Part:BBa_K3955102:Design
DB3DB3 peptide fused with amyL signal peptide
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
In order for DB3DB3 to be successfully secreted extracellularly, it needed to be distinguishable from SLPmod by being larger than it was. We therefore repeated the sequence 3 times and introduced cleavege sites for pancreatic elastase in between the repeats, by adding an alanine. Pancreatic elastase was chosen as a peptidase since it naturally occurs in the colon, which would be the target organ of our potential future implementation.
Codons were chosen manually to reduce the sequence repeats in the nucleotide sequence but still mainly use the most common codons for L. reuteri, our intended chassi.
Source
Peptide sequence: Klein A, Ziehm T, Tusche M, Buitenhuis J, Bartnik D, Boeddrich A et al. Optimization of the All-D Peptide D3 for Aβ Oligomer Elimination. PLOS ONE. 2016;11(4):e0153035.
Secretion signal peptide sequence:
Wu C, Chung T. Green fluorescent protein is a reliable reporter for screening signal peptides functional in Lactobacillus reuteri. Journal of Microbiological Methods. 2006;67(1):181-186.
References
1. Klein A, Ziehm T, Tusche M, Buitenhuis J, Bartnik D, Boeddrich A et al. Optimization of the All-D Peptide D3 for Aβ Oligomer Elimination. PLOS ONE. 2016;11(4):e0153035.
2. Perov S, Lidor O, Salinas N, Golan N, Tayeb- Fligelman E, Deshmukh M et al. Structural Insights into Curli CsgA Cross-β Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents. PLOS Pathogens. 2019;15(8):e1007978.
3. YUUKT T, NOMURA T, TEZUKA H, TSUBOI A, YAMAGATA H, TSUKAGOSHI N et al. Complete Nucleotide Sequence of a Gene Coding for Heat- and pH-Stable α-Amylase of Bacillus licheniformis: Comparison of the Amino Acid Sequences of Three Bacterial Liquefying α-Amylases Deduced from the DNA Sequences1. The Journal of Biochemistry. 1985;98(5):1147-1156.
4. Wu C, Chung T. Green fluorescent protein is a reliable reporter for screening signal peptides functional in Lactobacillus reuteri. Journal of Microbiological Methods. 2006;67(1):181-186.