Regulation of nuclear NF-κB oscillation by a diffusion coefficient and its biological implications

The transcription factor NF-κB shuttles between the cytoplasm and the nucleus, and nuclear NF-κB is known to oscillate with a cycle of 1.5-2.5 h following the application of external stimuli. Oscillation pattern of NF-κB is implicated in regulation of the gene expression profile. In a previous report, we found that the oscillation pattern of nuclear NF-κB in a computational 3D spherical cell was regulated by spatial parameters such as nuclear to cytoplasmic volume ratio, nuclear transport, locus of protein synthesis, and diffusion coefficient. Here we report analyses and a biological implication for the regulation of oscillation pattern by diffusion coefficient. Our analyses show that the "reset" of nuclear NF-κB, defined as the return of nuclear NF-κB to the initial level or lower, was crucial for the oscillation; this was confirmed by the flux analysis. In addition, we found that the distant cytoplasmic location from the nucleus acted as a "reservoir" for storing newly synthesized IκBα. When the diffusion coefficient of proteins was large (≥ 10-11 m2/s), a larger amount of IκBα was stored in the "reservoir" with a large flux by diffusion. Subsequently, stored IκBα diffused back to the nucleus, where nuclear NF-κB was "reset" to the initial state. This initiated the next oscillation cycle. When the diffusion coefficient was small (≤ 10-13 m2/s), oscillation of nuclear NF-κB was not observed because a smaller amount of IκBα was stored in the "reservoir" and there was incomplete "reset" of nuclear NF-κB. If the diffusion coefficient for IκBα was increased to 10-11 m2/s keeping other proteins at 10-13 m2/s, the oscillation was rescued confirming the "reset" and "reservoir" hypothesis. Finally, we showed altered effective value of diffusion coefficient by diffusion obstacles. Thus, organelle crowding seen in stressed cells possibly changes the oscillation pattern by controlling the effective diffusion coefficient.