Difference between revisions of "Team:Tec-Monterrey/Description"

Latest revision as of 02:43, 18 October 2018

Overview

CRISPR-Cas technology has the capability of storing information. This year, iGEM team Tec-Monterrey aims to use the CRISPR-Cas system to store specific DNA sequences in the genome of E. coli in order to save information about the environment surrounding the bacteria. To make this possible, Cas1-Cas2 proteins, which create the protospacer acquisition in the CRISPR system, are used to insert a synthetic DNA sequence in the CRISPR array within the genome of the bacteria. This synthetic sequence is produced by a second system, called SCRIBE. The final step of our project is reading out the inserted DNA sequence. Specific primers for polymerase chain reaction (PCR) are used to amplify a section of the CRISPR array where the sequence is inserted. Taking together both systems, our project intends to act as a biological tape recorder capable of sensing external stimuli in the environment and storing their presence in the genome.

System Functionality

The construct shown in Figure 1 codes for the SCRIBE system adaptation.
This system generates single-stranded DNA inside of living cells in response to gene regulatory signals.
It is composed of 3 main components:

A reverse transcriptase protein
One
msr
RNA moiety which acts as a primer for the RT.
A second RNA moiety, called
msd
, which represents a template for the reverse transcriptase. This sequence contains the
message of interest
.

Figure 2: Retrotranscriptase action

This hybrid

RNA-ssDNA

molecule contains the

message of interest

.
This message has a PAM sequence, a crucial component for the identification by the CRISPR-Cas complex. (Figure 3)

Figure 4: Cas 1 and Cas 2 construct

These proteins (Figure 5) have to detect the PAM sequence in order to enable their function as endonucleases, in other words, their activity to work as scissors that cut DNA sequences.

Figure 6: Message insertion

Figure 1: Construct for SCRIBE system

Then, the retrotranscriptase acts on the

msd

(RNA) sequence and produces a hybrid RNA-ssDNA molecule called

msDNA

, as shown in Figure 2.

Figure 3: Message acquisition by Cas proteins

Here is where our beloved

CRISPR-Cas

complex comes into place. (Figure 4)

CRISPR-Cas

is a prokaryotic immune system that protects bacteria from phages and plasmids. With this complex, foreign DNA, in the form of spacers, is incorporated into the bacteria’s genome, specifically at the CRISPR locus. This acquisition of new DNA generates a memory of each “infection”.
Several Cas proteins are involved in this system, but Cas1 and Cas2 are the only proteins needed for acquisition of new spacers.

Figure 5: Cas 1 and Cas 2 complex

Once the PAM sequence is detected, the Cas1-Cas2 complex cuts the target sequence and integrates it into the bacteria’s genome, as shown in Figure 6.

References

Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Science. 358, 1457–1461 (2017).

A. Levy et al. Nature. 520, 505–510 (2015).

S. L. Shipman et al. Science. 353, aaf1175 (2016).

E. S. Lander. Cell. 164, 18–28 (2016).

Nuñez, J. K., Kranzusch, P. J., Noeske, J., Wright, A., Davies, C. & Doudna, J. Nat. Struct. Mol. Biol. 21, 528–534 (2014).

Díez-Villaseñor, C., Guzmán, N., Almendros, C., García-Martínez, J. & Mojica, F. J. RNA Biology. 10, 792-802 (2013).

Yosef, I., Goren, M. & Qimron, U. Nucleic Acids Research. 40, 5569–5576 (2012).

Yosef, I., Shitrit, D., Goren, M., Burstein, D., Pupko, T. & Qimron U. Proceedings of the National Academy of Sciences. 110, 14396-14401 (2013).

Nuñez, J. K. Mechanism of CRISPR–Cas Immunological Memory. (2016). Doctoral dissertation, UC Berkeley

Xue, C., Whitis, N., Sashital, D. Molecular Cell. 64, 826–834 (2016).

Church, G., Gao, Y., Kosuri, S. Science. 337, 1628 (2012).

Panda, D. et al. 3 Biotech. 8, 239 (2018).

Farzadfard, F., Lu, T. Science. 346 (2014).

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+<!------------------------------------------------------------------------------------------------------------------------>
+<!----------------------------------------------------- sidebar dots navigation ------------------------------------------>
+<!------------------------------------------------------------------------------------------------------------------------>
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+    <nav class="cd-vertical-nav">
+        <ul class="vertical-nav">
+            <li><a href="#page-top"><span class="label">Header<br><br></span></a></li>
+            <li><a href="#overview"><span class="label">Overview<br><br></span></a></li>
+            <li><a href="#system"><span class="label">System<br><br></span></a></li>
+            <li><a href="#references"><span class="label">References<br><br></span></a></li>
+        </ul>
+    </nav>
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    <header class="masthead" id="page-top">
@@ Line 54: / Line 156: @@
    <div class="articulo">
-     <section id="description" class="seccion-responsiva">
+     <section id="overview" class="seccion-responsiva">
        <div class="body-title">Overview</div>
-        CRISPR-Cas technology has the capability of storing information. This year, iGEM team Tec-Monterrey aims to use the CRISPR-Cas system to store specific DNA sequences in the genome of E. coli in order to save information about the environment surrounding the bacteria. To make this possible, Cas1-Cas2 proteins, which create the protospacer acquisition in the CRISPR system, are used to insert a synthetic DNA sequence in the CRISPR array within the genome of the bacteria. This synthetic sequence is produced by a second system, called SCRIBE. The final step of our project is reading out the inserted DNA sequence. Specific primers for polymerase chain reaction (PCR) are used to amplify a section of the CRISPR array where the sequence is inserted. Taking together both systems, our project intends to act as a biological tape recorder capable of sensing external stimuli in the environment and storing their presence in the genome.
+<br>
+        CRISPR-Cas technology has the capability of storing information. This year, iGEM team Tec-Monterrey aims to use the CRISPR-Cas system to store specific DNA sequences in the genome of <i>E. coli</i> in order to save information about the environment surrounding the bacteria. To make this possible, Cas1-Cas2 proteins, which create the protospacer acquisition in the CRISPR system, are used to insert a synthetic DNA sequence in the CRISPR array within the genome of the bacteria. This synthetic sequence is produced by a second system, called SCRIBE. The final step of our project is reading out the inserted DNA sequence. Specific primers for polymerase chain reaction (PCR) are used to amplify a section of the CRISPR array where the sequence is inserted. Taking together both systems, our project intends to act as a biological tape recorder capable of sensing external stimuli in the environment and storing their presence in the genome.
      </section>
-   <div class="body-title">System Functionality</div>
+   <div class="body-title" style="margin: 5%;">System Functionality</div>
-     <section class="container-description">
+     <section id="system" class="container-description">
        <div class="main-info-container-left">
          <div class="main-info" style="margin-top: 0;"> <!-- Primero -->
-           Construct that codes for the SCRIBE system adaptation.
+           The construct shown in Figure 1 codes for the SCRIBE system adaptation.
            <br>
            This system generates single-stranded DNA inside of living cells in response to gene regulatory signals.
@@ Line 74: / Line 177: @@
              </li>
              <li>
-               One msr RNA moiety which acts as a primer for the RT.
+               One <h4 class="azul">msr</h4> RNA moiety which acts as a primer for the RT.
              </li>
              <li>
-               A second RNA moiety, called msd, which represents a template for the reverse transcriptase. This sequence contains the message of interest.
+               A second RNA moiety, called <h4 class="verde">msd</h4>, which represents a template for the reverse transcriptase. This sequence contains the <h4 class="rosa">message of interest</h4>.
              </li>
            </ul>
-          <img src="https://static.igem.org/mediawiki/2018/d/df/T--Tec-Monterrey--Design_Scribe_System.png">
          </div>
-         <div class="main-info" style="margin-top: 50vh;"> <!-- Tercero -->
+         <div class="main-info" style="margin-top: 5%;"> <!-- Segundo -->
-          Hybrid RNA-ssDNA molecule which contains the message of interest.
+           <img class="gif" src="https://static.igem.org/mediawiki/2018/3/3a/T--Tec-Monterrey--Gif_RT.gif">
-          <br>
+          <div class="leyenda">Figure 2: Retrotranscriptase action</div>
-          This message has a PAM sequence, a crucial component for the identification by the CRISPR-Cas complex.
-           <img src="https://static.igem.org/mediawiki/2018/7/7a/T--Tec-Monterrey--Design_Scribe2.png">
          </div>
-         <div class="main-info" style="margin-top:85vh;"> <!-- Quinto -->
+        <br>
-           These proteins have to detect the PAM sequence in order to enable their function as endonucleases, in other words, their activity to work as scissors that cut DNA sequences.
+         <div class="main-info" style="margin-top:25%;"> <!-- Tercero -->
+           This hybrid <h4 class="azul">RNA-ssDNA</h4> molecule contains the <h4 class="rosa">message of interest</h4>.
            <br>
-           Crispr-cas complex is conformed by two dimers of cas 1 and one dime of cas 2, forming a hexamer.
+           This message has a PAM sequence, a crucial component for the identification by the CRISPR-Cas complex. (Figure 3)
-          <img src="https://static.igem.org/mediawiki/2018/4/42/T--Tec-Monterrey--Design_Cas1_2.png">
          </div>
-         <div class="main-info" style="margin-top: 50vh;"> <!-- Septimo -->
+         <div class="main-info" style="margin-top: 60%;"> <!-- Cuarto -->
+          <img class="gif" src="https://static.igem.org/mediawiki/2018/4/43/T--Tec-Monterrey--Gif_Cas1_2.gif">
+          <div class="leyenda">Figure 4: Cas 1 and Cas 2 construct</div>
+        </div>
+        <div class="main-info" style="margin-top:40%;"> <!-- Quinto -->
+          These proteins (Figure 5) have to detect the PAM sequence in order to enable their function as endonucleases, in other words, their activity to work as scissors that cut DNA sequences.
+        </div>
+        <div class="main-info" style="margin-top:20%;"> <!-- Sexto -->
            <img class="gif" src="https://static.igem.org/mediawiki/2018/8/8a/T--Tec-Monterrey--Gif_Integration.gif">
+          <div class="leyenda">Figure 6: Message insertion</div>
          </div>
        </div>
        <div class="main-info-container-right">
-         <div class="main-info"> <!-- Segundo -->
+         <div class="main-info" style="margin-top: 1%;"> <!-- Primero -->
-           The retrotranscriptase acts on the msd (RNA) sequence and produces a hybrid RNA-ssDNA molecule called msDNA.
+          <img class="gif" src="https://static.igem.org/mediawiki/2018/d/df/T--Tec-Monterrey--Design_Scribe_System.png">
-           <img class="gif" src="https://static.igem.org/mediawiki/2018/3/3a/T--Tec-Monterrey--Gif_RT.gif">
+          <div class="leyenda">Figure 1: Construct for SCRIBE system</div>
+        </div>
+        <div class="main-info" style="margin-top: 28%;"> <!-- Segundo -->
+           Then, the retrotranscriptase acts on the <h4 class="verde">msd</h4> (RNA) sequence and produces a hybrid RNA-ssDNA molecule called <h4 class="azul">msDNA</h4>, as shown in Figure 2.
+         </div>
+        <div class="main-info" style="margin-top: 35%;"> <!-- Tercero -->
+           <img class="gif" src="https://static.igem.org/mediawiki/2018/d/d3/T--Tec-Monterrey--Cas_Video.gif">
+          <div class="leyenda">Figure 3: Message acquisition by Cas proteins</div>
          </div>
-         <div class="main-info" style="margin-top: 50vh;"> <!-- Cuarto -->
+         <div class="main-info" style="margin-top: 28%;"> <!-- Cuarto -->
-           Here is where our loved CRISPR-Cas complex comes into place.
+           Here is where our beloved <h4 class="celeste">CRISPR-Cas</h4> complex comes into place. (Figure 4)
            <br>
-           CRISPR-Cas is a prokaryotic immune system that protects bacteria from phages and plasmids. With this complex, foreign DNA in the form of spacers is incorporated into the bacteria’s genome, specifically at the  CRISPR locus. This acquisition of new DNA generates a memory of each “infection”.
+           <h4 class="celeste">CRISPR-Cas</h4> is a prokaryotic immune system that protects bacteria from phages and plasmids. With this complex, <b>foreign DNA</b>, in the form of <b><i>spacers</i></b>, is incorporated into the bacteria’s genome, specifically at the  CRISPR locus. This <b><i>acquisition</i></b> of new DNA generates a memory of each “infection”.
            <br>
            Several Cas proteins are involved in this system, but Cas1 and Cas2 are the only proteins needed for acquisition of new spacers.
-          <br>
-          <img class="gif" src="https://static.igem.org/mediawiki/2018/4/43/T--Tec-Monterrey--Gif_Cas1_2.gif">
          </div>
-         <div class="main-info" style="margin-top: 50vh;"> <!-- Sexto -->
+         <div class="main-info" style="margin-top:20%;"> <!-- Quinto -->
-          Once the PAM sequence is detected, the Cas1-Cas2 complex cuts the target sequence and integrates it into the bacteria’s genome.
+           <img src="https://static.igem.org/mediawiki/2018/4/42/T--Tec-Monterrey--Design_Cas1_2.png">
-           <img class="gif" src="https://static.igem.org/mediawiki/2018/8/8a/T--Tec-Monterrey--Gif_Integration.gif">
+          <div class="leyenda">Figure 5: Cas 1 and Cas 2 complex</div>
          </div>
-         <div class="main-info"> <!-- Octavo -->
+         <div class="main-info" style="margin-top:35%;"> <!-- Sexto -->
+          Once the PAM sequence is detected, the Cas1-Cas2 complex cuts the target sequence and integrates it into the bacteria’s genome, as shown in Figure 6.
          </div>
        </div>
@@ Line 122: / Line 236: @@
      </section>
-     <section id="references-interLab" class="seccion-responsiva">
+     <section id="references" class="seccion-responsiva">
       	<div class="referencias">
            <div class="body-title">References</div>
+<br>
-          Amlinger, L., Hoekzema, M., Wagner, E. G. H., Koskiniemi, S. & Lundgren, M. Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. (2017).doi: 10.1038/s41598-017-10876-z.
+Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. <i>Science</i>. 358, 1457–1461 (2017).
-          <br>
+<br><br>
-          <br>
+A. Levy et al. <i>Nature</i>. 520, 505–510 (2015).
-          Díez-Villaseñor, C., Guzmán, N. M., Almendros, C., García-Martínez, J. & Mojica, F. J. M. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. (2013). doi:10.4161/rna.24023
+<br><br>
-          <br>
+S. L. Shipman et al. <i>Science</i>. 353, aaf1175 (2016).
-          <br>
+<br><br>
-          Farzadfard, F., & Lu, T. K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science. (2014). doi: 10.1126/science.1256272.
+E. S. Lander. <i>Cell</i>. 164, 18–28 (2016).
-          <br>
+<br><br>
-          <br>
+Nuñez, J. K., Kranzusch, P. J., Noeske, J., Wright, A., Davies, C. & Doudna, J. <i>Nat. Struct. Mol. Biol</i>. 21, 528–534 (2014).
-          Levy, A., Goren, M. G., Yosef, I., Auster, O., Manor, M., Amitai, G., Edgar, R., Qimron, U. & Sorek, R. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature. (2015). doi:10.1038/nature14302
+<br><br>
-          <br>
+Díez-Villaseñor, C., Guzmán, N., Almendros, C., García-Martínez, J. & Mojica, F. J. <i>RNA Biology</i>. 10, 792-802 (2013).
-          <br>
+<br><br>
-          Nuñez, J. K. Mechanism of CRISPR–Cas Immunological Memory. (2016). Doctoral dissertation, UC Berkeley
+Yosef, I., Goren, M. & Qimron, U. <i>Nucleic Acids Research</i>. 40, 5569–5576 (2012).
-          <br>
+<br><br>
-          <br>
+Yosef, I., Shitrit, D., Goren, M., Burstein, D., Pupko, T. & Qimron U. <i>Proceedings of the National Academy of Sciences</i>. 110, 14396-14401 (2013).
-          Nuñez, J. K., Kranzusch P, Noeske J, Wright A, Davies C, Doudna J. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat. Struct. Mol. Biol. (2014). doi:10.1038/nsmb.2820
+<br><br>
-          <br>
+Nuñez, J. K. Mechanism of CRISPR–Cas Immunological Memory. (2016). Doctoral dissertation, UC Berkeley
-          <br>
+<br><br>
-          Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Multiplex recording of cellular events over time on CRISPR biological tape. Science. (2017). doi:10.1126/science.aao0958
+Xue, C., Whitis, N., Sashital, D. <i>Molecular Cell</i>. 64, 826–834 (2016).
-          <br>
+<br><br>
-          <br>
+Church, G., Gao, Y., Kosuri, S. <i>Science</i>. 337, 1628 (2012).
-          Shipman, S. L., Nivala, J., Macklis, J. D., & Church, G. M. Molecular recordings by directed CRISPR spacer acquisition. Science. (2016). doi: 10.1126/science.aaf1175
+<br><br>
-          <br>
+Panda, D. et al. <i>3 Biotech</i>. 8, 239 (2018).
-          <br>
+<br><br>
-          Tang, W., & Liu, D. R. Rewritable multi-event analog recording in bacterial and mammalian cells. Science. (2018). doi: 10.1126/science.aap8992
+Farzadfard, F., Lu, T. <i>Science</i>. 346 (2014).
            <br>
            </div>

Difference between revisions of "Team:Tec-Monterrey/Description"

Latest revision as of 02:43, 18 October 2018

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msr

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