The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics
Fig 3
The effective dephosphorylation rate is the main determinant of which behaviour is produced.
(A,B) The magnitude of the single pulse response (A) and stochastic pulsing (B) behaviours across kP-pstress-space. The regions where either behaviour occurs are similar to that of the kP ⋅ pstress = C curve (show for various values, green dashed lines). (C,D) Parameter substitutions generate a parameter pprod = pstress ⋅ kP, to which both behaviours are sensitive, and a parameter pfrac = pstress/kP, to which both behaviours are insensitive. While the regions corresponding to either behaviour are adjacent, they do not overlap. The stochastic pulsing behaviour exists for slightly larger values of pprod, as compared to the single response pulse behaviour. (E,F) For 4096 different parameter sets, we characterise both behaviours’ sensitivity to change (, E, and
, F) in the parameters pprod, pfrac, kB5, and kD5 (Section 4.5.4). We do this by evaluating
and
for the four different parameters across all 4096 parameter sets. We then put each set of 4096 evaluations in ascending order and plot them in E and F. For a few parameter sets, the behaviours show some sensitivity to kB5. However, pprod has the far largest effect on either behaviour. In both cases, changes to pfrac and kD5 have little effect on the system. Hence, these lines coincide (both following the x-axis closely). Parameter values and other details on simulation conditions for this figure are described in S2 and S5 Tables.