Abstract
BackgroundImportins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its inhibitor, IκBα, which masks nuclear localization sequence of NF-κB. In response to TNFα or LPS, IκBα is degraded, which allows importins to bind NF-κB and shepherd it across nuclear pores. NF-κB nuclear activity is terminated when newly synthesized IκBα enters the nucleus, binds NF-κB and exportin which directs the complex to the cytoplasm. Although importins/exportins are known to regulate spatiotemporal kinetics of NF-κB and other transcription factors governing innate immunity, the mechanistic details of these interactions have not been elucidated and mathematically modelled.ResultsBased on our quantitative experimental data, we pursue NF-κB system modelling by explicitly including NF-κB–importin and IκBα–exportin binding to show that the competition between importins and IκBα enables NF-κB nuclear translocation despite high levels of IκBα. These interactions reduce the effective relaxation time and allow the NF-κB regulatory pathway to respond to recurrent TNFα pulses of 45-min period, which is about twice shorter than the characteristic period of NF-κB oscillations. By stochastic simulations of model dynamics we demonstrate that randomly appearing, short TNFα pulses can be converted to essentially digital pulses of NF-κB activity, provided that intervals between input pulses are not shorter than 1 h.ConclusionsBy including interactions involving importin-α and exportin we bring the modelling of spatiotemporal kinetics of transcription factors to a more mechanistic level. Basing on the analysis of the pursued model we estimated the information transmission rate of the NF-κB pathway as 1 bit per hour.ReviewersThis article was reviewed by Marek Kimmel, James Faeder and William Hlavacek.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0164-z) contains supplementary material.
Highlights
Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors
Localization of a Transcription factor (TF) can be dynamically regulated by its conformational change or association with other molecules affecting the accessibility of the nuclear localization signal (NLS) or nuclear export signal (NES) for karyopherin binding [5,6,7]
We chose this technique in addition to Western blotting (WB) to obtain information about the levels and localization of NF-κB and IκBα in single cells
Summary
Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. In the best recognized pathway of nuclear protein export, exportin 1 (XPO1) functions both in NES recognition and as a carrier. Cargoes possessing both NLS and NES sequences undergo continuous shuttling between the cytoplasmic and the nuclear compartment. GTPases are essential for active nuclear transport, but due to their abundance [8, 9], they do not limit the rates of nuclear transport processes Instead, these rates can be limited by diffusion or active transport along microtubules [10], as the karyopherin:cargo complexes are formed anywhere in a cellular compartment, and need to translocate first into the vicinity of the nuclear envelope before translocation across a NPC can occur
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