Difference between revisions of "Part:BBa K4260011"

Revision as of 20:28, 10 October 2022

Coding sequence for Isoeugenol Monooxygenase: RBS, signal peptide pelB and Iso

Type:Coding sequence

Designed by:Claudia Angélica García Alonso

Group:iGEM_TecCEM

Fig. 1 Design scheme of the coding sequence.

Design

These part contains the coding sequence of Isoeugenol monooxygenase (IsoMo), reported by Yamada, Okada, Yoshida & Nagasawa [1] (gene Iso), and has an approximate size of 54 kDa; these enzyme comes from Pseudomonas putida IE27. This par also has as an RBS for stimulate de translation of the IsoMo enzyme, using an existing part (BBa_B0030)[2], as well as a signal peptide called pelB, because of its codon optimization for Escherichia coli , as it was decided that the IsoMo enzyme would be directed to the periplasm for the application we needed (for more information check out BBa_K4260007), these was also taken for an existing part (BBa_J32015). [3]

Usage and biology

Isougenol monooxygenase’s tertiary structure model of gene Iso did not exist, therefore it was obtained with I-TASSER, allowing to observe that it is composed mainly of β sheets.

IsoMo is responsible for the direct conversion of isoeugenol to vanillin, requiring only oxygen for the reaction, which can be very convenient when trying to carry this reaction in a prokaryotic cell. It commonly occurs that, when trying to have a prokaryote express too many genes, it gets stressed and does not express them.

The model shown in Figure 3 was useful for the performance of molecular docking, in order to observe its behavior when put in contact with its substrate isoeugenol. The molecular docking was not a blind-type because previously reported residues of the active site were used as reference: H176, H218, H282, H471, E135, E349 & E413 [3]. The final binding score (ΔG°) was of -6.4 and a possible hydrogen bond was shown in methionine 350 (Figure 4).

Fig. 3 3D model of Isoeugenol Monooxygenase, Iso.

This helped confirm the affinity of the enzyme for its substrate, as well as the interaction between the two molecules. After observing these results, it was determined that Iso coding sequence was a good option for the expression of isoeugenol monooxygenase.

Fig. 4 Results of molecular docking, performed with AutodockVina.
A bond of 2.399 Å is formed between isoeugenol and Met350.

Application

For more information about the enzyme and its possible application as a selection marker, please check out BBa:K4260007.BBa:K4260006.

Biosafety

Although this coding sequence comes from a Pseudomona bacteria, it is not associated with the pathogenicity of the microorganism itself.

References

[1] Yamada, M., Okada, Y., Yoshida, T., & Nagasawa, T. (2008). Vanillin production using Escherichia coli cells over-expressing isoeugenol monooxygenase of Pseudomonas putida. Biotechnology letters, 30(4), 665-670.

[2] https://parts.igem.org/Part:BBa_B0030

[3] https://parts.igem.org/Part:BBa_J32015

@@ Line 11: / Line 11: @@
 <center>
 <img style="vertical-align: bottom;)" width=90% src="https://static.igem.org/mediawiki/parts/c/c5/Nc_22_11.png">
+</center>
 </br>
 <center><strong>Fig. 1 </strong> Design scheme of the coding sequence.</center>
 </br>
-</html>
-<p align="justify"><H3>Design</H3></p>
+<H3>Design</H3>
 <p align = "justify">These part contains the coding sequence of Isoeugenol monooxygenase (IsoMo), reported by Yamada, Okada, Yoshida & Nagasawa [1] (gene Iso), and has an approximate size of 54 kDa; these enzyme comes from <em>Pseudomonas putida</em> IE27. This par also has as an RBS for stimulate de translation of the IsoMo enzyme, using an existing part <a href=""https://parts.igem.org/Part:BBa_B0030">(BBa_B0030</a>)[2], as well as a signal peptide called pelB, because of its codon optimization for Escherichia coli , as it was decided that the IsoMo enzyme would be directed to the periplasm for the application we needed (for more information check out BBa_K4260007), these was also taken for an existing part  <a href=""https://parts.igem.org/Part:BBa_J32015">(BBa_J32015</a>). [3]
 <br></br>
-<H3>Sources, usage and biology</H3>
+<H3>Usage and biology</H3>
-<H4><em>IemR: Transcriptional activator</em></H4>
-<br></br>
-<p align = "justify">The transcriptional activator is coded by gene IemR, from <em>Pseudomonas nitroreducens </em>Jin1,  (951 bp long) and has a size of about 34.6 kDa. It is specific for the transcription of the Isoeugenol Monooxygenase gene Iem [3]; however, it was decided to employ gene Iso and not IemR because unlike Iem the first one does not lead to the formation of undesired co-products of the reaction like acetaldehyde or vanillic acid [1].
-</p>
-<center><img style="vertical-align: top;)" width=90% src="https://static.igem.org/mediawiki/parts/f/f1/ActivadorTransc_IemR.png"></center>
-<center><strong>Fig. 2 </strong>3D model of IemR, transcriptional activator of Iso.</center>
-<br></br>
-<H4><em>Promoter region</em></H4>
-<p align = "justify">The promoter region and the transcriptional activator were evaluated by Ryu, Seo, Park, Ahn, Chong, Sadowsky & Hur (2013) [4] as the transcription regulation system for IsoMo. Eugenol and isoeugenol were evaluated as inducers of the transcription of IemR and hence, the expression of Iem. They concluded that isoeugenol was the better activator, and that by inducing the transcription of Iem, and its traduction, more production of isoeugenol monooxygenase was observed in the bacteria. </p>
-<H4><em>Promoter region</em></H4>
 <table>
@@ Line 55: / Line 43: @@
 <H4><em>Application</em></H4>
-<p align = "justify">In order to know more information about the enzyme and a possible application as a selection marker, please check out <a href="https://parts.igem.org/Part:BBa_K4260006">BBa:K4260006.</a></p>
+<p align = "justify">For more information about the enzyme and its possible application as a selection marker, please check out BBa:K4260007.<a href="https://parts.igem.org/Part:BBa_K4260006">BBa:K4260006.</a></p>
 <H4><em>Biosafety</em></H4>
-<p align = "justify">In spite of the two coded proteins being from Pseudomonas bacteria, no hazards were dealt with, because none of them are associated with the pathogenicity of these microorganisms. </p>
+<p align = "justify">Although this coding sequence comes from a Pseudomona bacteria,  it is not associated with the pathogenicity of the microorganism itself. </p>
 <hr>
 <H3>References</H3>
 <p align = "justify">[1] Yamada, M., Okada, Y., Yoshida, T., & Nagasawa, T. (2008). Vanillin production using Escherichia coli cells over-expressing isoeugenol monooxygenase of Pseudomonas putida. Biotechnology letters, 30(4), 665-670.</p>
+<p align = "justify">[2] <a href="https://parts.igem.org/Part:BBa_B0030">https://parts.igem.org/Part:BBa_B0030</a></p>
-<p align = "justify">[2] <a href="https://parts.igem.org/Part:BBa_J32015">https://parts.igem.org/Part:BBa_J32015</a></p>
+<p align = "justify">[3] <a href=" https://parts.igem.org/Part:BBa_J32015 "> https://parts.igem.org/Part:BBa_J32015 </a></p>
-<p align = "justify">[3] Ryu, J. Y., Seo, J., Park, S., Ahn, J. H., Chong, Y., Sadowsky, M. J., & Hur, H. G. (2013). Characterization of an isoeugenol monooxygenase (Iem) from Pseudomonas nitroreducens Jin1 that transforms isoeugenol to vanillin. Bioscience, biotechnology, and biochemistry, 120715.</p>
-<p align = "justify">[4] Ryu, J. Y., Seo, J., Ahn, J. H., Sadowsky, M. J., & Hur, H. G. (2012). Transcriptional control of the isoeugenol monooxygenase of Pseudomonas nitroreducens Jin1 in Escherichia coli. Bioscience, biotechnology, and biochemistry, 76(10), 1891-1896.
-</p>
 </html>
-[[File:Nc 22 11.png|300px|thumb|right|<i><b>Fig.1:</b>RecA intein mediated biosensor behavior in the presence endocrine disrupting chemicals (EDCs).</i>]]