title: A traffic flow model for bio-polymerization processes.
abstract: Bio-polymerization processes like transcription and translation are central to proper function of a cell. The speed at which the bio-polymer grows is affected both by the number of pauses of elongation machinery, as well the number of bio-polymers due to crowding effects. In order to quantify these effects in fast transcribing ribosome genes, we rigorously show that a classical traffic flow model is the limit of a mean occupancy ODE model. We compare the simulation of this model to a stochastic model and evaluate the combined effect of the polymerase density and the existence of pauses on the instantaneous transcription rate of ribosomal genes.
authors: Department of Mathematical Sciences, Montana State University, Bozeman, MT, 59717-2400, USA.
authors: Lisa
authors: L
authors: Davis
authors: Tomáš
authors: T
authors: Gedeon
authors: Jakub
authors: J
authors: Gedeon
authors: Jennifer
authors: J
authors: Thorenson
mesh_terms: D003198:Computer Simulation; D012321:DNA-Directed RNA Polymerases / Q000502:physiology*; D020459:Genes, rRNA / Q000502:physiology*; D008390:Markov Chains; D008954:Models, Biological; D014176:Protein Biosynthesis / Q000502:physiology*; D012270:Ribosomes / Q000502:physiology*; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D012321:DNA-Directed RNA Polymerases
references: Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8797-8
references: 19470457
references: Science. 1998 Jul 31;281(5377):660-5
references: 9685251
references: J Mol Biol. 1998 May 1;278(2):307-16
references: 9571053
references: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1994 Jun;49(6):5303-5309
references: 9961857
references: J Mol Biol. 1990 May 5;213(1):123-34
references: 2187097
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Aug;68(2 Pt 1):021910
references: 14525009
references: Biopolymers. 1968;6(1):1-5
references: 5641411
references: J Theor Biol. 1980 Sep 21;86(2):279-313
references: 7442295
references: J Biol Chem. 1995 Aug 4;270(31):18335-40
references: 7629155
references: Proc Natl Acad Sci U S A. 1989 Jul;86(14):5301-5
references: 2526335
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2004;70(1 Pt 2):016108
references: 15324130
references: Nature. 2007 Apr 12;446(7137):820-3
references: 17361130
references: Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8900-5
references: 19416863
references: Biochemistry. 1989 Sep 19;28(19):7829-42
references: 2482070
references: Phys Rev A. 1992 Jan 15;45(2):618-625
references: 9907026
references: EMBO J. 1993 Nov;12(11):4305-15
references: 8223440
references: Mol Microbiol. 1999 Jun;32(6):1296-304
references: 10383769
references: Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4439-44
references: 16537373
references: Cell. 2003 Nov 14;115(4):437-47
references: 14622598
references: Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18159-64
references: 19017803
references: J Biol Chem. 1997 May 9;272(19):12265-71
references: 9139668
references: J Mol Biol. 2004 Nov 19;344(2):335-49
references: 15522289
references: PLoS Comput Biol. 2010 Apr 01;6(4):e1000726
references: 20369012
references: J Bacteriol. 2009 Jun;191(11):3740-6
references: 19329648