Difference between revisions of "Team:XJTLU-CHINA/Lysis"

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<div class="container">
 
<div class="container">
 
<h1>AcmA and the application of the toggle switch in our project</h1>
 
<h1>AcmA and the application of the toggle switch in our project</h1>
 +
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/f/fc/Lysis_figure1.png" height=600 width=600>
 +
<p class="form"><b>Figure 1.</b>&nbsp;&nbsp;&nbsp;&nbsp;Construction of the AMPs-Toggle Switch-Autolysin cassette. The upstream sensing device for <i>S. aureus</i> is omitted, which can be seen at the Sensing Device module.</p> 
 +
<p>Considering low efficiency and complexity of conventional secretory pathway, this year, we built a based-on-lysis system for aiming at releasing AMPs (antimicrobial peptides) efficiently. Therefore, we designed the acmA gene to be preceded by a bistable toggle switch so as to make cell lysis more regimented (see the reason in the following section). The switch we used was the lacI-tetR regulated expression system. The tetR linked downstream to plac is constituitively transcribed when free from the repression of the LacI repressor protein. This leads to the expression of TetR protein and subsequently an inhibitive effect on AcmA expression. Hence, under the normal situation in a host bacterial cell (such as <i>L. lactis</i>), the expression of AcmA autolysin is always inhibited. In this case, <i>L. lactis</i> can keep its integrity and maintain the capability of sensing <i>S. aureus</i>. Thereafter, with the initiation of P2 by phosphorylated AgrA (the mechanism can be seen at the <a href="">Sensing Device module</a>) and the expression of LacI, the switch turns on the ptet promoter and the expression of AcmA starts, as subsequently elicits the autolysis process and the accumulated AMPs burst out, culminating the extermination of the pathogen—<i>S. aureus</i> in the gut.</p>
 +
<hr>
 
<h1>The reason of utilization of the lacI-tetR regulatory switch</h1>
 
<h1>The reason of utilization of the lacI-tetR regulatory switch</h1>
 +
<p>Considering the prompt effect of AcmA on cell number (see Figure 2), after its induction, there might be a relatively early cell lysis (decrease in OD) occurring before AMPs are accumulated to a concentration at which pathogenic bacteria can be effectively killed. In the light of this finding, we adopted a lacI-tetR regulatory switch to postpone the autolysis process. </p>
 +
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/3/39/Lysis_figure2.png" height=600 width=600>
 +
<p class="form"><b>Figure 2.</b>&nbsp;&nbsp;&nbsp;&nbsp;</p> 
 +
<p>Buist’s demonstration of the effect of overexpression (A, B & C) of AcmA (1997). The optical density of the bacterial cells was measured at OD<sub>600</sub>. After the induction of AcmA with mitomycin at the stationary phase (10 hours in the graph), there was a conspicuous decrease in bacterial optical density during the next 2 days. <br>
 +
In Buist’s work, A, C, D respectively represents the <i>L. lactis</i> that contains different kind of plasmids harboring the acmA gene and B stands (which is not shown in the graph) for the bacteria that does not have the acmA gene.</p>
 +
<hr>
 +
 
<h1>AcmA in <i>Lactococcus lactis</i></h1>
 
<h1>AcmA in <i>Lactococcus lactis</i></h1>
 
<h3>Enzymatic function</h3>
 
<h3>Enzymatic function</h3>
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<p>As a broad-range autolysin due to its similar lysis mechanism to the other autolysin family members, i.e. hydrolyzing N-acetylmuramyl-1,4-β-N-acetylglucosamine bonds in the peptidoglycan, it is not clear whether AcmA has any adverse effects on the enteric microbiome. If AcmA lyse other gram-positive bacteria, the homeostasis of intestinal bacterial community may be affected.</p>
 
<p>As a broad-range autolysin due to its similar lysis mechanism to the other autolysin family members, i.e. hydrolyzing N-acetylmuramyl-1,4-β-N-acetylglucosamine bonds in the peptidoglycan, it is not clear whether AcmA has any adverse effects on the enteric microbiome. If AcmA lyse other gram-positive bacteria, the homeostasis of intestinal bacterial community may be affected.</p>
 
<hr>
 
<hr>
 +
 
<h1>Testing the expression of autolysin in <i>L. lactis</i></h1>
 
<h1>Testing the expression of autolysin in <i>L. lactis</i></h1>
 +
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/d/d4/Lysis_figure3.png" height=600 width=600>
 +
<p class="form"><b>Figure 3.</b>&nbsp;&nbsp;&nbsp;&nbsp;Construction of the autolysin part (Main elements in pNZ8148 haboring acmA, the detailed result of the assembly of BBa_K2309004 in the pNZ8148 plasmid can be seen at <i>Figure 4</i>)</p> 
 +
<p>Before we assembled all of our parts together, we tested each independent functional part. The acmA gene along with an upstream RBS was first joined to pNZ8148 which contains a nisin-inducible promoter and a terminator (Figure 3), and then the whole construct was transformed into the <i>Lactococcus lactis</i> NZ9000 strain. After the bacteria was cultured to the stationary phase, nisin was added to induce the expression of the AcmA protein. We employed an experimental procedure similar to Buist, et al. (1997). In their experiment (see their result at <i>Figure 2</i>, after induction with mitomycin, the bacteria cells at the stationary phase had a prominent decrease in optical density in several hours. (Buist et al., 1997)</p>
 +
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/d/db/Lysis_figure4.png" height=600 width=600>
 +
<p class="form"><b>Figure 4.</b>&nbsp;&nbsp;&nbsp;&nbsp;Integrated plasmid construction of the testing part (The detailed illustration of pNZ8148 harboring the acmA gene)</p> 
 +
<hr>
 
<h1>Testing Protocol</h1>
 
<h1>Testing Protocol</h1>
 
<h3>Nisin-induced lysis of <i>L. lactis</i></h3>
 
<h3>Nisin-induced lysis of <i>L. lactis</i></h3>
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Smith, Thomas J., Blackman, Steve A. and Foster, Simon J. (2000) ‘Autolysins of Bacillus subtilis: multiple enzymes with multiple functions’, Microbiology, 146, pp. 249-262, Emerald Insight [Online]. DOI: 10.1099/00221287-146-2-249  
 
Smith, Thomas J., Blackman, Steve A. and Foster, Simon J. (2000) ‘Autolysins of Bacillus subtilis: multiple enzymes with multiple functions’, Microbiology, 146, pp. 249-262, Emerald Insight [Online]. DOI: 10.1099/00221287-146-2-249  
 
</p>
 
</p>
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/7/70/Modeling_on_the_sensing_device.png" height=600 width=600>
 
<p>Table 1 Definitions of the parameters</p>
 
    <div class="table" align="center">
 
        <br>
 
        <table border="1" cellpadding="5">
 
            <colgroup>
 
                <col width="70">
 
                <col width="350">
 
                <col width="70">
 
                <col width="150">
 
                <col width="250">
 
            </colgroup>
 
 
            <tr>
 
                <th>Parameters</th>
 
                <th>Pate constant for</th>
 
                <th>Value</th>
 
                <th>Units</th>
 
                <th>Note</th>
 
            </tr>
 
 
            <tr>
 
                <td>α<sub>pi</sub></td>
 
                <td>Phosphorylation of AgrA</td>
 
                <td>10<sup>[1]</sup></td>
 
                <td>μmol<sup>-1</sup> ml<sup>-1</sup> h<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td>α<sub>pidi</sub></td>
 
                <td>Dephosphorylation of AgrA</td>
 
                <td>1<sup>[1]</sup></td>
 
                <td>h<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td>μ<sub>x</sub></td>
 
                <td>Degradation and dilution</td>
 
                <td>2<sup>[1]</sup></td>
 
                <td>h<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td>α<sub>cbind</sub></td>
 
                <td>AgrC that anchors to the cell membrane</td>
 
                <td>10</td>
 
                <td>μmol<sup>-1</sup> ml<sup>-1</sup> h<sup>-1</sup></td>
 
                <td>Assume the same as α<sub>pi</sub></td>
 
            </tr>
 
 
            <tr>
 
                <td>α<sub>bind</sub></td>
 
                <td>Binding of AIP to AgrC</td>
 
                <td>1<sup>[1]</sup></td>
 
                <td>μmol<sup>-1</sup> ml<sup>-1</sup> h<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td>α<sub>unbind</sub></td>
 
                <td>Separation of AIP from AgrC</td>
 
                <td>0.1<sup>[1]<sup></td>
 
                <td>h<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
        </table>
 
    </div>
 
<div class="table" align="center">
 
        <br>
 
        <table border="1" cellpadding="5">
 
            <colgroup>
 
                <col width="70">
 
                <col width="350">
 
                <col width="70">
 
                <col width="110">
 
                <col width="250">
 
            </colgroup>
 
 
            <tr>
 
                <th>Parameters</th>
 
                <th>Definitions</th>
 
                <th>Value</th>
 
                <th>Units</th>
 
                <th>Note</th>
 
            </tr>
 
 
            <tr>
 
                <td>X</td>
 
                <td>Nisin</td>
 
                <td>1.42×10<sup>-7[2]</sup></td>
 
                <td>μmol ml<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td>k<sub>2</sub></td>
 
                <td>The Phosphorylated AgrA concentration required for half-maximal transcription rate of P2</td>
 
                <td>1<sup>[1]</sup></td>
 
                <td>μmol  ml<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td>β<sub>1</sub></td>
 
                <td>Maximum transcription rate of pnisA</td>
 
                <td>10</td>
 
                <td>μmol  h<sup>-1</sup></td>
 
                <td>Assume the same as β<sub>2</sub></td>
 
            </tr>
 
 
            <tr>
 
                <td>β<sub>2</sub></td>
 
                <td>Maximum transcription rate of P2</td>
 
                <td>10<sup>[1]</sup></td>
 
                <td>μmol h<sup>-1</sup></tb>
 
                <td></td>
 
            </tr>
 
        </table>
 
    </div>
 
<p>Table 2 Definitions of the variables</p>
 
<div class="table" align="center">
 
        <br>
 
        <table border="1" cellpadding="5">
 
            <colgroup>
 
                <col width="70">
 
                <col width="350">
 
                <col width="120">
 
            </colgroup>
 
 
            <tr>
 
                <th>Variables</th>
 
                <th>Concentration of </th>
 
                <th>Units</th>
 
            </tr>
 
 
            <tr>
 
                <td>A</td>
 
                <td>AgrA</td>
 
                <td>μmol&nbsp; ml<sup>-1</sup></td>
 
            </tr>
 
 
            <tr>
 
                <td>C</td>
 
                <td>AgrC</td>
 
                <td>μmol ml<sup>-1</sup></td>
 
            </tr>
 
 
            <tr>
 
                <td>C<sub>bind</sub></td>
 
                <td>AgrC that anchors to the cell membrane</td>
 
                <td>μmol ml<sup>-1</sup></td>
 
            </tr>
 
           
 
            <tr>
 
                <td>AIP</td>
 
                <td>Free AIP molecules</td>
 
                <td>μmol ml<sup>-1</sup></td>
 
            </tr>
 
           
 
            <tr>
 
                <td>C<sub>p</sub></td>
 
                <td>AIP-bound AgrC</td>
 
                <td>μmol ml<sup>-1</sup></td>
 
            </tr>
 
           
 
            <tr>
 
                <td>A<sub>pi</sub></td>
 
                <td>The phosphorylated AgrA</td>
 
                <td>μmol ml<sup>-1</sup></td>
 
            </tr>
 
           
 
            <tr>
 
                <td>sfGFP</td>
 
                <td>The product of P2 promoter</td>
 
                <td>μmol ml<sup>-1</sup></td>
 
            </tr>     
 
        </table>
 
    </div>
 
<p>The three Hill equations represent the rates of translation of AgrA, AgrC and sfGFP. Β<sub>1</sub> is the highest efficiency for the promoter pnisA to initiate the transcription of the agrC and agrA genes, and β<sub>2</sub> is the highest efficiency for the promoter P2 to initiate the transcription of the sfGFP gene. X is the concentration of nisin which is needed to activate the promoter pnisA, to this extent, k<sub>1</sub> equals to the concentration of A<sub>pi</sub> when the rate of reaction is up to half of V<sub>max</sub>. K<sub>2</sub>, which is controlled by another regulatory factor, is the concentration of phosphorylated AgrA when the rate of reaction is up to half of V<sub>max</sub>.</p>
 
<p>By assuming that 0.25 μM of AIP molecules is present in the intestine, we run the MATLAB script to check whether AIP molecules can successfully activate the promoter P2 by binding to AgrC and phosphorylating AgrA. We set the threshold concentration of sfGFP to be 0.5 μM, and at this point, we consider the promoter P2 is activated. The results are shown below.</p>
 
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/9/9e/State_values.png" height=600 width=600>
 
<p class="form"><b>Fig 1.</b>&nbsp;&nbsp;&nbsp;&nbsp;State values of AgrA, Cbind, AgrC, Cp, Api and sfGFP.</p> 
 
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/b/be/Individual_display_of_6_variables.png" height=700 width=700>
 
<p class="form"><b>Fig 2.</b>&nbsp;&nbsp;&nbsp;&nbsp;Individual display of 6 variables</p> 
 
<p>As it is shown in the second graph (values are hard to observe in the first one), concentration of sfGFP reaches 0.5 μM at the third hour. Therefore, we made a conclusion that the amount of AIP molecules can activate the promoter P2 to transcribe the genes downstream.</p>
 
<h1>Modelling on peptide synthesis and cell lysis</h1>
 
<p>Our design uses the tandem repeat strategy to express three copies of each peptide gene, LL-37, GF-17 and Grammistin-Pp1, aiming to producing peptides quickly and at a higher rate. To release the peptides to kill <i>Staphylococcus aureus</i> in the intestine, we choose lysis of the cells instead of secretion. A lysis gene is used to open up the cells, then all the peptides will surely be released into the guts. In addition, we plan to use a toggle switch to provide more time for peptide synthesis before lysis. When the cells are lysed, it will result in the release of intracellular proteins and stop all life activities. Therefore, we use modeling to identify:</p>
 
<ol>
 
<li>How long does cell lysis take from the point of induction?</li>
 
<li>At this time point, how much peptides are produced by the gene circuit?</li>
 
</ol>
 
<p>Results: </br>
 
Inspired by the team TU-Delft (2013), we came up with the idea that the promoters P2, plac and ptet may serve as binary switches between the active and inactive promoter states instead of continuous activities from fully on to fully off. We used the parameter--s, a binary state descriptor, to refer to the situation when a promoter produces one of the two levels of activity: on or off.</p>
 
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/6/6f/Modelling_on_peptide_synthesis_and_cell_lysis.png" height=350 width=350>
 
<p>Table 3 Definitions of parameters</p>
 
<div class="table" align="center">
 
        <br>
 
        <table border="1" cellpadding="5">
 
            <colgroup>
 
                <col width="70">
 
                <col width="350">
 
                <col width="70">
 
                <col width="150">
 
                <col width="250">
 
            </colgroup>
 
 
            <tr>
 
                <th>Parameters</th>
 
                <th>Definitions</th>
 
                <th>Value</th>
 
                <th>Units</th>
 
                <th>Note</th>
 
            </tr>
 
 
            <tr>
 
                <td><i>a</i></td>
 
                <td>translation rate per amino acid</td>
 
                <td>1020<sup>[3]</sup></td>
 
                <td>Min<sup>-1</sup> amino acids residues<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td><i>c<sub>p2</sub></i></td>
 
                <td>maximum transcription rate of P2</td>
 
                <td>0.17<sup>[1]</sup></td>
 
                <td>μmol  min<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td><i>c<sub>tetR</sub></i></td>
 
                <td>maximum transcription rate of ptet</td>
 
                <td>2.79<sup>[3]</sup></td>
 
                <td>μmol<sup>-1</sup>  min<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
           
 
            <tr>
 
                <td><i>c<sub>plac</sub></i></td>
 
                <td>maximum transcription rate of plac</td>
 
                <td>2.79</td>
 
                <td>μmol<sup>-1</sup>  min<sup>-1</sup></td>
 
                <td>Assume the same as <i>c<sub>tetR</sub></i> </td>
 
            </tr>
 
           
 
            <tr>
 
                <td><i>d<sub>mRNA</sub></i></td>
 
                <td>degradation rate of mRNA</td>
 
                <td>0.288<sup>[4]</sup></td>
 
                <td>min<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
           
 
            <tr>
 
                <td><i>d<sub>Lacl</sub></i></td>
 
                <td>degradation rate of Lacl</td>
 
                <td>0.1386<sup>[4]</sup></td>
 
                <td>min<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>d<sub>tetR</sub></i></td>
 
                <td>degradation rate of tetR</td>
 
                <td>0.1386<sup>[4]</sup></td>
 
                <td>min<sup>-1</sup></td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>d<sub>AcmA</sub></i></td>
 
                <td>degradation rate of AcmA</td>
 
                <td>0.0063</td>
 
                <td>min<sup>-1</sup></td>
 
                <td>Assume the same as GFP</td>
 
            </tr>
 
            <tr>
 
                <td><i>d<sub>GFn</sub></i></td>
 
                <td>degradation rate of GFn</td>
 
                <td>0.0021</td>
 
                <td>min<sup>-1</sup></td>
 
                <td>Assume the one-third of GFP</td>
 
            </tr>
 
            <tr>
 
                <td><i>d<sub>Gram</sub></i></td>
 
                <td>degradation rate of Gran</td>
 
                <td>0.0021</td>
 
                <td>min<sup>-1</sup></td>
 
                <td>Assume the one-third of GFP</td>
 
            </tr>
 
            <tr>
 
                <td><i>d<sub>LLn</sub></i></td>
 
                <td>degradation rate of LLn</td>
 
                <td>0.0021</td>
 
                <td>min<sup>-1</sup></td>
 
                <td>Assume the one-third of GFP</td>
 
            </tr>
 
            <tr>
 
                <td><i>l<sub>p2</sub></i></td>
 
                <td>Leakage factor of P2</td>
 
                <td>0.002</td>
 
                <td>-</td>
 
                <td>Assume the same as <i>l<sub>tetR</sub></i></td>
 
            </tr>
 
            <tr>
 
                <td><i>l<sub>tetR</sub></i></td>
 
                <td>Leakage factor of tetR</td>
 
                <td>0.002<sup>[3]</sup></td>
 
                <td>-</td>
 
                <td></td>
 
            </tr>
 
 
            <tr>
 
                <td><i>l<sub>plac</sub></i></td>
 
                <td>Leakage factor of plac</td>
 
                <td>0.002</td>
 
                <td>-</td>
 
                <td>Assume the same as <i>l<sub>tetR</sub></i></td>
 
            </tr>
 
            <tr>
 
                <td><i>S<sub>Lacl</sub></i></td>
 
                <td>length of Lacl</td>
 
                <td>371</td>
 
                <td>Amino Acid residues</td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>S<sub>tetR</sub></i></td>
 
                <td>length of tetR</td>
 
                <td>226</td>
 
                <td>Amino Acid residues</td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>S<sub>AcmA</sub></i></td>
 
                <td>length of AcmA</td>
 
                <td>438</td>
 
                <td>Amino Acid residues</td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>S</i></td>
 
                <td>Activation/Inactivation</td>
 
                <td>0/1<sup>[3]</sup></td>
 
                <td>-</td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>k<sub>Lacl</sub></i></td>
 
                <td>dissociation constant of plac</td>
 
                <td>6</td>
 
                <td>μmol</td>
 
                <td>Assume the same as <i>k<sub>tetR</sub></i></td>
 
            </tr>
 
            <tr>
 
                <td><i>k<sub>tetR</sub></i></td>
 
                <td>dissociation constant of ptet</td>
 
                <td>6<sup>[3]</sup></td>
 
                <td>μmol</td>
 
                <td></td>
 
            </tr>
 
            <tr>
 
                <td><i>n<sub>tetR</sub></i></td>
 
                <td>Hills coefficient</td>
 
                <td>3<sup>[3]</sup></td>
 
                <td>-</td>
 
                <td></td>
 
            </tr>
 
 
 
            <tr>
 
                <td><i>n<sub>Lacl</sub></i></td>
 
                <td>Hills coefficient</td>
 
                <td>3</td>
 
                <td>-</td>
 
                <td>Assume the same as <i>n<sub>tetR</sub></i></td>
 
            </tr>
 
        </table>
 
    </div>
 
<div class="table" align="center">
 
        <br>
 
        <table border="1" cellpadding="5">
 
            <colgroup>
 
                <col width="70">
 
                <col width="330">
 
            </colgroup>
 
 
            <tr>
 
                <th>Variables</th>
 
                <th>Concentration of </th>
 
            </tr>
 
 
            <tr>
 
                <td>LacIm</td>
 
                <td>Transcribed LacI</td>
 
            </tr>
 
 
            <tr>
 
                <td>tetRm</td>
 
                <td>Transcribed TetR</td>
 
            </tr>
 
 
            <tr>
 
                <td>AcmAm</td>
 
                <td>Transcribed AcmA</td>
 
            </tr>
 
 
            <tr>
 
                <td>GFnm</td>
 
                <td>Transcribed GF-17 (n=1,2,3)</td>
 
            </tr>
 
 
            <tr>
 
                <td>Granm</td>
 
                <td>Transcribed Grammistin-Pp1 (n=1,2,3)</td>
 
            </tr>
 
 
            <tr>
 
                <td>LLnm</td>
 
                <td>Transcribed LL-37 (n=1,2,3)</td>
 
            </tr>
 
 
            <tr>
 
                <td>LacI</td>
 
                <td>Translated Lacl</td>
 
            </tr>
 
 
            <tr>
 
                <td>tetR</td>
 
                <td>Translated tetR</td>
 
            </tr>
 
 
            <tr>
 
                <td>GFn</td>
 
                <td>Translated GF-17 (n=1,2,3)</td>
 
            </tr>
 
 
            <tr>
 
                <td>Gran</td>
 
                <td>Translated Grammistin-Pp1 (n=1,2,3)</td>
 
            </tr>
 
 
            <tr>
 
                <td>LLn</td>
 
                <td>Translated LL-37 (n=1,2,3)</td>
 
            </tr>
 
        </table>
 
    </div>
 
<p>By running the Matlab script, we obtained the results shown below.</p>
 
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/a/aa/Figure_3_State_values_.png" height=600 width=600>
 
<p class="form"><b>Fig 3.</b>&nbsp;&nbsp;&nbsp;&nbsp;State values of LacIm, GFnm, Granm, LLnm, tetRm, AcmAm, LacI, tetR, AcmA, GFn, Gran, LLn.</p>
 
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/f/f8/Individual_display_of_transcribed.png" height=600 width=600>
 
<p class="form"><b>Fig 4.</b>&nbsp;&nbsp;&nbsp;&nbsp;Individual display of transcribed LacIm, GFnm, Granm, LLnm, tetRm and AcmAm</p>
 
<img class="img-responsive center-block" src="https://static.igem.org/mediawiki/2017/c/cc/Figure_5_Individual_display_of_translated.png" height=600 width=600>
 
<p class="form"><b>Fig 5.</b>&nbsp;&nbsp;&nbsp;&nbsp;Individual display of translated LacI, tetR, AcmA, GFn, Gran and LLn.</p>
 
 
 
<p>From these graphs, we can make a general conclusion that the shift between the two states controlled by LacI and TetR takes at least 20 minutes. By the time the promoter P2 initiates the transcription and later efficiently translation of the mRNA of the tandem repeat genes (ll-37, gf-17, and grammistin-Pp1), the antimicrobial peptides are capable of being synthesized at high rates. When the repression of the promoter ptet (tetR) is relieved and the lysis gene acmA (AcmAm) starts to be transcribed, the antimicrobial peptides can be accumulated to high concentrations. Thereafter, enough amounts of antimicrobial peptides will be released to eradicate <i>Staphylococcus aureus</i> through the cell lysis.</p>
 
<p>References<br>
 
[1] Z. Cai, et al. “A simulation of Synthetic <i>agr</i> System in <i>E. coli</i>,”<i>in Bioinformatics Research and Applications</i>. Charlotte, NC: Springer, 2013, pp76-86.<br>
 
[2] NICE Expression System for <i>Lactococcus lactis</i>. MoBITec GmbH, Germany, 2010.<br>
 
[3] Team: TU-Delft (2013). <i>Timer Plus Sumo</i> [Online]. Available: <a href="https://2013.igem.org/Team:TU-Delft/Timer_Plus_Sumo">https://2013.igem.org/Team:TU-Delft/Timer_Plus_Sumo</a><br>
 
[4] C. Wu, H. Lee, and B. Chen, "Robust synthetic gene network design via library-based search method," Bioinformatics, vol. 27, pp. 2700-2706, Oct. 2011.</p>
 
  
 
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Revision as of 10:49, 27 October 2017

Lysis

Lysis

AcmA and the application of the toggle switch in our project

Figure 1.    Construction of the AMPs-Toggle Switch-Autolysin cassette. The upstream sensing device for S. aureus is omitted, which can be seen at the Sensing Device module.

Considering low efficiency and complexity of conventional secretory pathway, this year, we built a based-on-lysis system for aiming at releasing AMPs (antimicrobial peptides) efficiently. Therefore, we designed the acmA gene to be preceded by a bistable toggle switch so as to make cell lysis more regimented (see the reason in the following section). The switch we used was the lacI-tetR regulated expression system. The tetR linked downstream to plac is constituitively transcribed when free from the repression of the LacI repressor protein. This leads to the expression of TetR protein and subsequently an inhibitive effect on AcmA expression. Hence, under the normal situation in a host bacterial cell (such as L. lactis), the expression of AcmA autolysin is always inhibited. In this case, L. lactis can keep its integrity and maintain the capability of sensing S. aureus. Thereafter, with the initiation of P2 by phosphorylated AgrA (the mechanism can be seen at the Sensing Device module) and the expression of LacI, the switch turns on the ptet promoter and the expression of AcmA starts, as subsequently elicits the autolysis process and the accumulated AMPs burst out, culminating the extermination of the pathogen—S. aureus in the gut.


The reason of utilization of the lacI-tetR regulatory switch

Considering the prompt effect of AcmA on cell number (see Figure 2), after its induction, there might be a relatively early cell lysis (decrease in OD) occurring before AMPs are accumulated to a concentration at which pathogenic bacteria can be effectively killed. In the light of this finding, we adopted a lacI-tetR regulatory switch to postpone the autolysis process.

Figure 2.    

Buist’s demonstration of the effect of overexpression (A, B & C) of AcmA (1997). The optical density of the bacterial cells was measured at OD600. After the induction of AcmA with mitomycin at the stationary phase (10 hours in the graph), there was a conspicuous decrease in bacterial optical density during the next 2 days.
In Buist’s work, A, C, D respectively represents the L. lactis that contains different kind of plasmids harboring the acmA gene and B stands (which is not shown in the graph) for the bacteria that does not have the acmA gene.


AcmA in Lactococcus lactis

Enzymatic function

N-acetylmuramidase, AcmA, is an autolysin protein of Lactococcus lactis, which is responsible for cell wall hydrolysis at the stationary phase and is involved in cell division of this organism(Buist, et al., 1997). Consisting of two different domains in the structure, a glucosaminidase domain at the N-terminus and three so-called LysM domains at the C-terminus, the enzyme can specifically bind to peptidoglycan of L. lactis and of other Gram-positive bacteria. Peptidoglycan is a major component in the outer plasma membrane of Gram-positive bacteria and forms a mesh-like layer on the exterior of the cell. The known mechanism on the function of AcmA to date is that it can hydrolyze the N-acetylmuramyl-1,4-β-N-acetylglucosamine bonds in the peptidoglycan, whereby the peptidoglycan chain is broken and thus contribute to the cell lysis occurred to stationary L.lactis.

Physiological effects

The physiological functions of AcmA in the bacteria contribute to cell division, separation, motility, cell-wall turnover and other physiological processes (Smith, Blackman & Foster, 2000). However, overproduction of AcmA in L. lactis can cause cell autolysis, and hence its name (Buist, et al., 1997).


Merits and a possible concern of employing AcmA

Merits:

  1. Since AcmA is an endogenous molecule of Lactococcus lactis, the expression of AcmA in its original host is much more natural and applicable.
  2. Compared to other secretion systems, the autolysis process makes the secretion of AMPs more thorough because it does not require an energy consuming secretory system.

Concern:

As a broad-range autolysin due to its similar lysis mechanism to the other autolysin family members, i.e. hydrolyzing N-acetylmuramyl-1,4-β-N-acetylglucosamine bonds in the peptidoglycan, it is not clear whether AcmA has any adverse effects on the enteric microbiome. If AcmA lyse other gram-positive bacteria, the homeostasis of intestinal bacterial community may be affected.


Testing the expression of autolysin in L. lactis

Figure 3.    Construction of the autolysin part (Main elements in pNZ8148 haboring acmA, the detailed result of the assembly of BBa_K2309004 in the pNZ8148 plasmid can be seen at Figure 4)

Before we assembled all of our parts together, we tested each independent functional part. The acmA gene along with an upstream RBS was first joined to pNZ8148 which contains a nisin-inducible promoter and a terminator (Figure 3), and then the whole construct was transformed into the Lactococcus lactis NZ9000 strain. After the bacteria was cultured to the stationary phase, nisin was added to induce the expression of the AcmA protein. We employed an experimental procedure similar to Buist, et al. (1997). In their experiment (see their result at Figure 2, after induction with mitomycin, the bacteria cells at the stationary phase had a prominent decrease in optical density in several hours. (Buist et al., 1997)

Figure 4.    Integrated plasmid construction of the testing part (The detailed illustration of pNZ8148 harboring the acmA gene)


Testing Protocol

Nisin-induced lysis of L. lactis

  1. Inoculate a colony of pNZ8148-acmA transformed L. lactis and a colony of non-transformed L. lactis separately into M17 broth (containing 10 g/ml chloramphenicol) and incubate at 30℃ without shaking.
  2. Dilute the two overnight cultures 25-fold with M17 broth and transfer the diluted cultures in a 96-well plate, with 8 repeats for the transformant and 1 for the negative control. Put the plate in a plate reader, and read successive OD600 value until bacteria grow to the stationary phase.
  3. Induce the transformant bacteria with different concentrations (0.1-5 ng/ml) of nisin when the OD600 reaches 3. Continue to measure their optical density for 2 days (can be longer).

References

Buist, G., et al. (1997) ‘Autolysis of Lactococcus lactis Caused by Induced Overproduction of Its Major Autolysin, AcmA’, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, July 1997, pp. 2722-2728
Smith, Thomas J., Blackman, Steve A. and Foster, Simon J. (2000) ‘Autolysins of Bacillus subtilis: multiple enzymes with multiple functions’, Microbiology, 146, pp. 249-262, Emerald Insight [Online]. DOI: 10.1099/00221287-146-2-249

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