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Model

First, we extract the fermentation test data of the engineered strain CSY1297 from the Nature article.

Use computer modeling to get the simple linear regression shown in the figure 1.

Figure1.

Because we use low-density cell (LDC) fermentation in the laboratory, the obtained OD600 range is between 0 and 2, while the model OD600 range is between 21 and 27. There is a huge difference between the two and it is not suitable for predicting the fermentation performance of our strains.

Then we extracted fermentation test data from the Nature Communications article. The engineered bacterial strain constructed in this article is genetically the closest to our bacteria, and the article uses the same LDC fermentation as ours. Data are as follows:

Use computer modeling to get the simple linear regression shown in the figure2.

Figure 2

The fit between the linear model and the data is low. After optimizing the parameters of the equation, we get the modified simple linear regression shown in the figure 3.

Figure 3.

The fit between modified simple linear model and the data is still low, so we get the polynomial use to get the following model (figure 4).

Figure 4.

After furthering the possible parameters, we get the modified polynomial linear regression shown in figure 5.

Figure 5.

Continue to optimize, we get the polynomial linear regression-2 shown in figure 6.

Figure 6.

The R-squared reaches 0.9855, which can be used to predict the performance of our engineered bacteria to produce tropine. Substituting the time and the OD600 value we tested in the laboratory into the model to get figures 7.

Figure 7.

The results show that when the OD600 of our engineered bacteria reaches a certain value, the output of tropine will increase sharply, indicating that our engineered bacteria have great industrial application prospects.

Reference

1. Prashanth Srinivasan & Christina D. Smolke. Biosynthesis of medicinal tropane alkaloids in yeast.Nature | Vol 585 | 24 September 2020 | 614-619
2. Prashanth Srinivasan & Christina D. Smolke. Engineering a microbial biosynthesis platform for de novo production of tropane alkaloids.NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-11588-w

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