Week 2 HW: DNA Design

Homework Record

0. Kernel Set-Up

1. Expression Target

🍬 What molecule are you expressing?

A trio of enzymes for a pathway to biosynthesize capsaicin (the TRPV1-activating molecule) from vanillin and a fatty acid precursor.

🍬 What is the sequence?

Pun1/AT3 (capsaicin synthase) GU300812.1, GenBank (NCBI), from Capsicum chinense (ghost pepper).
pAMT (aminotransferase) LC032106.1, GenBank (NCBI), from Capsicum chinense (cultivar habanero).
ACS1 (acyl-CoA synthetase) EU616571, GenBank (NCBI), from Capsicum annuum. Note: the exact ghost-pepper variant used in the original patent work differs from this by a single amino acid substitution (Ile476Val) — using the publicly available annuum sequence rather than pulling the patent-only variant.

🍬 Which host/chassis are you using?

The whole mechanism relies on the natural SCOBY growth, which involves strains of bacteria and yeast in symbiosis. Spicy SCOBY proposes Komagateibacter Rhaeticus strain P 1463 and S. cerevisiae, respectively. Since the yeast is easier to engineer than the bacteria, S. Cerevisiae is the organism which this project will be working with, while K. Rhaeticus is coming along for the ride, but mostly left alone to spin its cellulose as it is bound to do.

The strain selection for the bacterial agent in the SCOBY stems from prior experiments by Gilbert et al. (2021), in their syn-SCOBY investigations with S. Cerevisiae, which also informed the yeast tinkering in this project.

🍬 Where does the product go?

Cytoplasm: These are the same compartment the plant naturally makes them in, so no signal peptide or targeting sequence needed; it maintains default cytoplasmic expression.

2. Genetic Bits & Bobs

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3. Genes, assemble!

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4. Optimisation

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5. From Build to Design

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6. The Unknown

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AI Use

Claude AI was used to find specific relevant papers, patents and other supporting documents to enable the homework assignments. It was also used to explain concepts and clarify misunderstandings/mistakes by providing non-AI information and context. It did also assist with the use of the Asimov Kernel platform and markdown formatting.

References

Gilbert, C., Tang, T-C., Ott, W., Dorr, B.A., Shaw, W.M., Sun, G.L., Lu, T.K. and Ellis, T. (2021) ‘Living materials with programmable functionalities grown from engineered microbial co-cultures’, Nature Materials, 20, pp. 691–700. doi: 10.1038/s41563-020-00857-5.