Team:SJTU-BioX-Shanghai/Part1 Connect

From 2014.igem.org

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<h2 id="testmethod:">Test Method:</h2>
<h2 id="testmethod:">Test Method:</h2>
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<li>pBluescript II KS(+) is chosen as the <strong><em>connector</em></strong> for test for several reasons: </li>
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<li>pBluescript II KS(+) is chosen as the <strong><em>connector</em></strong> for test for several reasons:  
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<p><center><img src="http://2014.igem.org/wiki/images/8/81/Pks_ii_original.png"></img></center></p>
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<p><center><img src="http://2014.igem.org/wiki/images/8/81/Pks_ii_original.png"></img></center></p></li>
<li>After checking the sequence of pBluescript II KS(+), we chose TTCGATATCAAGCT as the recognition sequence for test and designed TAL1.
<li>After checking the sequence of pBluescript II KS(+), we chose TTCGATATCAAGCT as the recognition sequence for test and designed TAL1.
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<p><center><img src="http://2014.igem.org/wiki/images/e/e6/Free_TAL1.png"></img></center></p>
<p><center><img src="http://2014.igem.org/wiki/images/e/e6/Free_TAL1.png"></img></center></p>
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<li>Considering our multiple-enzyme system may be applied in the following experiment, we choose pRSFDuet&#8211;1(<em>NOVAGEN</em>) as the expression vector.</li>
<li>Considering our multiple-enzyme system may be applied in the following experiment, we choose pRSFDuet&#8211;1(<em>NOVAGEN</em>) as the expression vector.</li>
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<p><center><img src="http://2014.igem.org/wiki/images/d/d3/Prsf.png"></img></center></p>
<p><center><img src="http://2014.igem.org/wiki/images/d/d3/Prsf.png"></img></center></p>
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<li>Similar to the cross-linked ChIP, we use formaldehyde to cross-link <strong><em>connectee</em></strong> and <strong><em>connector</em></strong></p>
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<li>Similar to the cross-linked ChIP, we use formaldehyde to cross-link <strong><em>connectee</em></strong> and <strong><em>connector</em></strong></p></li>
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<li>After that we do immunoprecipitation to get the protein-plasmid complex and digest protein</p>
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<li>After that we do immunoprecipitation to get the protein-plasmid complex and digest protein</p></li>
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<li>Finally, we use PCR to check whether there is any existing plasmid DNA.</p>
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<li>Finally, we use PCR to check whether there is any existing plasmid DNA.</p></li>
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<h2 id="aconvenientpart:">A Convenient Part:</h2>
<h2 id="aconvenientpart:">A Convenient Part:</h2>

Revision as of 05:40, 17 October 2014

Basic Test

——One Connectee Binds Connector

Connectee:


Schematic Introduction


At first, tests should be taken to check whether TAL can bind plasmid DNA in prokaryotic system. Here we use E.coli. As mentioned in the overview, in order for the protein to bind to the plasmid–the connector, we have designed two kinds of delicate fusion proteins–the connectee. One is anchored to the cell membrane, the other is free in the cytoplasm. Both of them consist of linkers and various sections, which are shown in the schematic diagrams below.

.
  1. TAL effector–a transactivator-like protein.
    TAL effector can bind DNA with target sequence. The 2012 Freiburg iGEM team has offered us a whole set of 96 TAL-protein direpeat bioparts, with which we are supposed to build functional TAL proteins. Since each TAL protein can identify a 14-nucleotide target sequence, the first and fourteenth nucleotide being Thymin, all the 96 parts can be used to identify more than 16 million different nucleotide sequences, which makes it very convenient for us to choose a sequence for the fusion protein to bind to.

  2. Membrane anchor system–ssDsbA-Lgt.
    ssDsbA is the signal sequence of DsbA which can direct the fusion protein to the periplasm. Lgt is a transmembrane protein.
    The membrane anchor system has been identified by iGEM12_SJTU-BioX-Shanghai.


  3. Fluorescent protein.
    CFP is a Cyan Fluorescent Protein which has an excitation peak at 439 nm and an emission peak at 476 nm.
    YFP is a Yellow Fluorescent Protein which has an excitation peak at 514 nm and an emission peak at 527 nm.
    mRFP is a Red Fluorescent Protein which has an excitation peak at 584 nm and an emission peak at 607 nm.


Connectee 1:

The first kind of connectee is designed to be tested on the membrane, which is composed of three major domains, membrane anchor system(ssDsbA-Lgt), mRFP and TAL effector.

The reason why we choose a membrane anchor is that:

  1. TAL could bind nucleoid which may bring some negative effect on bacteria growth.
  2. Membrane scaffold is a natural scaffold.
  3. Exogenous proteins often form inactive inclusion body when expressed in the prokaryotic system

The membrane anchor system (ssDsbA-Lgt) comes from BBa_K771000 designed by iGEM12_SJTU-BioX-Shanghai; mRFP comes from BBa_E1010 designed by Antiquity; TAL effector comes from TAL-Protein DiRepeats (BBa_K747000 to BBa_K747095) designed by iGEM12_Freiburg. We use Helical Linker to connect mRFP and Lgt, in accord with iGEM12_SJTU-BioX-Shanghai. While in consideration of any possible stereospecific blockade when TAL binds plasmid DNA, we choose Flexible Linker to connect Lgt and TAL effector.

Connectee 2:

The second kind of connectee is designed to be tested in the cytoplasm, which only contains TAL effector.

Connector:

As iGEM12_Freiburg designed, we can choose a 14-nucleotide-long Transactivator-like (TAL) protein TXXXXXXXXXXXXT to recognize the same sequence on the plasmid DNA.
The plasmid here we called connector.

The principle for choosing a TAL recognizing sequence:

I. It does not exist in expression vector

II. It does not exist in the sequence of connectee

Test Method:

  1. pBluescript II KS(+) is chosen as the connector for test for several reasons: I. High copy number
    II.Medium length—2961bp
    III. Easy to test whether binding a TAL may affect gene expression—lacI & blue-white spot screening

  2. After checking the sequence of pBluescript II KS(+), we chose TTCGATATCAAGCT as the recognition sequence for test and designed TAL1.

    Two kinds of connectee with TAL1 are shown below:


  3. Considering our multiple-enzyme system may be applied in the following experiment, we choose pRSFDuet–1(NOVAGEN) as the expression vector.
  4. Similar to the cross-linked ChIP, we use formaldehyde to cross-link connectee and connector

  5. After that we do immunoprecipitation to get the protein-plasmid complex and digest protein

  6. Finally, we use PCR to check whether there is any existing plasmid DNA.

A Convenient Part:

In order to be used cooperatively with TAL-Protein DiRepeats (BBa_K747000 to BBa_K747095), we also design a part named ssDsbA-mRFP-Lgt-TAL adapter-His Tag (BBa_K1453000).

This part consists of T1 sequence, T14 sequence and two sites for type II restriction enzyme BsmBI. When digested with BsmBI, this part can produce two sticky-ends. One can complement with the first TAL-Protein DiRepeat (Bba_K747000 to Bba_K747015) at 5’ of the sequence, while the other can complement with the sixth TAL-Protein DiRepeat (Bba_K747080 to Bba_K747095) at 3’.

With the rest of TAL-Protein DiRepeats (Bba_K747016 to Bba_K747079), users can synthesize a 14-nucleotide-long Transactivator-like (TAL) protein to recognize their own connector and design their own polymerization. (Golden Gate Cloning)

For more details about membrane anchor, please view this page.

For more details about TAL and Golden Gate Cloning, please view this page.

References:

  1. GONTERO, Brigitte, María Luz CÁRDENAS, and Jacques RICARD. “A functional five‐enzyme complex of chloroplasts involved in the Calvin cycle.” European journal of biochemistry 173.2 (1988): 437–443.
  2. Bogdanove, Adam J., and Daniel F. Voytas. “TAL effector: customizable proteins for DNA targeting.” Science 333.6051 (2011): 1843–1846.
  3. Deng, Dong, et al. “Structural basis for sequence-specific recognition of DNA by TAL effector.” Science 335.6069 (2012): 720–723.
  4. Pailler, J., W. Aucher, et al. (2012). “Phosphatidylglycerol: prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane.” Journal of bacteriology 194(9): 2142–2151.
  5. Schierle, C. F., M. Berkmen, et al. (2003). “The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway.” Journal of bacteriology 185(19): 5706–5713.
  6. Scholze, H. & Boch, J. TAL effector are remote controls for gene activation. ‘‘Current Opinion in Microbiology’’ 14, 47–53 (2011).

  7. Moscou, M. J. & Bogdanove, A. J. A Simple Cipher Governs DNA Recognition by TAL Effector. ‘‘Science’’ 326, 1501–1501 (2009).
  8. Conrado, R. J., G. C. Wu, et al. (2012). “DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency.” Nucleic acids research 40(4): 1879–1889.
  9. Yang, Zhong, et al. “Highly efficient production of soluble proteins from insoluble inclusion bodies by a two-step-denaturing and refolding method.” PloS one 6.7 (2011): e22981.