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What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Mahmutovic A, Berg OG, Elf J - Nucleic Acids Res. (2015)

Bottom Line: Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value.This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed.For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.

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The dependence of the parameter space on the total number of searching proteins and the genome size showing how the front of the semi-transparent cyan regions in Figure 2 would move under different assumptions. The blue, green and magenta lines correspond to 4, 5 and 6 searching proteins, respectively, while the black dashed line represents an 85% vacancy around the operator site (vOP) and a vacancy of 70% elsewhere. The chi-square values depend weakly on the genome size as tested by simulations. The acceptable 1D diffusion constant is pushed toward lower values by either increasing the number of searching proteins or decreasing the genome size.
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Figure 6: The dependence of the parameter space on the total number of searching proteins and the genome size showing how the front of the semi-transparent cyan regions in Figure 2 would move under different assumptions. The blue, green and magenta lines correspond to 4, 5 and 6 searching proteins, respectively, while the black dashed line represents an 85% vacancy around the operator site (vOP) and a vacancy of 70% elsewhere. The chi-square values depend weakly on the genome size as tested by simulations. The acceptable 1D diffusion constant is pushed toward lower values by either increasing the number of searching proteins or decreasing the genome size.

Mentions: When looking at which of the experimental input parameters are most uncertain we find that there are considerable uncertainty in both the DNA vacancy v and in the estimated number (N ≈ 3–5) of repressors participating in the search. The number of proteins does not influence the chi-square fits in Figure 2, but the total search time is influenced in direct proportion. Thus, if N > 5, the overlap region would be pushed toward lower α and D1 (Figure 6). The DNA vacancy has been assumed to be uniform over the chromosome; however, it could be very different around the operator regions as compared to the bulk of the DNA, for instance if parts of the genome are excluded due to local folds or if DNA binding proteins themselves are clustered in regions of the chromosome other than the operator regions (55). This would have the effect of lowering the occupancy around the operator site while allowing for more DNA binding molecules overall. Taking this effect into account, the overlap between the cyan region and the red chi-square values would increase, which would also allow for lower D1 values (Figure 6).


What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Mahmutovic A, Berg OG, Elf J - Nucleic Acids Res. (2015)

The dependence of the parameter space on the total number of searching proteins and the genome size showing how the front of the semi-transparent cyan regions in Figure 2 would move under different assumptions. The blue, green and magenta lines correspond to 4, 5 and 6 searching proteins, respectively, while the black dashed line represents an 85% vacancy around the operator site (vOP) and a vacancy of 70% elsewhere. The chi-square values depend weakly on the genome size as tested by simulations. The acceptable 1D diffusion constant is pushed toward lower values by either increasing the number of searching proteins or decreasing the genome size.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402528&req=5

Figure 6: The dependence of the parameter space on the total number of searching proteins and the genome size showing how the front of the semi-transparent cyan regions in Figure 2 would move under different assumptions. The blue, green and magenta lines correspond to 4, 5 and 6 searching proteins, respectively, while the black dashed line represents an 85% vacancy around the operator site (vOP) and a vacancy of 70% elsewhere. The chi-square values depend weakly on the genome size as tested by simulations. The acceptable 1D diffusion constant is pushed toward lower values by either increasing the number of searching proteins or decreasing the genome size.
Mentions: When looking at which of the experimental input parameters are most uncertain we find that there are considerable uncertainty in both the DNA vacancy v and in the estimated number (N ≈ 3–5) of repressors participating in the search. The number of proteins does not influence the chi-square fits in Figure 2, but the total search time is influenced in direct proportion. Thus, if N > 5, the overlap region would be pushed toward lower α and D1 (Figure 6). The DNA vacancy has been assumed to be uniform over the chromosome; however, it could be very different around the operator regions as compared to the bulk of the DNA, for instance if parts of the genome are excluded due to local folds or if DNA binding proteins themselves are clustered in regions of the chromosome other than the operator regions (55). This would have the effect of lowering the occupancy around the operator site while allowing for more DNA binding molecules overall. Taking this effect into account, the overlap between the cyan region and the red chi-square values would increase, which would also allow for lower D1 values (Figure 6).

Bottom Line: Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value.This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed.For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.

Show MeSH
Related in: MedlinePlus