Difference between revisions of "Part:BBa K2599003"
 
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<div style="width:40%; padding-left: 20%;"><p style="padding-top: 10px; font-size: 10px; text-align: center;"><b>Figure 1.</b> Basic part of Enterocin B</p></div>
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<div style="width:40%; padding-left: 30%;"><p style="padding-top: 10px; font-size: 10px; text-align: center;"><b>Figure 1.</b> Basic part of Enterocin B</p></div>
  
  
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The bacteriocins inhibit their target organisms through pore formation. Though the mechanism of each inhibition is vary from species to species, the general process is conserved. To see more details, please search for our project page.
 
The bacteriocins inhibit their target organisms through pore formation. Though the mechanism of each inhibition is vary from species to species, the general process is conserved. To see more details, please search for our project page.
  
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Enterocin A and enterocin B have very similar inhibitory spectra. It interact with anionic lipids that are abundantly present in the membranes of Gram-positive bacteria. And according to the reference, enterocin B is inhibitory to some strains that are not sensitive to enterocin A. Furthermore, enterocin B is able to kill the bacteria that survive from the enterocin A treatment.
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Since enterocin B belongs to class II bacteriocin, it is a small and heat stable peptide with a narrow spectrum of activity. Also, Enterocin A and enterocin B have very similar inhibitory spectra. They both interact with anionic lipids that are abundantly present in the membranes of Gram-positive bacteria. And according to the reference, enterocin B is inhibitory to some strains that are not sensitive to enterocin A. Furthermore, enterocin B is able to kill the bacteria that survive from the enterocin A treatment.
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<div style="width:40%; padding-left: 30%;"><p style="padding-top: 20px; font-size: 10px; text-align: center;"><b>Figure 2.</b> Mechanism of bacteriocin</p></div>
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Enterocin B is a short peptide that will degrade in a short time. After degradation, this antibacterial peptide is harmless to our environment.
 
Enterocin B is a short peptide that will degrade in a short time. After degradation, this antibacterial peptide is harmless to our environment.
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<p style="padding-top:10px;font-size:20px;"><b>Peptide Prediction</b></p>
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NCTU_Formosa 2017 had compeleted a [http://2017.igem.org/Team:NCTU_Formosa/Model peptide prediction model] that can predict
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peptide for new function. In this model, they used scoring card method (SCM) for machine learning. This year, NCTU_Formosa 2018 continued to use the same method for predicting antimicrobial peptide, in order to seek more candidates for our project.
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Enterocin B is one of the existing peptides that we predicted to show the function of antimicrobial activity. The score of our prediction is 464.36.
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{{#tag:html|<img style="width: 70%; padding-left: 15%;" src="https://static.igem.org/mediawiki/2018/2/2f/T--NCTU_Formosa--B_card.png" alt="" />}}
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<div style="width:40%; padding-left: 30%;"><p style="padding-top: 10px; font-size: 10px; text-align: center;"><b>Figure 3.</b> The prediction result of Enterocin B.</p></div>
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===Cloning===
 
===Cloning===
  
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We conbined our toxic gene to pSB1C3 backbone and conducted PCR to check the size of our part. The enterocin B sequence length is around 210 b.p.
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We conbined our toxic gene to pSB1C3 backbone and conducted PCR to check the size of our part. The Enterocin B sequence length is around 210 b.p. and the length of PCR product should be around 260 b.p.
  
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{{#tag:html|<img style="width: 20%; padding-left: 40%;" src="https://static.igem.org/mediawiki/2018/3/37/T--NCTU_Formosa--B_basic.png" alt="" />}}
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<div style="width:40%; padding-left: 30%;"><p style="padding-top: 10px; font-size: 10px; text-align: center;"><b>Figure 4.</b> Agarose gel electrophoretic pattern of Taq PCR product.</p></div>
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More experiment results of Enterocin B, please look for the composite part [https://parts.igem.org/Part:BBa_K2599011 BBa_K2599011]
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<p style="padding-top:10px;font-size:20px;"><b>Safety</b></p>
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In the future, we are going to spray our bio-stimulator into the environment. To make sure whether the bacteria contain anti-microbial peptide will not exist in the final product, we design the processing standards in the laboratory.
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Bacteriocins are usually heat stable, we use high-temperature sterilization to double make sure our peptide solution does not contain any living E. coli. However, peptides may degrades after long time sterilization. To find out the best fitted time for sterilization, we boiled our bacteriocins for 0, 15, 30, and 45 minutes, and put them on LB Agar plate and cultured it at 37℃ for 16 hours.
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From the result of the plate, we can easily observe that bacteria exists only in the sample that is not boiled. After fifteen minutes of sterilization, there are no alive bacterias exist.
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{{#tag:html|<img style="width: 30%; padding-left: 35%;" src="https://static.igem.org/mediawiki/2018/9/9e/T--NCTU_Formosa--B_safety_plate.png" alt="" />}}
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<div style="width:70%; padding-left: 15%;"><p style="padding-top: 10px; font-size: 10px; text-align: center;"><b>Figure 5.</b> LB Agar plate of sterilization of Durancin+intein+CBD. (A)Negative control:LB broth. (B)Sterilize for 0 minutes. (C)Sterilize for 15 minutes. (D)Sterilize for 30 minutes. (E)Sterilize for 45 minutes.  </p></div>
  
  
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<partinfo>BBa_K2599003 parameters</partinfo>
 
<partinfo>BBa_K2599003 parameters</partinfo>
 
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<p style="padding-top:10px;font-size:20px;"><b>Reference</b></p>
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1. Casaus, P., et al. (1997). "Enterocin B, a new bacteriocin from Enterococcus faecium T136 which can act synergistically with enterocin A." Microbiology 143(7): 2287-2294.
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2. Franz, C. M., et al. (1999). "Atypical genetic locus associated with constitutive production of enterocin B by Enterococcus faecium BFE 900." Appl Environ Microbiol 65(5): 2170-2178.

Latest revision as of 18:53, 17 October 2018


Antimicrobial peptide - Enterocin B

This biobrick is the basic part of the enterocin B, more information please look for the composite part [1].



Figure 1. Basic part of Enterocin B


Introduction

Same as enterocin A, enterocin B is also from Enterococcus faecium that contains disulfide bridge. However, enterocin B does not belong to the pediocin family of bacteriocins. The primary translation product was a 71 aa peptide containing a leader peptide, and it is found to be a heat-stable bacteriocins, which can synergistically act with enterocin A.


Mechanism of Enterocin B

The bacteriocins inhibit their target organisms through pore formation. Though the mechanism of each inhibition is vary from species to species, the general process is conserved. To see more details, please search for our project page.

Since enterocin B belongs to class II bacteriocin, it is a small and heat stable peptide with a narrow spectrum of activity. Also, Enterocin A and enterocin B have very similar inhibitory spectra. They both interact with anionic lipids that are abundantly present in the membranes of Gram-positive bacteria. And according to the reference, enterocin B is inhibitory to some strains that are not sensitive to enterocin A. Furthermore, enterocin B is able to kill the bacteria that survive from the enterocin A treatment.


Figure 2. Mechanism of bacteriocin


Features of Enterocin B

1. Species Specific

Bacteriocins are antimicrobial peptides that will kill or inhibit bcterial strains closely related or non-related to produced bacteria, but will not harm the bacteria themselves by specific immunity proteins. The organisims that Enterocin B targets including Enterococcus faecalis, Bacillus subtilis, Bacillus coagulans, etc. More target organisms can be found on [http://bactibase.hammamilab.org/BAC101 bactibase].

2. Eco-friendly

Since enterocin B is a polypeptide naturally produced by bacteria itself and can inhibit other bacteria without much environment impact. It don't pose threat to other organisms like farm animals or humans. Therefore, this toxin will not cause safety problem.

3. Biodegradable

Enterocin B is a short peptide that will degrade in a short time. After degradation, this antibacterial peptide is harmless to our environment.


Peptide Prediction

NCTU_Formosa 2017 had compeleted a [http://2017.igem.org/Team:NCTU_Formosa/Model peptide prediction model] that can predict peptide for new function. In this model, they used scoring card method (SCM) for machine learning. This year, NCTU_Formosa 2018 continued to use the same method for predicting antimicrobial peptide, in order to seek more candidates for our project.

Enterocin B is one of the existing peptides that we predicted to show the function of antimicrobial activity. The score of our prediction is 464.36.


Figure 3. The prediction result of Enterocin B.



Experiment Result

Cloning

We conbined our toxic gene to pSB1C3 backbone and conducted PCR to check the size of our part. The Enterocin B sequence length is around 210 b.p. and the length of PCR product should be around 260 b.p.


Figure 4. Agarose gel electrophoretic pattern of Taq PCR product.


More experiment results of Enterocin B, please look for the composite part BBa_K2599011

Safety

In the future, we are going to spray our bio-stimulator into the environment. To make sure whether the bacteria contain anti-microbial peptide will not exist in the final product, we design the processing standards in the laboratory.

Bacteriocins are usually heat stable, we use high-temperature sterilization to double make sure our peptide solution does not contain any living E. coli. However, peptides may degrades after long time sterilization. To find out the best fitted time for sterilization, we boiled our bacteriocins for 0, 15, 30, and 45 minutes, and put them on LB Agar plate and cultured it at 37℃ for 16 hours.

From the result of the plate, we can easily observe that bacteria exists only in the sample that is not boiled. After fifteen minutes of sterilization, there are no alive bacterias exist.


Figure 5. LB Agar plate of sterilization of Durancin+intein+CBD. (A)Negative control:LB broth. (B)Sterilize for 0 minutes. (C)Sterilize for 15 minutes. (D)Sterilize for 30 minutes. (E)Sterilize for 45 minutes.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Reference


Reference

1. Casaus, P., et al. (1997). "Enterocin B, a new bacteriocin from Enterococcus faecium T136 which can act synergistically with enterocin A." Microbiology 143(7): 2287-2294.

2. Franz, C. M., et al. (1999). "Atypical genetic locus associated with constitutive production of enterocin B by Enterococcus faecium BFE 900." Appl Environ Microbiol 65(5): 2170-2178.