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PLOS ONE  2013 

In Vivo Facilitated Diffusion Model

DOI: 10.1371/journal.pone.0053956

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Abstract:

Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and one-dimensional sliding along the DNA contour is still beneficial in the crowded interior of cells is highly disputed. Here we use a simple model for the bacterial genome inside the cell and present a semi-analytical model for the in vivo target search of transcription factors within the facilitated diffusion framework. Without having to resort to extensive simulations we determine the mean search time of a lac repressor in a living E. coli cell by including parameters deduced from experimental measurements. The results agree very well with experimental findings, and thus the facilitated diffusion picture emerges as a quantitative approach to gene regulation in living bacteria cells. Furthermore we see that the search time is not very sensitive to the parameters characterizing the DNA configuration and that the cell seems to operate very close to optimal conditions for target localization. Local searches as implied by the colocalization mechanism are only found to mildly accelerate the mean search time within our model.

References

[1]  Riggs AD, Bourgeois S, Cohn M (1970) The lac repressor-operator interaction: Iii. kinetic studies. J Mol Biol 53: 401–417.
[2]  von Smoluchowski M (1916) Three presentations on diffusion, molecular movement according to brown and coagulation of colloid particles. Physikal Zeitschr 17: 557–571.
[3]  Berg OG, Winter RB, Von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. models and theory. Biochemistry 20: 6929–6948.
[4]  Winter RB, Berg OG, Von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. the escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry 20: 6961–6977.
[5]  Slutsky M, Mirny L (2004) Kinetics of protein-dna interaction: Facilitated target location in sequence-dependent potential. Biophys J 87: 4021–4035.
[6]  Lomholt MA, van den Broek B, Kalisch SMJ, Wuite GJL, Metzler R (2009) Facilitated diffusion with dna coiling. Proc Natl Acad Sci USA 106: 8204–8208.
[7]  Zhou HX (2011) Rapid search for specific sites on dna through conformational switch of non-specifically bound proteins. Proc Natl Acad Sci USA 108: 8651–8656.
[8]  Sheinman M, Bénichou O, Kafri Y, Voituriez R (2012) Classes of fast and specific search mechanisms for proteins on dna. Rep Prog Phys 75: 026601.
[9]  Mirny L, Slutsky M, Wunderlich Z, Tafvizi A, Leith J, et al. (2009) How a protein searches for its site on DNA: the mechanism of facilitated diffusion. J Phys A Math Gen 42: 434013..
[10]  Kolomeisky AB (2011) Physics of protein-DNA interactions: mechanisms of facilitated target search. Phys Chem Chem Phys 13: 2088–2095..
[11]  Sokolov I, Metzler R, Pant K, Williams M (2005) Target search of n sliding proteins on a dna. Biophys J 89: 895–902.
[12]  Gowers DM, Wilson GG, Halford SE (2005) Measurement of the contributions of 1d and 3d pathways to the translocation of a protein along dna. Proc Natl Acad Sci USA 102: 15883–15888.
[13]  Wang YM, Austin RH, Cox EC (2006) Single molecule measurements of repressor protein 1d diffusion on dna. Phys Rev Lett 97: 048302.
[14]  Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA (2007) How gene order is influenced by the biophysics of transcription regulation. Proc Natl Acad Sci USA 104: 13948–13953.
[15]  Bonnet I, Biebricher A, Porté PL, Loverdo C, Bénichou O, et al. (2008) Sliding and jumping of single ecorv restriction enzymes on non-cognate dna. Nucleic Acids Res 36: 4118–4127.
[16]  van den Broek B, Lomholt MA, Kalisch SMJ, Metzler R, Wuite GJL (2008) How dna coiling enhances target localization by proteins. Proc Natl Acad Sci USA 105: 15738–15742.
[17]  Konopka MC, Shkel IA, Cayley S, Record MT, Weisshaar JC (2006) Crowding and confinement effects on protein diffusion in vivo. J Bacteriol 188: 6115–6123.
[18]  Kühn T, Ihalainen TO, Hyv?luoma J, Dross N, Willman SF, et al. (2011) Protein diffusion in mammalian cell cytoplasm. PLoS One 6: e22962.
[19]  Elf J, Li GW, Xie XS (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316: 1191–1194.
[20]  Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, et al. (2012) The lac repressor displays facilitated diffusion in living cells. Science 336: 1595–1598.
[21]  Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276: 10577–10580.
[22]  Morelli MJ, Allen RJ, ten Wolde PR (2011) Effects of macromolecular crowding on genetic networks. Biophys J 101: 2882–2891.
[23]  Golding I, Cox EC (2006) Physical nature of bacterial cytoplasm. Phys Rev Lett 96: 098102.
[24]  Weber SC, Spakowitz AJ, Theriot JA (2010) Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm. Phys Rev Lett 104: 238102.
[25]  Jeon JH, Tejedor V, Burov S, Barkai E, Selhuber-Unkel C, et al. (2011) In Vivo anomalous diffusion and weak ergodicity breaking of lipid granules. Phys Rev Lett 106: 048103.
[26]  Metzler R, Klafter J (2000) The random walk's guide to anomalous diffusion: a fractional dynamics approach. Phys Rep 339: 1–77.
[27]  Barkai E, Garini Y, Metzler R (2012) Strange kinetics of single molecules in living cells. Phys Today 65(8): 29–35.
[28]  Banks D, Fradin C (2005) Anomalous diffusion of proteins due to molecular crowding. Biophys J 89: 2960–2971.
[29]  Weiss M, Elsner M, Kartberg F, Nilsson T (2004) Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys J 87: 3518–3524.
[30]  Koslover EF, Diaz de la Rosa MA, Spakowitz AJ (2011) Theoretical and computational modeling of target-site search kinetics in vitro and in vivo. Biophys J 101: 856–865.
[31]  Bénichou O, Chevalier C, Meyer B, Voituriez R (2011) Facilitated diffusion of proteins on chromatin. Phys Rev Lett 106: 038102..
[32]  Foffano G, Marenduzzo D, Orlandini E (2012) Facilitated diffusion on confined dna. Phys Rev E Stat Nonlin Soft Matter Phys 85: 021919.
[33]  Rocha EPC (2008) The organization of the bacterial genome. Annu Rev Genet 42: 211–233.
[34]  Kim J, Yoshimura SH, Hizume K, Ohniwa RL, Ishihama A, et al. (2004) Fundamental structural units of the escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res 32: 1982–1992.
[35]  Postow L, Hardy C, Arsuaga J, Cozzarelli N (2004) Topological domain structure of the escherichia coli chromosome. Genes Dev 18: 1766–1779.
[36]  Romantsov T, Fishov I, Krichevsky O (2007) Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy. Biophys J 92: 2875–2884.
[37]  Umbarger MA, Toro E, Wright MA, Porreca GJ, Bau D, et al. (2011) The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 44: 252–264.
[38]  Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, et al. (2004) Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial dna replication. Proc Natl Acad Sci USA 101: 9257–9262.
[39]  Jun S, Wright A (2010) Entropy as the driver of chromosome segregation. Nat Rev Microbiol 8: 600–607.
[40]  Jung Y, Jeon C, Kim J, Jeong H, Jun S, et al. (2012) Ring polymers as model bacterial chromosomes: confinement, chain topology, single chain statistics, and how they interact. Soft Matter 8: 2095–2102.
[41]  Buenemann M, Lenz P (2010) A geometrical model for dna organization in bacteria. PLoS One 5: e13806.
[42]  Junier I, Martin O, Képès F (2010) Spatial and topological organization of dna chains induced by gene co-localization. PLoS Comput Biol 6: e1000678.
[43]  Fritsche M, Li S, Heermann DW, Wiggins PA (2012) A model for escherichia coli chromosome packaging supports transcription factor-induced dna domain formation. Nucleic Acids Res 40: 972–980.
[44]  Bauer M, Metzler R (2012) Generalized facilitated diffusion model for dna-binding proteins with search and recognition states. Biophys J 102: 2321–2330.
[45]  Sheinman M, Kafri Y (2009) The effects of intersegmental transfers on target location by proteins. Phys Biol 6: 016003..
[46]  Madras N, Orlitsky A, Shepp L (1990) Monte carlo generation of self-avoiding walks with fixed endpoints and fixed length. J Stat Phys 58: 159–183.
[47]  Reingruber J, Holcman D (2010) Narrow escape for a stochastically gated brownian ligand. J Phys Condens Matter 22: 065103.
[48]  Coppey M, Bénichou O, Voituriez R, Moreau M (2004) Kinetics of target site localization of a protein in DNA: a stochastic approach. Biophys J 87: 1640–1649.
[49]  Wunderlich Z, Mirny LA (2008) Spatial effects on the speed and reliability of protein-dna search. Nucleic Acids Res 36: 3570–3578.
[50]  Bénichou O, Chevalier C, Klafter J, Meyer B, Voituriez R (2010) Geometry-controlled kinetics. Nat Chem 2: 472–477.
[51]  Meyer B, Chevalier C, Voituriez R, Bénichou O (2010) Universality classes of first-passage-time distribution in confined media. Phys Rev E Stat Nonlin Soft Matter Phys 83: 051116..
[52]  Guigas G, Weiss M (2008) Sampling the cell with anomalous diffusion - The discovery of slowness. Biophys J 94: 90–94.
[53]  Lomholt MA, Zaid IM, Metzler R (2007) Subdiffusion and weak ergodicity breaking in the presence of a reactive boundary. Phys Rev Lett 98: 200603.
[54]  Hellmann M, Heermann DW, Weiss M (2012) Enhancing phosphorylation cascades by anomalous diffusion. EPL 97: 58004.
[55]  Sereshki LE, Lomholt MA, Metzler R (2012) A solution to the subdiffusion-efficiency paradox: inactive states enhance reaction efficiency at subdiffusion conditions in living cells. EPL 97: 20008.

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