Difference between revisions of "Part:BBa K4260007"

 
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<strong><font size=5>Isoeugenol monooxygenase, normal coding sequence: Promoter +RBS+pelB+Iso+rrnB T1 terminator
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<br><strong>Type:</strong>Coding sequence</br>
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<br><strong>Designed by:</strong>Claudia Angélica García Alonso</br>
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<br><strong>Group:</strong>iGEM_TecCEM</br>
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<br></br>
  
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BBa_K4260006 is a composite part that aims to work as a selection marker for the replacement of antibiotic-based selection markers. Isoeugenol monooxygenase (coded by gene Iso) is an enzyme present in Pseudomonas bacteria, that converts isoeugenol to vanillin directly.  
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It is well known that antibiotics are necessary in synthetic biology experimental procedures. Therefore iGEM TecCEM created BBa_K4260007 a sequence designed for the replacement of tradicional selection markers, antibiotics; being our main focus the most commonly used microorganism Escherichia coli; in order to prevent more serious problems in the future due to antibiotic-resistant microorganisms. The sequence encodes the gene of Isoeugenol Monooxygenase (IsoMo), that allows bacteria to direct the enzyme to the periplasm with pelB signal sequence. With IsoMo we aim to confer bacteria the ability to resist isoeugenol, an inhibitory agent added to culture mediums.  
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Isoeugenol is an aromatic compound found in clover and cinnamon essential oils, that has proved to have an inhibitory effect on different microorganisms; however, this genetic construct was designed for its expression in Escherichia coli. Its antimicrobial activity resides in altering the integrity of the inner membrane of the bacteria, leading to fluid spillage and cell death. Therefore, by directing the enzyme to the periplasm of the bacteria, only transformed cells could survive when exposed to isoeugenol.
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Isoeugenol acts on the inner membrane of bacteria, making it lose its integrity and causing the cell to spill out.
  
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<img style="vertical-align: bottom;)" width=90% src="https://static.igem.org/mediawiki/parts/2/2e/Nc_22_07.png">
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<center><strong>Fig. 1 </strong> Designed scheme of the composite part.</center>
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<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
  
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<H3>Design</H3>
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<span class='h3bb'>Sequence and Features</span>
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<p align = "justify">In this composite part there can be found a modified gene, by codon optimization, from Pseudomonas putida IE27, reported by Yamada, Okada, Yoshida & Nagasawa in 2008 [1], Isoeugenol monooxygenase (IsoMo), that makes able to metabolize this compound, which allows a one-step conversion of it into vanillin, as well as pelB and an RBS, using a registered part from iGEM_TecCEM <a href=""https://parts.igem.org/Part:BBa_K4260011">(BBa_K4260011</a>) [2]. Within this part there is also a constitutive promoter for ensuring the transcription of genes despite any other conditions, for this aim we use <a href=""https://parts.igem.org/Part:BBa_J23100">(BBa_J23100</a>) [3], as it has been reported this promoter has been characterized as one of the most efficient constitutive promoters. For the terminator another registered part was used rrnB <a href=""https://parts.igem.org/Part:BBa_B0010">(BBa_B0010</a>). [4]
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<partinfo>BBa_K4260007 SequenceAndFeatures</partinfo>
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===Functional Parameters===
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<H3>Characterization</H3>
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<partinfo>BBa_K4260007 parameters</partinfo>
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<br></br>
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<H3>Usage and biology</H3>
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<td valign="top"><img style="vertical-align: top;)"  width="300" height="300"  src="https://static.igem.org/mediawiki/parts/b/be/Electrophoresis_Nc_22.png"></td>
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<td><p align = "justify">In particular this sequence was inserted in 2 E coli strains, DH5 and BL21, for the ligatión pJET was used, as we were aiming to characterize our IsoMo enzyme, all transformed cells were grown in LB media with Ampicillin to ensure that all the bacteria will inherit the vector. For analyzing that the transformation of Nc_22 in those strains was successful we performed a series of experiments; first of all a plasmid purificatión was performed and with the help of an electrophoresis gel we proved that the plasmid was there.
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<td><center><strong>Fig. 3 </strong>3D model of Isoeugenol Monooxygenase, Iso.
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<p align = "justify">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.</p>
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<br><center><img style="vertical-align: top;)"  width="300" height="200" src="https://static.igem.org/mediawiki/parts/5/59/Docking_monox_isoeugenol.png"></center></br>
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<center><strong>Fig. 4 </strong>Results of molecular docking, performed with AutodockVina.</center>
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<br><center>A bond of 2.399 Å is formed between isoeugenol and Met350.</center></br>
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<H4><em>Application</em></H4>
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<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>
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<H4><em>Biosafety</em></H4>
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<p align = "justify">Although this coding sequence comes from a Pseudomona bacteria,  it is not associated with the pathogenicity of the microorganism itself. </p>
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<hr>
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<H3>References</H3>
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<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>
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<p align = "justify">[2] <a href="https://parts.igem.org/Part:BBa_B0030">https://parts.igem.org/Part:BBa_B0030</a></p>
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<p align = "justify">[3] <a href=" https://parts.igem.org/Part:BBa_J32015 "> https://parts.igem.org/Part:BBa_J32015 </a></p>
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Revision as of 00:42, 11 October 2022


Isoeugenol monooxygenase, normal coding sequence: Promoter +RBS+pelB+Iso+rrnB T1 terminator


Type:Coding sequence

Designed by:Claudia Angélica García Alonso

Group:iGEM_TecCEM


It is well known that antibiotics are necessary in synthetic biology experimental procedures. Therefore iGEM TecCEM created BBa_K4260007 a sequence designed for the replacement of tradicional selection markers, antibiotics; being our main focus the most commonly used microorganism Escherichia coli; in order to prevent more serious problems in the future due to antibiotic-resistant microorganisms. The sequence encodes the gene of Isoeugenol Monooxygenase (IsoMo), that allows bacteria to direct the enzyme to the periplasm with pelB signal sequence. With IsoMo we aim to confer bacteria the ability to resist isoeugenol, an inhibitory agent added to culture mediums. Isoeugenol acts on the inner membrane of bacteria, making it lose its integrity and causing the cell to spill out.


Fig. 1 Designed scheme of the composite part.

Design

In this composite part there can be found a modified gene, by codon optimization, from Pseudomonas putida IE27, reported by Yamada, Okada, Yoshida & Nagasawa in 2008 [1], Isoeugenol monooxygenase (IsoMo), that makes able to metabolize this compound, which allows a one-step conversion of it into vanillin, as well as pelB and an RBS, using a registered part from iGEM_TecCEM (BBa_K4260011) [2]. Within this part there is also a constitutive promoter for ensuring the transcription of genes despite any other conditions, for this aim we use (BBa_J23100) [3], as it has been reported this promoter has been characterized as one of the most efficient constitutive promoters. For the terminator another registered part was used rrnB (BBa_B0010). [4]

Characterization



Usage and biology

In particular this sequence was inserted in 2 E coli strains, DH5 and BL21, for the ligatión pJET was used, as we were aiming to characterize our IsoMo enzyme, all transformed cells were grown in LB media with Ampicillin to ensure that all the bacteria will inherit the vector. For analyzing that the transformation of Nc_22 in those strains was successful we performed a series of experiments; first of all a plasmid purificatión was performed and with the help of an electrophoresis gel we proved that the plasmid was there.

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