Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks

Nagar, A and Valleriani, A and Lipowsky, R (2011) Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks. Journal of Statistical Physics, 145 (5). pp. 1385-1404. ISSN 0022-4715

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We investigate the role of degradation of mRNA on protein synthesis using the totally asymmetric simple exclusion process (TASEP) as the underlying model for ribosome dynamics. mRNA degradation has a strong effect on the lifetime distribution of the mRNA, which in turn affects polysome statistics such as the number of ribosomes present on an mRNA strand of a given size. An average over mRNA of all ages is equivalent to an average over possible configurations of the corresponding TASEP-both before steady state and in steady state. To evaluate the relevant quantities for the translation problem, we first study the approach towards steady state of the TASEP, starting with an empty lattice representing an unloaded mRNA. When approaching the high density phase, the system shows two distinct phases with the entry and exit boundaries taking control of the density at their respective ends in the second phase. The approach towards the maximal current phase exhibits the surprising property that the ribosome entry flux can exceed the maximum possible steady state value. In all phases, the averaging over the mRNA age distribution shows a decrease in the average ribosome density profile as a function of distance from the entry boundary. For entry/exit parameters corresponding to the high density phase of TASEP, the average ribosome density profile also has a maximum near the exit end.

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Additional Information: We thank Sophia Rudorf, Carlus Deneke, and Stefan Klumpp for stimulating interac- tions. The research of A.N. was supported by the German Federal Ministry of Education and Research in the framework of GoFORSys. Figure 1 was designed in collaboration with Susann Valleriani.
Uncontrolled Keywords: Degradation; mRNA translation; TASEP
Subjects: Physics
Divisions: Department of Physics
Depositing User: Team Library
Date Deposited: 29 Oct 2014 08:10
Last Modified: 14 Aug 2017 07:03
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