Difference between revisions of "Team:Tec-Chihuahua/Parts"

 
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    <div class="parts8-bg"><br><br>
 
<center><img src="https://static.igem.org/mediawiki/2018/c/c9/T--Tec-Chihuahua--Partsletters.png" width="13%" height="4%"/></center>
 
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<b><h3>Basic Parts Used</h3></b>
 
<br>
 
<b>Promoter T7 and RBS <a href="http://parts.igem.org/Part:BBa_K525998">[BBa_K525998]</a></b><br>
 
<p align="justify">This unregulated T7 promoter, which has an integrated RBS, has high levels of transcription when the T7 RNA polymerase is present; thus, in order to express BioBricks™ under the control of this promoter, a bacteria carrying a T7 polymerase gene has to be used.
 
For our proof of concept, we needed to express our proteins in large quantities. The two bacteria used to test our three enzymes, <i>Escherichia coli</i> BL21(DE3) and <i>Erwinia amylovora</i>, both contain the T7 polymerase gene.
 
</p><br>
 
<b>RBS (Elowitz 1999) - defines RBS efficiency  <a href="http://parts.igem.org/Part:BBa_B0034">[BBa_B0034]</a></b>
 
<p align="justify">A Ribosome Binding Site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation. This RBS is based on the Elowitz repressilator.
 
As our final BioBrick™ contains the three genes that code for our three enzymes, we added RBS sequences between each to increase translation efficiency.
 
</p><br>
 
<b>Autoinducer inactivation enzyme from <i>Bacillus</i>; hydrolyzes acetyl homoserine lactone <a href="http://parts.igem.org/Part:BBa_C0060">[BBa_C0060]</a></b>
 
<p align="justify">This gene encodes for the aiiA enzyme, which catalyzes the degradation of N-acyl-homoserine lactones (AHLs), which are quorum sensing autoinducers.
 
The lack of communication caused by the decrease of AHLs will result in the inability to sense population density and coordinate the expression of target genes, which in the case of several Gram-negative bacteria, like <i>Erwinia amylovora</i>, include virulence factors.
 
</p><br>
 
<b>yhjH Gene From <i>E.coli</i> str. K12 <a href="http://parts.igem.org/Part:BBa_K861090">[BBa_K861090]</a></b>
 
<p align="justify">This gene encodes for the yhjH enzyme, which contains a EAL domain that catalyzes the reaction of c-di-GMP into GMP.
 
C-di-GMP can serve as a second messenger to inhibit motility and increase biofilm formation and adhesion of bacteria, hence, the expression of this gene can make the bacteria more motile.
 
</p><br>
 
<b>epsE Molecular Clutch Gene of <i>B. subtilis</i> <a href="http://parts.igem.org/Part:BBa_K143032">[BBa_K14303]</a></b>
 
<p align="justify">This gene encodes for the epsE enzyme, which has been suggested to function in a manner similar to a molecular clutch. If expressed inside a cell, it will disengage the flagellum from the motor proteins in the cell membrane, causing the cell to be unable to swim effectively.
 
epsE could potentially be used as a controller of bacterial movement, promoting biofilm formation and inhibiting motility.
 
</p><br>
 
<b>T1 from <i>E. coli</i> rrnB <a href="http://parts.igem.org/Part:BBa_B0010">[BBa_B0010]</a></b>
 
                      <p align="justify">A transcriptional terminator consisting of a 64 bp stem-loop.
 
For the construction of our genetic circuitry, an efficient and reliable terminator was needed.
 
</p>
 
<br>
 
  
<b><h3>Generated Intermediate Parts</h3></b><br><br>
+
<groupparts>
<b>(T7 promoter + RBS) + (aiiA) <a href="http://parts.igem.org/Part:BBa_K2471006">[BBa_K2471006]</a></b><br>
+
  <h3><b>Basic Parts Used</b></h3><br>
<i>(BBa_K525998) + (BBa_C0060)</i><br><br>
+
  
<b>(T7 promoter + RBS) + (yhjH) <a href="http://parts.igem.org/Part:BBa_K2471007">[BBa_K2471007]</a></b><br>
+
  <b>Promoter T7 and RBS <a href="http://parts.igem.org/Part:BBa_K525998">[BBa_K525998]</a></b><br>
<i>(BBa_K525998) + (BBa_K861090)</i><br><br>
+
      <p align="justify"> This unregulated T7 promoter, which has an integrated RBS, has high levels of transcription when the T7 RNA polymerase is present; thus, in order to induce expression of this BioBrick™ under the control IPTG will be used.
 +
      </p><br>
  
<b>(T7 promoter + RBS) + (epsE) <a href="http://parts.igem.org/Part:BBa_K2471008">[BBa_K2471008]</a></b><br>
+
  <b>PelB leader sequence<a href="http://parts.igem.org/Part:BBa_J32015"> [BBa_J32015]</a></b>
<i>(BBa_K525998) + (BBa_K143032)</i><br><br>
+
      <p align="justify">The pelB leader sequence is a sequence of amino acids which, when attached to a protein, directs the protein to the bacterial periplasm. Protein secretion can increase the stability of cloned gene products. It was shown that the half-life of the recombinant proinsulin is increased 10-fold when the protein is secreted to the periplasmic space.
 +
      </p><br>
  
<b>(RBS) + (yhjH) <a href="http://parts.igem.org/Part:BBa_K2471009">[BBa_K2471009]</a></b><br>
+
  <b>Defensin 1 <a href="http://parts.igem.org/Part:BBa_K1104301">[BBa_K1104301]</a></b>
<i>(BBa_B0034) + (BBa_K861090)</i><br><br>
+
      <p align="justify">Defensin 1 is synthesized in salivary glands and it plays an important role in the social immunity system of the bee, meaning that it is commonly passed through generations.
 +
Defensins unpolarize inner membranes by causing an ionic outer flow using preexistent channels. Apart from these processes, they are responsible for respiratory inhibition 3 minutes after they are added by directly attacking the respiration chain components.
 +
      </p><br>
  
<b>(RBS) + (epsE) <a href="http://parts.igem.org/Part:BBa_K2471010">[BBa_K2471010]</a></b><br>
+
  <b> Abaecin <a href="http://parts.igem.org/Part:BBa_K1104300">[BBa_K1104300]</a></b>
<i>(BBa_B0034) + (BBa_K143032)</i><br><br>
+
      <p align="justify"> Antimicrobial peptide that shows activity against both Gram-negative and positive bacteria. When being alone, it shows no activity against E. coli, at least at concentrations up to 200 μM. Hymenoptaecin a native peptide showed activity starting at 2μM concentration. When working together, helps by opening channels for the abaecin, which then gets to attack the DnaK, getting to interfere with a proper folding of the proteins.
 +
      </p><br>
  
<b>(T7 promoter + RBS) + (aiiA) + (RBS) + (yhjH) <a href="http://parts.igem.org/Part:BBa_K2471011">[BBa_K2471011]</a></b><br>
+
  <b>T1 from <i>E. coli</i> rrnB <a href="http://parts.igem.org/Part:BBa_B0010">[BBa_B0010]</a></b>
<i>(BBa_K525998) + (BBa_C0060) + (BBa_B0034) + (BBa_K8610)</i><br><br>
+
      <p align="justify">A transcriptional terminator consisting of a 64 bp stem-loop. For the construction of our genetic circuitry, an efficient and reliable terminator was needed.
 +
      </p><br>
  
<b>(RBS) + (epsE) + (T1 terminator) <a href="http://parts.igem.org/Part:BBa_K2471012">[BBa_K2471012]</a></b><br>
+
<b><h3>New Additions to the Parts Registry</h3></b><br>
<i>(BBa_B0034) + (BBa_K143032) + (BBa_B0010)</i><br><br>
+
  
<b><h3>Composite Parts of our Creation</h3><br><br></b>
+
<b>Modified 6xHis-tag <a href=" http://parts.igem.org/Part:BBa_K2834002">[BBa_K2834002]</a></b>
 +
<p align="justify"> A silently mutated amino acid motif in proteins that consists of  six histidine (His) residues, often at the N- or C-terminus of the protein. Polyhistidine-tags are often used for affinity purification of polyhistidine-tagged recombinant proteins expressed in Escherichia coli  and other prokaryotic expression systems.</p><br>
  
<b>(T7 promoter + RBS) + (aiiA) + (T1 terminator) <a href="http://parts.igem.org/Part:BBa_K2471000">[BBa_K2471000]</a></b><br>
+
<b>Apidaecin <a href="http://parts.igem.org/Part:BBa_K2834000">[BBa_K2834000]</a></b>
<i>(BBa_K525998) + (BBa_C0060) + (BBa_B0010)</i><br>
+
<p align="justify"> It affects mainly Gram-negative bacteria, killing it impressively fast. Its mechanism of action is pretty unique. It has a total lack of pore-forming activity and its efficiency depends on the enantiomer used, meaning it has stereospecificity. Apidaecin gets to the ribosome 70s and the DnaK protein, leading to a protein synthesis inhibition when getting in contact with the ribosome, however, DnaK is the final target. This DnaK has an essential role in the folding of the proteins and in the DNA replication process, especially in the lambda phage.</p>
<p>This BioBrick™ contains the necessary genetic circuitry to constitutively express the aiiA gene, that when expressed, results in the production of the aiiA enzyme, and thus, the disruption of the quorum sensing thanks to the decrease in AHLs.</p><br>
+
<p id="validated"></p><br>
  
<b>(T7 promoter + RBS) + (yhjH) + (T1 terminator) <a href="http://parts.igem.org/Part:BBa_K2471001">[BBa_K2471001]</a></b><br>
+
<b><h3>Composite Parts in our Creation</h3></b><br>
<i>(BBa_K525998) + (BBa_K861090) + (BBa_B0010)</i><br>
+
<p>This BioBrick™ contains the necessary genetic circuitry to constitutively express the yhjH gene, that when expressed, results in the production of the yhjH enzyme, that catalyzes the reaction of c-di-GMP to GMP, which will inhibit biofilm formation and promote motility.</p><br>
+
  
<b>(T7 promoter + RBS) + (epsE) + (T1 terminator) <a href="http://parts.igem.org/Part:BBa_K2471002">[BBa_K2471002]</a></b><br>
 
<i>(BBa_K525998) + (BBa_K143032) + (BBa_B0010)</i><br>
 
<p>This BioBrick™ contains the necessary genetic circuitry to constitutively express the epsE gene, that when expressed, results in the production of the epsE enzyme. This will cause the detachment of the flagellum from the motor proteins in the cell membrane, promoting biofilm formation and inhibiting motility.</p><br>
 
  
<b>(T7 promoter + RBS) + (aiiA) + (RBS) + (yhjH) + (RBS) + (epsE) + (T1 terminator)<a href="http://parts.igem.org/Part:BBa_K2471003"> [BBa_K2471003]</a></b><br>
+
  <b><p align="center">(T7 promoter + RBS) + (PelB) + (Defensin1) + (6x His-Tag) + (T1 terminator)</p> 
<i>(BBa_K525998) + (BBa_C0060) + (BBa_B0034) + (BBa_K861090) + (BBa_B0034) + (BBa_K143032) + (BBa_B0010)</i><br>
+
  <center><a href="http://parts.igem.org/Part:BBa_K2834005">[BBa_K2834005]</a></b></center><br>
<p>This BioBrick™ contains the necessary genetic circuitry to constitutively express the aiiA, yhjH and epsE genes, that when expressed, results in the production of the three enzymes of the same name. The combined effect of these will cause the cell to be unable to communicate (quorum quenching), move (motility inhibition) and form biofilm (decrease of ci-d-GMP).</p><br>
+
  <img class="giro" src="https://static.igem.org/mediawiki/2018/a/ae/T--Tec-Chihuahua--A.png"/>
 +
  <i>(BBa_K525998) + (BBa_J32015) + (BBa_K1104301) + (BBa_K2834002) + (BBa_B0010)
 +
</i><br>
 +
  <p align="justify">This BioBrick™ contains the necessary genetic circuitry to be induced by IPTG and express the Defensin 1 peptide which will be transferred to the periplasmic region by the pelB. Post sonication this peptide can be isolated with the 6x His-Tag using an antiHis column.</p><br>
  
<b><h3>New Additions to the Parts Registry</h3></b><br><br>
 
<b>N-acyl homoserine lactonase from <i>Bacillus</i> sp. A24 <a href="http://parts.igem.org/Part:BBa_K2471013">[BBa_K2471013]</a></b><br>
 
<p align="justify">This aiiA gene comes from Bacillus sp. 240B1. Expression of aiiA in transformed <i>Erwinia carotovora</i> strain SCG1 significantly reduced the release of autoinducers, decreased extracellular pectolytic enzyme activities, and attenuated pathogenicity on potato, eggplant, chinese cabbage, carrot, celery, cauliflower, and tobacco. The successful degradation of AHLs makes this gene a great alternative to inhibit several of the virulence factors from <i>Erwinia amylovora</i>. The results given by Dong <i>et al</i>. encouraged the potential applications of this gene in the future, “Our results show that the aiiA gene product inhibits virulence of <i>E. carotovora</i> when expressed in the pathogen” (Dong, <i>et al</i>., 2000).</p><br>
 
  
<b>Glycosyltransferase family 2 protein from <i>Bacillus subtilis</i> <a href="http://parts.igem.org/Part:BBa_K2471014">[BBa_K2471014]</a></b><br>
+
    <p align="center"><b>(T7 promoter + RBS) + (PelB) + (Abaecin) + (6x His-Tag) + (T1 terminator)</p> 
<p align="justify">The protein produced arrests flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix. The clutch is a simple, rapid, and potentially reversible form of motility control. epsE is sufficient to inhibit motility and does so by arresting flagellar rotation (Blair, K. M., 2008). Though the EPS operon is normally repressed in <i>B. subtilis</i>, it's beneficial for the original copy of the epsE gene to be knocked out if its synthetically expressed. Although many bacterial flagellar assemblies contain proteins that are similar in shape, there is no guarantee that the epsE gene will function correctly in any host cell other than <i>B. subtilis</i>.</p><br>
+
    <center><a href="http://parts.igem.org/Part:BBa_K2834006">[BBa_K2834006]</a></b></center><br>
 +
    <img class="giro" src="https://static.igem.org/mediawiki/2018/9/91/T--Tec-Chihuahua--B.png"/>
 +
    <i>(BBa_K525998) + (BBa_J32015) + (BBa_K1104300) + (BBa_K2834002) + (BBa_B0010)</i><br>
 +
    <p align="justify">This BioBrick™ contains the necessary genetic circuitry to be induced by IPTG and express the Abaecin peptide which will be transferred to the periplasmic region by the pelB. Post sonication this peptide can be isolated with the 6x His-Tag using a antiHis column.</p><br>
  
<b>Expressible N-acyl homoserine lactonase from <i>Bacillus sp</i>. A24 <a href="http://parts.igem.org/Part:BBa_K2471004">[BBa_K2471004]</a></b><br>
+
    <p align="center"><b>(T7 promoter + RBS) + (PelB) + (Apidaecin) + (6x His-Tag) + (T1 terminator)</b></p>
<p align="justify">This BioBrick™ counts with a T7 promoter (BBa_J64997), RBS (BBa_B0034), gene of interest (N-acyl homoserine lactonase; BBa_K2471013), and two terminators, T1 (BBa_B0010) and T7 (BBa_B0012). It was synthesized thanks to the sponsorship granted by IDT® and it codes for an aiiA enzyme, which catalyzes the degradation of N-acyl-homoserine lactones (AHLs).</p><br>
+
    <center><b><a href="http://parts.igem.org/Part:BBa_K2834003">[BBa_K2834003]</a></b></center><br>
 
+
    <img class="giro" src="https://static.igem.org/mediawiki/2018/0/03/T--Tec-Chihuahua--D.png" width="100%" height=80%"/><br>
<b>Expressible glycosyltransferase family 2 protein from <i>Bacillus subtilis</i> <a href="http://parts.igem.org/Part:BBa_K2471005">[BBa_K2471005]</a></b><br>
+
    <i>(BBa_K525998) + (BBa_J32015) + (BBa_K2834000) + (BBa_K2834002) + (BBa_B0010)</i><br>
<p align="justify">This BioBrick counts with a T7 promoter (BBa_J64997), RBS (BBa_B0034), gene of interest (glycosyltransferase family 2 protein; BBa_K2471014) and two terminators, T1 (BBa_B0010) and T7 (BBa_B0012). It codes for the epsE enzyme, that has been suggested to function in a similar way to a molecular clutch, could potentially be used as a controller of bacterial movement, promoting biofilm formation and inhibiting motility.</p><br><br>
+
    <p align="justify">This BioBrick™ contains the necessary genetic circuitry to be induced by IPTG and express the Apidaecin peptide which will be transferred to the periplasmic region by the pelB. Post sonication this peptide can be isolated with the 6x His-Tag using a antiHis column.</p><br>
  
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      <button class="collapsible"><h4 align="center"><b>References</b></h4></button>
 +
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  <ol><br>
 +
      <li>Ilyasov, R. A., Gaifullina, L. R., Saltykova, E. S., Poskryakov, A. V., & Nikolaenko, A. G. (2013). Defensins in the honeybee antiinfectious protection. Journal of Evolutionary Biochemistry and Physiology, 49(1), 1–9. https://doi.org/10.1134/s0022093013010015</li>
 +
      <li>Cociancich, S., Ghazi, A., Hetru, C., Hoffman, J. A., & Letellier, L. (1993). Insect Defensin, an Inducible Antibacterial Peptide, Forms Voltage-dependent Channels in Micrococcus luteus. The Journal of Biological Chemistry, 268(26), 19239-19245
 +
      <li>Shen, X., Ye, G., Cheng, X., Yu, C., Hu, C., Allosaar, I. (2010). Characterization of an abaecin-like antimicrobial peptide identified from a Pteromalus puparum cDNA clone. Retrieved from: https://www.sciencedirect.com/science/article/pii/S0022201110001114</li>
 +
      <li>Castle, M., Nazarian, A., Yi, S., Tempst, P. (1999). Lethal effects of apidaecin on Escherichia coli involve sequential molecular interactions with diverse targets. Retrieved from: http://www.jbc.org/content/274/46/32555.full.pdf</li>
 +
      <li>Cociancich, S., Ghazi, A., Hetru, C., Hoffman, J. A., & Letellier, L. (1993). Insect Defensin, an Inducible Antibacterial Peptide, Forms Voltage-dependent Channels in Micrococcus luteus. The Journal of Biological Chemistry, 268(26), 19239-19245</li>
 +
  </ol>
 +
<br>
 +
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<h4><p align="justify">References</p></h4><br>
+
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<p align="justify">Blair, K. M., Turner, L., Winkelman, J. T., Berg, H. C., & Kearns, D. B. (2008). A molecular clutch disables flagella in the <i>Bacillus subtilis</i> biofilm. science, 320(5883), 1636-1638.</p>
+
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<p align="justify">Dong, Y.-H., Xu, J.-L., Li, X.-Z., & Zhang, L.-H. (2000). aiiA, an enzyme that inactivates the acyl-homoserine lactone quorum-sensing signal and attenuates the virulence of <i>Erwinia carotovora</i>. Proceedings of the National Academy of Sciences of the United States of America, 97(7), 3526–3531.</p><br>
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Latest revision as of 23:15, 17 October 2018

Erwinions



Basic Parts Used


Promoter T7 and RBS [BBa_K525998]

This unregulated T7 promoter, which has an integrated RBS, has high levels of transcription when the T7 RNA polymerase is present; thus, in order to induce expression of this BioBrick™ under the control IPTG will be used.


PelB leader sequence [BBa_J32015]

The pelB leader sequence is a sequence of amino acids which, when attached to a protein, directs the protein to the bacterial periplasm. Protein secretion can increase the stability of cloned gene products. It was shown that the half-life of the recombinant proinsulin is increased 10-fold when the protein is secreted to the periplasmic space.


Defensin 1 [BBa_K1104301]

Defensin 1 is synthesized in salivary glands and it plays an important role in the social immunity system of the bee, meaning that it is commonly passed through generations. Defensins unpolarize inner membranes by causing an ionic outer flow using preexistent channels. Apart from these processes, they are responsible for respiratory inhibition 3 minutes after they are added by directly attacking the respiration chain components.


Abaecin [BBa_K1104300]

Antimicrobial peptide that shows activity against both Gram-negative and positive bacteria. When being alone, it shows no activity against E. coli, at least at concentrations up to 200 μM. Hymenoptaecin a native peptide showed activity starting at 2μM concentration. When working together, helps by opening channels for the abaecin, which then gets to attack the DnaK, getting to interfere with a proper folding of the proteins.


T1 from E. coli rrnB [BBa_B0010]

A transcriptional terminator consisting of a 64 bp stem-loop. For the construction of our genetic circuitry, an efficient and reliable terminator was needed.


New Additions to the Parts Registry


Modified 6xHis-tag [BBa_K2834002]

A silently mutated amino acid motif in proteins that consists of six histidine (His) residues, often at the N- or C-terminus of the protein. Polyhistidine-tags are often used for affinity purification of polyhistidine-tagged recombinant proteins expressed in Escherichia coli and other prokaryotic expression systems.


Apidaecin [BBa_K2834000]

It affects mainly Gram-negative bacteria, killing it impressively fast. Its mechanism of action is pretty unique. It has a total lack of pore-forming activity and its efficiency depends on the enantiomer used, meaning it has stereospecificity. Apidaecin gets to the ribosome 70s and the DnaK protein, leading to a protein synthesis inhibition when getting in contact with the ribosome, however, DnaK is the final target. This DnaK has an essential role in the folding of the proteins and in the DNA replication process, especially in the lambda phage.


Composite Parts in our Creation


(T7 promoter + RBS) + (PelB) + (Defensin1) + (6x His-Tag) + (T1 terminator)

[BBa_K2834005]

(BBa_K525998) + (BBa_J32015) + (BBa_K1104301) + (BBa_K2834002) + (BBa_B0010)

This BioBrick™ contains the necessary genetic circuitry to be induced by IPTG and express the Defensin 1 peptide which will be transferred to the periplasmic region by the pelB. Post sonication this peptide can be isolated with the 6x His-Tag using an antiHis column.


(T7 promoter + RBS) + (PelB) + (Abaecin) + (6x His-Tag) + (T1 terminator)

[BBa_K2834006]

(BBa_K525998) + (BBa_J32015) + (BBa_K1104300) + (BBa_K2834002) + (BBa_B0010)

This BioBrick™ contains the necessary genetic circuitry to be induced by IPTG and express the Abaecin peptide which will be transferred to the periplasmic region by the pelB. Post sonication this peptide can be isolated with the 6x His-Tag using a antiHis column.


(T7 promoter + RBS) + (PelB) + (Apidaecin) + (6x His-Tag) + (T1 terminator)

[BBa_K2834003]


(BBa_K525998) + (BBa_J32015) + (BBa_K2834000) + (BBa_K2834002) + (BBa_B0010)

This BioBrick™ contains the necessary genetic circuitry to be induced by IPTG and express the Apidaecin peptide which will be transferred to the periplasmic region by the pelB. Post sonication this peptide can be isolated with the 6x His-Tag using a antiHis column.



  1. Ilyasov, R. A., Gaifullina, L. R., Saltykova, E. S., Poskryakov, A. V., & Nikolaenko, A. G. (2013). Defensins in the honeybee antiinfectious protection. Journal of Evolutionary Biochemistry and Physiology, 49(1), 1–9. https://doi.org/10.1134/s0022093013010015
  2. Cociancich, S., Ghazi, A., Hetru, C., Hoffman, J. A., & Letellier, L. (1993). Insect Defensin, an Inducible Antibacterial Peptide, Forms Voltage-dependent Channels in Micrococcus luteus. The Journal of Biological Chemistry, 268(26), 19239-19245
  3. Shen, X., Ye, G., Cheng, X., Yu, C., Hu, C., Allosaar, I. (2010). Characterization of an abaecin-like antimicrobial peptide identified from a Pteromalus puparum cDNA clone. Retrieved from: https://www.sciencedirect.com/science/article/pii/S0022201110001114
  4. Castle, M., Nazarian, A., Yi, S., Tempst, P. (1999). Lethal effects of apidaecin on Escherichia coli involve sequential molecular interactions with diverse targets. Retrieved from: http://www.jbc.org/content/274/46/32555.full.pdf
  5. Cociancich, S., Ghazi, A., Hetru, C., Hoffman, J. A., & Letellier, L. (1993). Insect Defensin, an Inducible Antibacterial Peptide, Forms Voltage-dependent Channels in Micrococcus luteus. The Journal of Biological Chemistry, 268(26), 19239-19245