Team:Yale/Results

From 2014.igem.org

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<li><strong>T7 RNA polymerase design and creation</strong><p>
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<li><strong>T7 RNA polymerase design and creation</strong>
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The T7 Riboregulation System works by a “three-lock system.” The first lock is the cis- repressing RNA (crRNA), which is induced bysopropyl β-D-1-thiogalactopyranoside (IPTG). The second lock is the trans-activating RNA (taRNA), which is induced by anhydrous tetracycline (ATC).  If the taRNA is unlocked, it will bind to the crRNA, removing the hairpin and making the ribosomal binding site accessible for ribosomal binding, leading to translation of a specific protein, in this case, T7 RNA Polymerase. This system was initially developed by Dr. Farren Isaacs, and has been shown to work with chloramphenicol resistance (chloramphenical acetyl transferase gene) in place of the T7 gene. The plasmid was synthesized via Gibson assembly, and confirmed by sequencing.
The T7 Riboregulation System works by a “three-lock system.” The first lock is the cis- repressing RNA (crRNA), which is induced bysopropyl β-D-1-thiogalactopyranoside (IPTG). The second lock is the trans-activating RNA (taRNA), which is induced by anhydrous tetracycline (ATC).  If the taRNA is unlocked, it will bind to the crRNA, removing the hairpin and making the ribosomal binding site accessible for ribosomal binding, leading to translation of a specific protein, in this case, T7 RNA Polymerase. This system was initially developed by Dr. Farren Isaacs, and has been shown to work with chloramphenicol resistance (chloramphenical acetyl transferase gene) in place of the T7 gene. The plasmid was synthesized via Gibson assembly, and confirmed by sequencing.
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<li><strong>Functional Assays for Riboregulated T7 system</strong>  
<li><strong>Functional Assays for Riboregulated T7 system</strong>  
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<p>The P<sub>LlacO</sub> promoter controls the expression of the crRNA and is induced by IPTG. As specified above, we will use artificial riboregulatory elements to restrict translation of the mRNA sequence encoding the T7 RNA Polymerase. Specifically, the crRNA sequence will be inserted downstream of the promoter driving T7 RNA Polymerase and upstream of the ribosomal binding site (RBS).  
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<p>A second promoter, P<sub>LtetO</sub>, which is induced by ATC, will express the taRNA capable of interacting with the crRNA and releasing the RBS for docking of the T7 RNA polymerase. This will expose the RBS and allow for translation of T7 RNA Polymerase. Once the T7 RNA Polymerase is expressed, it can then bind to the T7 Promoter and lead to the expression of the gene of interest, such as LL-37. The ribo-regulated T7 RNA Polymerase (formally known as α12c) and the TolC selection marker will be ultimately incorporated into a conjugative plasmid and into the genome of <i>E. coli</i> to control for copy number. In this way, the cell can better regulate protein expression. A second pZ plasmid will contain the gene of interest expressed by a T7 promoter. Finally, the third plasmid will contain the OTS.
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Experimental plan for the GFP fluorescence assay testing the efficacy of the T7 riboregulation system. The T7 riboregulation system, pZE21_A12C_T7RNA, would express sfGFP behind a T7 promoter, in the plasmid pZA21. Either plasmid, and both plasmids together, were transformed into ECNR2 and induced with either IPTG and ATC. ECNR2 is the ancestral strain. A positive control was the same pZA21_T7sfGFP plasmid in ECNR2, and the same T7 RNA polymerase gene inserted in a regular pZE21 plasmid with a pLtetO promoter, and a negative control with the pZA21_T7sfGFP in ECNR2 without any plasmid that contains T7 RNA.</p>
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<p>The benefit of this type of system is that it is robust and can be easily re-engineered, portable in the form of plasmids, compatible across multiple <i>E. coli</i> strains, and efficient in that it does not require the cell to expend more energy on the constitutive synthesis of another protein. We hypothesize that by utilizing these two levels of control, we will be able to reduce the expression of T7 RNA polymerase and produce a system with zero basal expression of the gene of interest.</p></ul>
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<img src="https://static.igem.org/mediawiki/2014/f/ff/Yale_figure8.png">
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<i><strong>Figure 3.</strong> The functionalities behind the GFP assay.</i></center></p>
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<img src="https://static.igem.org/mediawiki/2014/0/03/Yale_figure9.png">
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<i><strong>Figure 4.</strong> Conformational assay to test the functionality of the pZA21_T7sfGFP, which is sfGFP placed behind the T7 promoter. The plasmid was transformed into a BL21(DE3) strain, which constitutively expresses T7 RNA polymerase. The strain, as well as untransformed BL21(DE3), were grown overnight and assayed using a Synergy H1 Biotek Platereader. </i></center></p>
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<img src="https://static.igem.org/mediawiki/2014/3/37/Yale_table_1.png">
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<i><strong>Table 1.</strong> Experimental conditions for the GFP assay. Each plasmid combination was paired with each inducer combination, and the conditions were made in sextuplicate.</i></center></p>
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Revision as of 03:02, 18 October 2014

Results

T7 Riboregulation System

  1. T7 RNA polymerase design and creation

    The T7 Riboregulation System works by a “three-lock system.” The first lock is the cis- repressing RNA (crRNA), which is induced bysopropyl β-D-1-thiogalactopyranoside (IPTG). The second lock is the trans-activating RNA (taRNA), which is induced by anhydrous tetracycline (ATC). If the taRNA is unlocked, it will bind to the crRNA, removing the hairpin and making the ribosomal binding site accessible for ribosomal binding, leading to translation of a specific protein, in this case, T7 RNA Polymerase. This system was initially developed by Dr. Farren Isaacs, and has been shown to work with chloramphenicol resistance (chloramphenical acetyl transferase gene) in place of the T7 gene. The plasmid was synthesized via Gibson assembly, and confirmed by sequencing.

    Figure 1. Preliminary gel screening of Mach 1 strains containing transformed pZE21_A12C_T7RNA plasmids created via Gibson Assembly.

    Figure 2. Sequencing data for T7 RNA polymerase construct, upstream of the taRNA and crRNA system. Image made using geneious.

    Currently the riboregulation system may have an issue with the internal T7 sequence, and while sequencing has been done, no successful data has been obtained.

  2. Functional Assays for Riboregulated T7 system

    Experimental plan for the GFP fluorescence assay testing the efficacy of the T7 riboregulation system. The T7 riboregulation system, pZE21_A12C_T7RNA, would express sfGFP behind a T7 promoter, in the plasmid pZA21. Either plasmid, and both plasmids together, were transformed into ECNR2 and induced with either IPTG and ATC. ECNR2 is the ancestral strain. A positive control was the same pZA21_T7sfGFP plasmid in ECNR2, and the same T7 RNA polymerase gene inserted in a regular pZE21 plasmid with a pLtetO promoter, and a negative control with the pZA21_T7sfGFP in ECNR2 without any plasmid that contains T7 RNA.

    Figure 3. The functionalities behind the GFP assay.

    Figure 4. Conformational assay to test the functionality of the pZA21_T7sfGFP, which is sfGFP placed behind the T7 promoter. The plasmid was transformed into a BL21(DE3) strain, which constitutively expresses T7 RNA polymerase. The strain, as well as untransformed BL21(DE3), were grown overnight and assayed using a Synergy H1 Biotek Platereader.

    Table 1. Experimental conditions for the GFP assay. Each plasmid combination was paired with each inducer combination, and the conditions were made in sextuplicate.

Adhesion Testing

  1. Mass Retention of Mussel Adhesion Proteins (MAPs) Under Stress

    Preliminary proof of concept testing was conducted on a commercially available MAP-based product known as Cell-Tak TM. Cell-TakTM is designed to facilitate cell adhesion to normally non-biocompatible surfaces such as microscope slides and petri dishes. We deposited ~20 µg films of Cell-Tak onto borosilicate substrates and proceeded to erode them under deionized H2O and 5% acetic acid. The results from this experiment are presented below and illustrate the design of our assay to test a variety of solvent and erosion conditions on MAP films. A balance that can read to uncertainties of 1 µg was used to determine the mass of protein remaining after subjecting the substrate to erosion. An exponential decay curve was fitted to these experiments giving decay rates of 0.002 µg/pass and 0.046 µg/pass for deionized H2O and 5% acetic acid, respectively. As lower pH reverses the coordination of L-DOPA, it is expected that the acidic conditions engender the higher rate of decay. This experiment presents a preliminary result that validates our ability to apply erosion onto MAP-coated surfaces. We intend to apply a similar protocol to metal and plastic surfaces as well as erode surfaces under different pH conditions to provide a more comprehensive picture of the optimal conditions for mussel adhesion.

    Figure X. (A) The erosion of Cell-Tak TM under conditions of DI water erosion. (B) The erosion of Cell-Tak TM under conditions of 5% acetic acid erosion.

  2. Determination of Surface Energies of MAP Films

    A contact angle measurement of a Cell-TakTM was recorded and served as an indication for presence of peptide on surfaces. The contact angle is measured between the surface of the drop and the table-top. Larger contact angles are indicative of more hydrophobic surfaces while shallower contact angles correspond to more wettable surfaces. A contact angle of 25.053º was obtained between an untreated silica substrate and a 2 µL drop of DI H2O. However, when surfaces were treated with the MAP, the contact angle increased to 62.007º, indicative of an increase in the hydrophobicity of our substrate. This result validates the evolutionary need for mussels to secrete proteins that are resistant to water in order to survive and anchor themselves in constantly wet environments.

    Figure X.(A) The profile photograph of a drop on an untreated silica substrate used for contact angle determination. (B) The profile photograph of a Cell-Tak TM treated surface used for contact angle determination.

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