Estimating the amount of AiiA per cell
AiiA is under the control of the lac promoter. The transcription and mRNA degradation rates help us estimate the amount of mRNA present on the cell.
“The half-life of protein A is assumed to be around 10 minutes which is similar to what is used in Elowitz’s repressilator model [1]. Furthermore, we assume that a more aggressive degradation tail can enable half-times on the order of two minutes for protein B.”
Modeling the Lux/AiiA Relaxation Oscillator
Christopher Batten
In the paper AiiA is called protein B. Therefore the degradation rate for AiiA with an aggressive degradation tail is 0.0058 s-1. This would give us a lower limit.
“Transcription initiation rate, km
Malan et al. (1984) measured the transcription initiation rate at P1 and report the following value: km ≈ 0.18min-1
mRNA degradation rate, jM
Kennell and Riezman (1977), measured a lacZ mRNA half-life of 1.5 min: ξM = 0.46min-1
lacZ mRNA translation initiation rate, кB
From Kennell and Riezman (1977), translation starts every 3.2 s at the lacZ mRNA. This leads to the following translation initiation rate: кB ≈ 18.8min-1”
Santillán M. and Mackey M. C. (2004). Influence of Catabolite Repression and Inducer Exclusion on the Bistable Behavior of the lac Operon. Biophys J 86:1282–1292
We modified both transcription initiation and translation rates by multiplying both rates by 4. This due to the fact that LuxR is a four times smaller than LacZ:
LacZ has a length of 1024 aa
LuxR has a length of 250 aa
Simulating with simbiology, AiiA reaches stationary state at almost 3500 molecules per cell.
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