An agent-based model for mRNA export through the nuclear pore complex

Molecular Biology of the Cell

Volumn 25, Issue 22, 2014, Pages 3643-3653

  Azimi, Mohammad ^a   Bulat, Evgeny ^a,b   Weis, Karsten ^b,c   Mofrad, Mohammad R K ^a  

^a Graduate Program in Chemical Biology   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NUCLEOPORIN;

ARTICLE; BINDING AFFINITY; CELL NUCLEUS MEMBRANE; CYTOPLASM; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR CROWDING; NUCLEAR PORE COMPLEX; PROTEIN LOCALIZATION; PROTEIN TRANSPORT; RNA TRANSPORT; STEADY STATE; ACTIVE TRANSPORT; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; CYTOLOGY; EUKARYOTIC CELL; HUMAN; KINETICS; METABOLISM; NUCLEAR PORE; TIME;

ACTIVE TRANSPORT, CELL NUCLEUS; ANIMALS; CYTOPLASM; EUKARYOTIC CELLS; HUMANS; KINETICS; MODELS, MOLECULAR; NUCLEAR PORE; NUCLEAR PORE COMPLEX PROTEINS; NUCLEIC ACID CONFORMATION; RNA TRANSPORT; RNA, MESSENGER; TIME FACTORS;

EID: 84908566730     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E14-06-1065     Document Type: Article

References (37)

1. Adam SA (2001). The nuclear pore complex. Genome Biol 2, REVIEWS0007.
2. Azimi M, Jamali Y, Mofrad MR (2011). Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion. PLoS One 6, e25306.
3. Azimi M, Mofrad MR (2013). Higher nucleoporin-Importinbeta affinity at the nuclear basket increases nucleocytoplasmic import. PLoS One 8, e81741.
4. Bonchev D, Thomas S, Apte A, Kier LB (2010). Cellular automata modelling of biomolecular networks dynamics. SAR QSAR Environ Res 21, 77-102.
5. Cheng H, Dufu K, Lee CS, Hsu JL, Dias A, Reed R (2006). Human mRNA export machinery recruited to the 5′ end of mRNA. Cell 127, 1389-1400.
6. Daneholt B (1997). A look at messenger RNP moving through the nuclear pore. Cell 88, 585-588.
7. Devillers J, Devillers H, Decourtye A, Aupinel P (2010). Internet resources for agent-based modelling. SAR QSAR Environ Res 21, 337-350.
8. Dong X, Foteinou PT, Calvano SE, Lowry SF, Androulakis IP (2010). Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One 5, e9249.
9. Grunwald D, Singer RH (2010). In vivo imaging of labelled endogenous beta-actin mRNA during nucleocytoplasmic transport. Nature 467, 604-607.
10. Hobeika M, Brockmann C, Gruessing F, Neuhaus D, Divita G, Stewart M, Dargemont C (2009). Structural requirements for the ubiquitin-associated domain of the mRNA export factor Mex67 to bind its specific targets, the transcription elongation THO complex component Hpr1 and nucleoporin FXFG repeats. J Biol Chem 284, 17575-17583.
11. Hodge CA, Tran EJ, Noble KN, Alcazar-Roman AR, Ben-Yishay R, Scarcelli JJ, Folkmann AW, Shav-Tal Y, Wente SR, Cole CN (2011). The Dbp5 cycle at the nuclear pore complex during mRNA export I: dbp5 mutants with defects in RNA binding and ATP hydrolysis define key steps for Nup159 and Gle1. Genes Dev 25, 1052-1064.
12. Jamali T, Jamali Y, Mehrbod M, Mofrad MRK (2011). Nuclear pore complex: biochemistry and biophysics of nucleocytoplasmic transport in health and disease. Int Rev Cell Mol Biol 287, 233-286.
13. Jamali Y, Jamali T, Mofrad MRK (2013). An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homooligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility. J Comput Phys 244, 264-278.
14. Kataoka N, Yong J, Kim VN, Velazquez F, Perkinson RA, Wang F, Dreyfuss G (2000). Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol Cell 6, 673-682.
15. Kohler A, Hurt E (2007). Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol 8, 761-773.
16. Le Hir H, Gatfield D, Izaurralde E, Moore MJ (2001). The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J 20, 4987-4997.
17. Le Hir H, Izaurralde E, Maquat LE, Moore MJ (2000). The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J 19, 6860-6869.
18. Loschberger A, van de Linde S, Dabauvalle MC, Rieger B, Heilemann M, Krohne G, Sauer M (2012). Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. J Cell Sci 125, 570-575.
19. Ma J, Liu Z, Michelotti N, Pitchiaya S, Veerapaneni R, Androsavich JR, Walter NG, Yang W (2013). High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat Commun 4, 2414.
20. Magee J, Warwicker J (2005). Simulation of non-specific protein-mRNA interactions. Nucleic Acids Res 33, 6694-6699.
21. Mehlin H, Daneholt B, Skoglund U (1992). Translocation of a specific premessenger ribonucleoprotein particle through the nuclear pore studied with electron microscope tomography. Cell 69, 605-613.
22. Mehlin H, Daneholt B, Skoglund U (1995). Structural interaction between the nuclear pore complex and a specific translocating RNP particle. J Cell Biol 129, 1205-1216.
23. Mohr D, Frey S, Fischer T, Guttler T, Gorlich D (2009). Characterisation of the passive permeability barrier of nuclear pore complexes. EMBO J 28, 2541-2553.
24. Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K (2011). A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature 472, 238-242.
25. Mor A, Suliman S, Ben-Yishay R, Yunger S, Brody Y, Shav-Tal Y (2010). Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells. Nat Cell Biol 12, 543-552.
26. Natalizio BJ, Wente SR (2013). Postage for the messenger: designating routes for nuclear mRNA export. Trends Cell Biol 23, 365-373.
27. Noble KN, Tran EJ, Alcazar-Roman AR, Hodge CA, Cole CN, Wente SR (2011). The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1. Genes Dev 25, 1065-1077.
28. Querido E, Chartrand P (2008). Using fluorescent proteins to study mRNA trafficking in living cells. Methods Cell Biol 85, 273-292.
29. Riddick G, Macara IG (2005). A systems analysis of importin-α-β mediated nuclear protein import. J Cell Biol 168, 1027-1038.
30. Rodriguez MS, Dargemont C, Stutz F (2004). Nuclear export of RNA. Biol Cell 96, 639-655.
31. Siebrasse JP, Kaminski T, Kubitscheck U (2012). Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy. Proc Natl Acad Sci USA 109, 9426-9431.
32. Stewart M (2007). Ratcheting mRNA out of the nucleus. Mol Cell 25, 327-330.
33. Tetenbaum-Novatt J, Hough LE, Mironska R, McKenney AS, Rout MP (2012). Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin-nucleoporin interactions. Mol Cell Proteomics 11, 31-46.
34. Tutucci E, Stutz F (2011). Keeping mRNPs in check during assembly and nuclear export. Nat Rev Mol Cell Biol 12, 377-384.
35. Vanzi F, Takagi Y, Shuman H, Cooperman BS, Goldman YE (2005). Mechanical studies of single ribosome/mRNA complexes. Biophys J 89, 1909-1919.
36. Visa N, Izaurralde E, Ferreira J, Daneholt B, Mattaj IW (1996). A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export. J Cell Biol 133, 5-14.
37. Yamada J, Phillips JL, Patel S, Goldfien G, Calestagne-Morelli A, Huang H, Reza R, Acheson J, Krishnan VV, Newsam S, et al. (2010). A bimodal distribution of two distinct categories of intrinsically disordered structures with separate functions in FG nucleoporins. Mol Cell Proteomics 9, 2205-2224.