Difference between revisions of "Part:BBa K2516003"

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Membrane-bound SuperNova (for C. reinhardtii)

This is a membrane-bound version of SuperNova protein, originally introduced by iGEM 2014 Carnegie Mellon team. Link: BBa_K1491017

SuperNova is a photosensitizing protein, which produces Reaction Oxygen Species (superoxide and singlet oxygen) under irradiation of 500-600nm wavelength light. It is a monomeric version of another photosensitizing protein called KillerRed. There are several advantages over KillerRed, SuperNova does not oligomerize inside the cell and does not interfere with mitotic cell division. This advantage allows performing targeted protein inactivation inside the cell by fusion to the target protein without loss of target protein function. [1]

The second application that seems very simple and powerful is light controlled safety system. SuperNova can be utilized as a killer switch for genetically modified organisms. Under irradiation of 500-600nm wavelength light, SuperNova will generate ROS and kill the cell. Its phototoxicity was proven in bacterial and mammalian cells. [1]

In case of KillerRed, it was proven that membrane-bound version is more toxic and kills the cell more rapidly. [2]

[Improvement]

Codon optimized for C. reinhardtii.

SuperNova protein was made membrane-bound by adding 4 sequences:

1) Signal peptide from Peptidyl serine alpha-galactosyltransferase gene (SGT1) (1-26 aa) [3].

It correctly predicted by SignalP 4.1 server [4] (predicts signal peptides) (Figure 1):

S score – probability of signal peptide Y score – probability of signal peptidase site C score – combined S and Y scores

2) (GGGGS)2 flexible linker (27-36 aa).

3) Transmembrane domain and C-terminus from SGT1 protein (37-74 aa). [3]

C-terminus was also added because it gave an optimal level of confidence in the presence of transmembrane domain both by TMHMM serve 2.0 and Philius transmembrane prediction server.

Transmembrane domain and signal peptide were correctly predicted by TMHMM server v2.0 (predicts transmembrane domains) [5](Figure 2):

4) (EAAAK)2 rigid linker (75-84 aa).

Total signal peptide, transmembrane domain and linkers were predicted by TMHMM server v2.0 and Philius transmembrane prediction server [6] with high confidence values: Type confidence = 0.91 and topology confidence = 0.93 (Figure 3):

Reference list:

1. Takemoto, K., Matsuda, T., Sakai, N., Fu, D., Noda, M., Uchiyama, S., ... & Ayabe, T. (2013). SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation. Scientific reports, 3, 2629.

2. Bulina, M. E., Lukyanov, K. A., Britanova, O. V., Onichtchouk, D., Lukyanov, S., & Chudakov, D. M. (2006). Chromophore-assisted light inactivation (CALI) using the phototoxic fluorescent protein KillerRed. Nature protocols, 1(2), 947-953.

3. The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017). http://www.uniprot.org/uniprot/H3JU05

4. Nielsen, H. (2017). Predicting Secretory Proteins with SignalP. Protein Function Prediction: Methods and Protocols, 59-73.

5. Krogh, A., Larsson, B., Von Heijne, G., & Sonnhammer, E. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of molecular biology, 305(3), 567-580.

6. Reynolds, S. M., Käll, L., Riffle, M. E., Bilmes, J. A., & Noble, W. S. (2008). Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS computational biology, 4(11), e1000213.

Sequence and Features