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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 effect of intersegment transfer on the parameter space for the intersegmental transfer rate, kIST = 100. The level curves correspond to chi-square values less than 3 measuring the goodness of fit of simulations to experiment for one of the two operator sites at distances 25, 45, 65, 115 and 203 bp. The chi-squared values come from simulations and the absolute time semi-transparent cyan region was calculated for the best fit combination of parameters with vacancy v = 0.85, the probability of specific binding pbind = 1.0 and the fraction of non-specific binding FB is equal to 90%. The cyan region in this figure shows where the absolute search time is in the interval 236 s (three proteins)–416 s (five proteins). The black horizontal lines aid in comparing the lowest attainable D1 values between the cases of no intersegment transfer (left: kIST = 0 s−1) and with intersegment transfer (right: kIST = 100 s−1).
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Figure 5: The effect of intersegment transfer on the parameter space for the intersegmental transfer rate, kIST = 100. The level curves correspond to chi-square values less than 3 measuring the goodness of fit of simulations to experiment for one of the two operator sites at distances 25, 45, 65, 115 and 203 bp. The chi-squared values come from simulations and the absolute time semi-transparent cyan region was calculated for the best fit combination of parameters with vacancy v = 0.85, the probability of specific binding pbind = 1.0 and the fraction of non-specific binding FB is equal to 90%. The cyan region in this figure shows where the absolute search time is in the interval 236 s (three proteins)–416 s (five proteins). The black horizontal lines aid in comparing the lowest attainable D1 values between the cases of no intersegment transfer (left: kIST = 0 s−1) and with intersegment transfer (right: kIST = 100 s−1).

Mentions: The process by which two DNA segments diffuse within binding distance of a protein capable of transiently binding both segments and therefore transfer from one segment to the other without dissociation is called intersegment transfer. We take this mode into account using the approach of (5). For the combination of parameters having no analytic counterpart we used simulations to get the chi-squared values. We find that intersegment transfer rates below ca 100 s−1 have a negligible effect on the minimal acceptable D1 value (Figure 5). The reason for the small effect is that intersegment transfer disrupts the sliding process which weakens the correlations in the two-operator data effectively increasing the required D1 value. At the same time, intersegment transfer increases the specific association rate, effectively decreasing D1. For higher values of kIST, the fit becomes increasingly bad, pushing the minimal acceptable D1 higher (Supplementary Figure S8).


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 effect of intersegment transfer on the parameter space for the intersegmental transfer rate, kIST = 100. The level curves correspond to chi-square values less than 3 measuring the goodness of fit of simulations to experiment for one of the two operator sites at distances 25, 45, 65, 115 and 203 bp. The chi-squared values come from simulations and the absolute time semi-transparent cyan region was calculated for the best fit combination of parameters with vacancy v = 0.85, the probability of specific binding pbind = 1.0 and the fraction of non-specific binding FB is equal to 90%. The cyan region in this figure shows where the absolute search time is in the interval 236 s (three proteins)–416 s (five proteins). The black horizontal lines aid in comparing the lowest attainable D1 values between the cases of no intersegment transfer (left: kIST = 0 s−1) and with intersegment transfer (right: kIST = 100 s−1).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: The effect of intersegment transfer on the parameter space for the intersegmental transfer rate, kIST = 100. The level curves correspond to chi-square values less than 3 measuring the goodness of fit of simulations to experiment for one of the two operator sites at distances 25, 45, 65, 115 and 203 bp. The chi-squared values come from simulations and the absolute time semi-transparent cyan region was calculated for the best fit combination of parameters with vacancy v = 0.85, the probability of specific binding pbind = 1.0 and the fraction of non-specific binding FB is equal to 90%. The cyan region in this figure shows where the absolute search time is in the interval 236 s (three proteins)–416 s (five proteins). The black horizontal lines aid in comparing the lowest attainable D1 values between the cases of no intersegment transfer (left: kIST = 0 s−1) and with intersegment transfer (right: kIST = 100 s−1).
Mentions: The process by which two DNA segments diffuse within binding distance of a protein capable of transiently binding both segments and therefore transfer from one segment to the other without dissociation is called intersegment transfer. We take this mode into account using the approach of (5). For the combination of parameters having no analytic counterpart we used simulations to get the chi-squared values. We find that intersegment transfer rates below ca 100 s−1 have a negligible effect on the minimal acceptable D1 value (Figure 5). The reason for the small effect is that intersegment transfer disrupts the sliding process which weakens the correlations in the two-operator data effectively increasing the required D1 value. At the same time, intersegment transfer increases the specific association rate, effectively decreasing D1. For higher values of kIST, the fit becomes increasingly bad, pushing the minimal acceptable D1 higher (Supplementary Figure S8).

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