Fig 1.
Schematic representation of the population dynamics model.
Diagrammatical representation of the best fitting model determined in [44]. The reproduction of cells is controlled by the abundance of nutrients N, and the sporulation is regulated by the concentration of a quorum-sensing signal S.
Fig 2.
Comparison of population dynamics and bont gene expression for C. botulinum type A1 cultures.
Data from the experimental results published in [26], [21], [22] and [23] for C. botulinum type A1 strains ATCC3502, Hall A-hyper, Hall A and Hall A respectively. Notice that toxin loci of these three strains are genetically identical with each other [9]. Comparison of the time courses measured in optical densities for the cultures (left) and the comparison of the bont gene expression time courses (right). Data normalized to the maximum OD (left) and maximum expression level (right) of the single original time course.
Fig 3.
Diagrammatic representation of the computational gene expression sub-model.
(Top Left) show the role of the BotR sigma factor, and of the three TCSs reported to regulate positively toxigenesis in C. botulinum Group I type A1 strain, along with the negative TCS regulator. (Top Right) our hypothesis of how the availability of nutrients (species N) regulates directly and indirectly (via CodY) toxin production, and how the quorum sensing signal (species S) together with the two positive TCS regulators, recognise the quorum-sensing pathway whose effect on toxin production was experimentally observed in the work of Cooksely and colleagues [28]. (Lower), the dashed arrows represent regulation mechanisms, whereas solid lines model mass transfer reactions. The species N (Nutrients) and S (quorum-sensing signal) are shared with the population sub-model. The state of each bacterial cell is assumed to be the same. Species CBO_0786, CBO_0787 (and their phospho forms), BotR and BoNT are subject to degradation (reactions not graphically depicted).
Fig 4.
States of the CBO0787/CBO0786, BotR and BoNT promoters.
The synthesis of the negative regulatory TCS, of the alternative sigma factor BotR and the BoNT protein are regulated by inhibitory and activator species. (A) shows the two possible states of prCBOi, the promoter for the polycistronic transcription of proteins CBO0787/CBO0786; (B) illustrates the three possible active states of prBR, the promoter of BotR; (C) details the possible states of the ntnh-bont operon promoter prBA: inactive, when not bound, inhibited by CodY1 and/or phosphorylated CBO_0786 inhibits transcription, and activated, by BotR and subsequently by phosphorylated CBO_RR and/or phosphorylated CBO_0607 for increasing levels of activation.
Fig 5.
Comparison of experimental data (from [59]) and model predicted results for WT.
(A) shows the population dynamics, where data measurements are in CFU/ml over time, while (B) illustrates the amount of toxin in the supernatant. In both plots, experimental data points are drawn as circles, while model predicted data are shown as continuous lines.
Table 1.
Experimental data from Zhang et al., 2013 [31].
Data for bont gene expression and supernatant toxin concentration of C. botulinum ATCC 3502 (wt) and cbo0786 mutant (mut), measured at mid-exponential (ME), late-exponential (LE) and early-stationary (ES) phases.
Fig 6.
Comparison of experimental and model predictions for concentration of toxin in the supernatant for wild-type and the cbo0786 mutant studied in [31].
(A): normalized concentration of toxin in the supernatant for C. botulinum ATCC 3502 (wt) and the cbo0786 mutant (mut) as reported in [31] (B): model prediction for toxin concentration in the supernatant (normalized) for wt and for the C786_M mutant (mut).
Table 2.
Experimental data from Zhang et al., 2014, [29].
Data for the supernatant toxin concentration of C. botulinum ATCC 3502 (wt) and codY mutant (mut), measured in μg/ml at various time points during the culture growth.
Fig 7.
Comparison of experimental results and model predictions for concentration of toxin in the supernatant for the wild-type and the codY mutant studied in [29].
(A): normalized observed concentration of toxin in the supernatant for C. botulinum ATCC 3502 (wt) and the codY mutant (mut), as reported in [29]. (B): model prediction for toxin concentration in the supernatant (normalized) for wt and for the CODY_M mutant (mut).
Table 3.
Experimental data from Connan et. al [30].
Data for supernatant toxin concentration of C. botulinum type A Hall (wt) and the mutants Hall/707 (CRR_M) and Hall/1146 (C607_M), measured during the Exponential growth phase (time 8 hours), the early stationary phase (time 12 hours) and the stationary phase (time 24 hours).
Fig 8.
Comparison of experimental results and model predictions for the concentration of toxin in the supernatant for the wild-type (wt) and two mutants studied in [30].
(A), experimentally measured amounts of toxin concentration in the supernatant, normalized by the maximal measured concentration (for wt, in the stationary phase) and reported on a log scale. (B), predicted toxin concentrations from our wt, CRR_M and C607_M mutant models, normalized by the maximal predicted concentration (for wt, in the stationary phase), log scale on the vertical axis.
Fig 9.
Comparison of predicted levels of toxin supernatant concentration, as obtained from the models of WT (continuous line) and of the double mutant strain CODY_M+C786_M (dashed line).
Our model produces a testable prediction for the phenotype of this mutant, which should be similar to WT as far as toxigenesis is concerned.