A generic 3D kinetic model of gene expression

• Autorzy: Vladimir Zhdanov
• Języki publikacji: EN

Abstrakty

EN

Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.

Słowa kluczowe

EN

subcellular processes; gene transcription; mRNA synthesis; mRNA translation; mRNA and protein diffusion and degradation

• Czasopismo: Open Physics
• Rocznik: 2012
• Tom: 10
• Numer: 2
• Strony: 533-537

Daty

wydano

2012-04-01

online

2012-03-31

Twórcy

autor

Vladimir Zhdanov,

Bibliografia

• [1] M. Kaern, T.C. Elston, W.J. Blake, J.J. Collins, Nature Rev. Genet. 6, 451 (2005) http://dx.doi.org/10.1038/nrg1615[Crossref]
• [2] J. Paulsson, Phys. Life Rev. 2, 157 (2005) http://dx.doi.org/10.1016/j.plrev.2005.03.003[Crossref]
• [3] J. Rausenberger, C. Fleck, J. Timmer, M. Kollmann, Progr. Biophys. Molec. Biol. 100, 57 (2009) http://dx.doi.org/10.1016/j.pbiomolbio.2009.06.003[Crossref]
• [4] A.S. Ribeiro, Math. Biosci. 223, 1 (2010) http://dx.doi.org/10.1016/j.mbs.2009.10.007[Crossref]
• [5] G. Tiana, S. Krishna, S. Pigolotti, M.H. Jensen, K. Sneppen, Phys. Biol. 4, R1 (2007) http://dx.doi.org/10.1088/1478-3975/4/2/R01[Crossref]
• [6] O. Purcell, N.J. Savery, C.S. Grierson, M. di Bernardo, J. Roy. Soc. Interface 7, 1503 (2010) http://dx.doi.org/10.1098/rsif.2010.0183[Crossref]
• [7] V.P. Zhdanov, Phys. Rep. 500, 1 (2011) http://dx.doi.org/10.1016/j.physrep.2010.12.002[Crossref]
• [8] U. Alon, Nature Rev. Genet. 8, 450 (2007) http://dx.doi.org/10.1038/nrg2102[Crossref]
• [9] G. Karlebach, R. Shamir, Nature Rev. Molec. Cell Biol. 9, 771 (2008)
• [10] M.C. Lagomarsino, B. Bassetti, G. Castellani, D. Remondini, Molec. Biosyst. 5, 335 (2009) http://dx.doi.org/10.1039/b816841p[Crossref]
• [11] D.F.T. Veiga, B. Dutta, G. Balazsi, Molec. Biosyst. 6, 469 (2010) http://dx.doi.org/10.1039/b916989j[Crossref]
• [12] M. Valencia-Burtona, et al., Proc. Natl. Acad. Sci. USA 106, 16399 (2009) http://dx.doi.org/10.1073/pnas.0907495106[Crossref]
• [13] J.H. Russell, K.C. Keiler, Proc. Natl. Acad. Sci. USA 106, 16405 (2009) http://dx.doi.org/10.1073/pnas.0904904106[Crossref]
• [14] P. Montero Llopis, et al., Nature 466, 77 (2010) http://dx.doi.org/10.1038/nature09152[Crossref]
• [15] K. Nevo-Dinur, A. Nussbaum-Shochat, S. Ben-Yehuda, O. Amster-Choder, Science 331, 1081 (2011) http://dx.doi.org/10.1126/science.1195691[Crossref]
• [16] D.Z. Rudner, R. Losick, Cold Spring Harb. Perspect. Biol. 2, a000307 (2010) http://dx.doi.org/10.1101/cshperspect.a000307[Crossref]
• [17] E. Evguenieva-Hackenberg, V. Roppelt, C. Lassek, G. Klug, RNA Biol. 8, 49 (2011) http://dx.doi.org/10.4161/rna.8.1.14066[Crossref]
• [18] N.E. Broude, Molec. Microbiol. 80, 1137 (2011) http://dx.doi.org/10.1111/j.1365-2958.2011.07652.x[Crossref]
• [19] K.C. Keiler, Curr. Opin. Microbiol. 14, 155 (2011) http://dx.doi.org/10.1016/j.mib.2011.01.009[Crossref]
• [20] J.T. Mika, B. Poolman, Curr. Opin. Biotechnol. 22, 117 (2011) http://dx.doi.org/10.1016/j.copbio.2010.09.009[Crossref]
• [21] S.A. Isaacson, C.S. Peskin, SIAM J. Sci. Comp. 28, 47 (2006) http://dx.doi.org/10.1137/040605060[Crossref]
• [22] V.P. Zhdanov, JETP Lett. 85, 302 (2007) http://dx.doi.org/10.1134/S0021364007060082[Crossref]
• [23] V.P. Zhdanov, Chem. Phys. Lett. 458, 247 (2008) http://dx.doi.org/10.1016/j.cplett.2008.03.047[Crossref]
• [24] V.P. Zhdanov, Biophys. Rev. Lett. 4, 267 (2009) http://dx.doi.org/10.1142/S1793048009001034[Crossref]
• [25] Q. Ma, G. Shi, S. Xu, Y. Zou, Neural Comput. Applic. 20, 507 (2011) http://dx.doi.org/10.1007/s00521-011-0575-9[Crossref]

Identyfikatory

DOI

10.2478/s11534-012-0011-5