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To incorporate the fluorescent amino acid at specific sites, we first had to choose the position and then use site directed mutagenesis to incorporate the amber stop codon at this position. For labeling issues, the fluorescent amino acid should not influence the protein folding or the activity. Furthermore, according to our expert Prof. Dr. Nedilijko Budisa, the yield of the protein could be influenced by the position the fluorescent amino acid is incorporated at. Therefore, we decided to try different positions at which the noncanonical amino acid is incorporated, all at permissive sites of the RuBisCo.<br> | To incorporate the fluorescent amino acid at specific sites, we first had to choose the position and then use site directed mutagenesis to incorporate the amber stop codon at this position. For labeling issues, the fluorescent amino acid should not influence the protein folding or the activity. Furthermore, according to our expert Prof. Dr. Nedilijko Budisa, the yield of the protein could be influenced by the position the fluorescent amino acid is incorporated at. Therefore, we decided to try different positions at which the noncanonical amino acid is incorporated, all at permissive sites of the RuBisCo.<br> | ||
The permissive sites were detected by the alignment with <a href=” http://www.ebi.ac.uk/Tools/msa/clustalo/”>Clustal Omega</a> of different analogical RuBisCo from <i>Thioalkalivibrio sulfidiphilus</i>, <i>Thioalkalivibrio denitrificans</i>,<i> Thiothrix nivea</i>, <i>Thermothiobacillus tepidarius</i>, <i>Acidobacillus caldus</i> and <i>Acidiferrobacter thiooxydans</i>. If amino acids at the same position are heterologous, the amino acid seems to be unimportant for the functioning and folding of the protein. These permissive sites of the enzyme are suitable for the incorporation of the noncanonical fluorescent amino acid. | The permissive sites were detected by the alignment with <a href=” http://www.ebi.ac.uk/Tools/msa/clustalo/”>Clustal Omega</a> of different analogical RuBisCo from <i>Thioalkalivibrio sulfidiphilus</i>, <i>Thioalkalivibrio denitrificans</i>,<i> Thiothrix nivea</i>, <i>Thermothiobacillus tepidarius</i>, <i>Acidobacillus caldus</i> and <i>Acidiferrobacter thiooxydans</i>. If amino acids at the same position are heterologous, the amino acid seems to be unimportant for the functioning and folding of the protein. These permissive sites of the enzyme are suitable for the incorporation of the noncanonical fluorescent amino acid. | ||
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<img class="figure image" src="https://2017.igem.org/File:T--Bielefeld-CeBiTec--SVI-Results-Labeling-Alignement.png"> | <img class="figure image" src="https://2017.igem.org/File:T--Bielefeld-CeBiTec--SVI-Results-Labeling-Alignement.png"> | ||
<p class="figure subtitle"><b>Figure 1:</b> Multiple amino acid sequence alignment of analogical small subunit RuBisCo variants from <i>Thioalkalivibrio sulfidiphilus</i>(WP_012639733.1), <i>Thioalkalivibrio denitrificans</i>(WP_058575622.1),<i> Thiothrix nivea</i>(WP_012823800.1), <i>Thermothiobacillus tepidarius</i>(WP_066099403), <i>Acidobacillus caldus</i>(WP_002708379.1) and <i>Acidiferrobacter thiooxydans</i>(WP_045467882.1).</p> | <p class="figure subtitle"><b>Figure 1:</b> Multiple amino acid sequence alignment of analogical small subunit RuBisCo variants from <i>Thioalkalivibrio sulfidiphilus</i>(WP_012639733.1), <i>Thioalkalivibrio denitrificans</i>(WP_058575622.1),<i> Thiothrix nivea</i>(WP_012823800.1), <i>Thermothiobacillus tepidarius</i>(WP_066099403), <i>Acidobacillus caldus</i>(WP_002708379.1) and <i>Acidiferrobacter thiooxydans</i>(WP_045467882.1).</p> |
Revision as of 13:22, 11 October 2017
Labeling
Short summary
To demonstrate the advantages of this tool, we want to colocalize the ribulose 1,5‑bisphosphat carboxylase oxygenase (RuBisCo) from Halobacillus neaplitanus and the carboxysome in E. coli cells. The carboxysome is labeled with the green fluorescent protein (GFP) and the RuBisCo should be labeled with the fluorescent amino acid at different positions and with the red fluorescent protein (RFP) to compare the advantages and disadvantages of both labeling strategies.
Evolved Tyrosine tRNA/aminoacyl-synthetase (TyrRS) for the incorporation of 7-hydroxy-L-coumaryl-ethylglycin (CouAA)
To test whether the synthetase really incorporates CouAA, we transformed the synthetase in pSB3C5 and our composite part BBa_ K2201331 as test protein in E. coli BL21 DE3. The part K2201231 contains the CDS for the protein Sup35 with an amber stop codon at position 21 under control of a T7-promoter. If the synthetase works, it will incorporate CouAA in response to the amber codon at position 21. However, we expressed the test protein, which contains a histidine tag, and purified it through NiNTA chromatography. The purified proteins were digested with trypsin and analyzed through MALDI TOF/TOF.
Construction of RuBisCo mutants containing the amber stop codon
The permissive sites were detected by the alignment with Clustal Omega of different analogical RuBisCo from Thioalkalivibrio sulfidiphilus, Thioalkalivibrio denitrificans, Thiothrix nivea, Thermothiobacillus tepidarius, Acidobacillus caldus and Acidiferrobacter thiooxydans. If amino acids at the same position are heterologous, the amino acid seems to be unimportant for the functioning and folding of the protein. These permissive sites of the enzyme are suitable for the incorporation of the noncanonical fluorescent amino acid.
Figure 1: Multiple amino acid sequence alignment of analogical small subunit RuBisCo variants from Thioalkalivibrio sulfidiphilus(WP_012639733.1), Thioalkalivibrio denitrificans(WP_058575622.1), Thiothrix nivea(WP_012823800.1), Thermothiobacillus tepidarius(WP_066099403), Acidobacillus caldus(WP_002708379.1) and Acidiferrobacter thiooxydans(WP_045467882.1).
Due to the alignment, we decided to incorporate the fluorescent amino acid at position 2 and position 111 of the small subunit, and at position 474 of the large subunit. In addition, we decided to try different combinations of this positions to find out if this intensifies the fluorescence signal. Thus,we constructed the following seven RuBisCo mutants: