quickly homogenize via rapid 3D diffusion to form a background pool of repressor. TFs can be recaptured into the nucleoid rate constant k2, and are diluted with rate constant β.
Mentions: where α is the rate of TF production, β is the rate constant for degradation or dilution, D1 and D3 are the intranucleoid and extranucleoid diffusion coefficients, respectively, k1 and k2 are nucleoid exclusion and capture rate constants, respectively, and f is the fraction of TFs initially confined to the nucleoid after translation. We postulate that hops through 3D space of short duration within the nucleoid can be coarse grained along with true 1D sliding along DNA into effective 1D diffusion along the nucleoid. Only when TFs escape into the cytoplasm for an extended 3D excursion they are considered to be undergoing true 3D diffusion, and this escape is assumed to occur with linear rate constant k1 as a result of nucleoid exclusion forces. In this view, the escape rate constant k1 serves as the degradation rate constant of the nucleoid-confined sub-population. After escape, TFs diffusing in 3D rapidly form a homogeneous background pool and can be recaptured by the nucleoid with linear rate constant k2. A cartoon illustrating this argument is shown in Figure 7. The steady-state solution of a simplified 1D version of this model yields an enhancement of TF concentration around the encoding gene located at a position x0 (Kuhlman and Cox, in preparation):

Bottom Line: Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene.We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid.We propose a model for intranucleoid diffusion that can reconcile these results with previous measurements of LacI diffusion, and we discuss the implications of these findings for gene regulation in bacteria and eukaryotes.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ, USA. tkuhlman@illinois.edu

ABSTRACT
The diffusion coefficient of the transcription factor LacI within living Escherichia coli has been measured directly by in vivo tracking to be D = 0.4 μm(2)/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell. Here, we test this expectation of spatial homogeneity by single-molecule visualization of LacI molecules non-specifically bound to DNA in fixed cells. Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene. We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid. Finally, we show that LacI inhomogeneity increases the strength with which targets located proximally to the LacI gene are regulated. We propose a model for intranucleoid diffusion that can reconcile these results with previous measurements of LacI diffusion, and we discuss the implications of these findings for gene regulation in bacteria and eukaryotes.

Show MeSH
Related in: MedlinePlus