Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks |
| |
Authors: | Apoorva Nagar Angelo Valleriani Reinhard Lipowsky |
| |
Institution: | (1) Center for Stochastic Processes in Science, Engineering and Department of Physics, Virginia Tech, Blacksburg, VA 24061-0435, USA |
| |
Abstract: | 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. |
| |
Keywords: | |
本文献已被 SpringerLink 等数据库收录! |
|