Coverage of mRNA by Ribosomes

Instructions
If you don't see a picture above with RNA and various regulatory buttons, please install newest version of Java.

mRNA selection : One can choose out of 18 mRNA sequences, which are the sequence of three kinds of codon ratess A, B, and C. One can change them by changing number in "mRNA selection" box. For detailed information about the mRNAs, see Pedersen et al. (2010).

PARAMETERS
(Initiation):

Initiation occurs as follows;
(i) Binding rate of ribosome is given by "on rate" (1/s). The default setting is 1/1.1 (1/sec).
(ii) When a ribosome bind to the first codon, the ribosome takes 0.2 sec to start translation when the start codon is AUG. For pIV1, which has starting codon GUG, it takes 0.5 sec to start translation.
The clearance time depends on the first eleven codons. It is the sum of [1/(rate to move for each codon)] for the first eleven codons.

(Elongation):

Elongation occurs stochastically. A ribosome occupies 11 codons, and it proceeds with a rate given to each codons.
One can chose the rate for each kind of codons. The default setting is 35 [1/s] for A, 8 [1/s] for B, 4.5 [1/s] for C. The mRNA sequence gives which codon is A, B, or C. In the middle, the color shows the position of A codon by grey, B codon by yellow, and C codon by orange. The table of codon dependent speed is given below.

(Termination):

The termination can take long time. One can choose the average time for a ribosome to leave from the termination site in the box of "terminate"(sec). The default setting is 0.5 sec.

The simulation speed can be controlled by the scroll bar.

Graphs

On the right top, one can see spatiotemporal plot of ribosome traffic. The spatial axis along mRNA is in horizontal direction, and time axis in vertical direction, and ribosome is shown as a read dot. One can see the effect of queueing clearly.

In the bottom, one can see two types of graphs.

If "Occupied (%)" is chosen, the percentage of time that a codon at a given position is covered by a ribosome is shown.

If "X codons free (%)" is chosen, the percentage of time that the codon at a given position to the codon X codon ahead are free is shown. The value of the window width X can be changed in the box "window width (codons)".

Philosophy

We found a correlation between the ribosome spacing in an early coding region predicted by above simulation and the functional half-life of mRNA. Detailed information is found in Pedersen et al. (2010).

References:

Margit Pedersen, Soren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen, and Steen Pedersen, "The functional half-life of an mRNA depends on the ribosome spacing in an early coding region", in preperation, (2010).

Namiko Mitarai, Kim Sneepen, and Steen Pedersen, "Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization" J. Mol. Biol. 382, p.236 (2008)