NDLI: Regulation of Nuclear NF-κB Oscillation by a Diffusion Coefficient and Its Biological Implications

Content Provider	PubMed Central
Author	Ohshima, Daisuke Ichikawa, Kazuhisa
Editor	Shih, Chiaho
Copyright Year	2014
Abstract	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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0109895
Starting Page	109895
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	10
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-10-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Regulation of Nuclear Factor κB (NF-κB) Transcriptional Activity via p65 Acetylation by the Chaperonin Containing TCP1 (CCT)

Regulation of the let-7a-3 Promoter by NF-κB

Roles of Spatial Parameters on the Oscillation of Nuclear NF-κB: Computer Simulations of a 3D Spherical Cell

Transcriptional Regulation of PIK3CA Oncogene by NF-κB in Ovarian Cancer Microenvironment

TDP-43 Inhibits NF-κB Activity by Blocking p65 Nuclear Translocation

Enhancement of Inflammatory Protein Expression and Nuclear Factor Κb (NF-Κb) Activity by Trichostatin A (TSA) in OP9 Preadipocytes

Negative Regulation of NF-κB by the ING4 Tumor Suppressor in Breast Cancer

In Vivo Circadian Oscillation of dCREB2 and NF-κB Activity in the Drosophila Nervous System

Quantification of Cellular NEMO Content and Its Impact on NF-κB Activation by Genotoxic Stress

Regulation of Nuclear NF-κB Oscillation by a Diffusion Coefficient and Its Biological Implications

Similar Documents

Regulation of Nuclear Factor κB (NF-κB) Transcriptional Activity via p65 Acetylation by the Chaperonin Containing TCP1 (CCT)

Regulation of the let-7a-3 Promoter by NF-κB

Roles of Spatial Parameters on the Oscillation of Nuclear NF-κB: Computer Simulations of a 3D Spherical Cell

Transcriptional Regulation of PIK3CA Oncogene by NF-κB in Ovarian Cancer Microenvironment

TDP-43 Inhibits NF-κB Activity by Blocking p65 Nuclear Translocation

Enhancement of Inflammatory Protein Expression and Nuclear Factor Κb (NF-Κb) Activity by Trichostatin A (TSA) in OP9 Preadipocytes

Negative Regulation of NF-κB by the ING4 Tumor Suppressor in Breast Cancer

In Vivo Circadian Oscillation of dCREB2 and NF-κB Activity in the Drosophila Nervous System

Quantification of Cellular NEMO Content and Its Impact on NF-κB Activation by Genotoxic Stress

Regulation of Nuclear NF-κB Oscillation by a Diffusion Coefficient and Its Biological Implications