Team:Bologna/Project

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T-REX Project

(Trans-Repressor of Expression)

The aim of our project is the design of a standard device to control the synthesis of any protein of interest. This "general-purpose" device, implemented in E. coli, acts at the translational level to allow silencing of protein expression faster than using regulated promoters. We named this device T-REX (Trans Repressor of Expression).
T-REX consists of two new BioBricks:

CIS-repressing, to be assembled upstream of the target protein coding sequence. It contains a ribosomal binding site (RBS);

TRANS-repressor, complementary to the CIS-repressing and placed under the control of a different promoter. For a better repressive effectiveness, the TRANS sequence contains also a RBS cover, released in two versions of different length (either 4 or 7 nucleotides).
The longer version covers also 3 nucleotides of the Shine-Dalgarno sequence.

Transcription of the target gene yields a mRNA strand - containing the CIS-repressing sequence at its 5' end - available for translation into protein by ribosomes (see Fig. 1, left panel). When the promoter controlling the TRANS coding sequence is active, it drives the transcription of an oligoribonucleotide complementary to the CIS mRNA sequence. The TRANS/CIS RNA duplex prevents ribosomes from binding to RBS on target mRNA, thus silencing protein synthesis. The amount of the TRANS-repressor regulates the rate of translation of the target mRNA (see Fig. 1, right panel)

Figure 1 - T-REX device

CIS and TRANS Parts Design

To identify CIS-repressing and TRANS-repressor DNA sequences, we developed BASER software. We used it to seek for two complementary 50bp non-coding sequences, whose transcribed RNAs:
a) feature maximal free energy in the secondary structure (i.e. reducing the probability of its intra-molecular annealing);
b) have minimal unwanted interactions with genomic mRNA;
c) present a minimal probability of partial/shifted hybridization with complementary strands.

Here below are the CIS-repressing and TRANS-repressor sequences. More details about BASER and its functioning can be found in the software section.

CIS-repressing
Prefix	non-coding TRANS target	RBS	Suffix
GAATTCGCGGCCGCTTCTAGAG	AACACAAACTATCACTTTAACAACACATTACATATACATTAAAATATTAC	AAAGAGGAGAAA	TACTAGTAGCGGCCGCTGCAG

TRANS-repressor (4)
Prefix	RBS cover	non-coding TRANS	Suffix
GAATTCGCGGCCGCTTCTAGAG	CTTT	GTAATATTTTAATGTATATGTAATGTGTTGTTAAAGTGATAGTTTGTGTT	TACTAGTAGCGGCCGCTGCAG

TRANS-repressor (7)
Prefix	RBS cover	non-coding TRANS	Suffix
GAATTCGCGGCCGCTTCTAGAG	CCTCTTT	GTAATATTTTAATGTATATGTAATGTGTTGTTAAAGTGATAGTTTGTGTT	TACTAGTAGCGGCCGCTGCAG

Testing Circuit

In order to test our T-REX device, we developed the following genetic circuit (Fig. 2):

Figure 2 - Genetic Circuit to test CIS and TRANS' mRNA functionality

The CIS-repressing sequence is assembled upstream of lac I (BBa_C0012), therefore the synthesis of LacI should be silenced/damped by the constitutively transcribed TRANS-repressor mRNA. To detect silencing of LacI, due to the action of T-REX, we realized a new inverter (BBa_K201001) consisting of a promoter regulated by LacI (BBa_K201008) and a GFP reporter (BBa_J04031).
We expect that a TRANS-repressor oligoribonucleotide with high affinity to CIS-repressing mRNA, inhibits the translation of LacI and then determines a maximally expressed GFP. Otherwise, in case of low TRANS/CIS affinity one should expect partially (or completely) repressed GFP expression.
To maximize the probability to silence the CIS transcript and switch on the GFP, we decided to use a high copy number (HCN) plasmid (pSB1A2) for the TRANS-repressor and a low copy number (LCN) plasmid (pSB3K3) for the LacI generator.
If the GFP inverter is unable to reveal the LacI reduction due to T-REX action, because of a high level of the free LacI concentration, IPTG can be supplied to reduce free LacI. In fact, the sensitivity of the GFP inverter to LacI variations depends on free LacI concentration. Using IPTG is thus possible to set actual LacI value in the region where the inverter has the highest sensitivity.

Mathematical Model

To characterize the T-REX device, we developed a mathematical model of the whole testing circuit considering the interaction between all its parts. Model equations were implemented in Simulink (Fig. 4) to simulate the circuit and it intermediate parts. After the identification of model parameters on the data obtained from experiments with the intermediate parts, the GFP level as a function of the TRANS/CIS affinity was predicted by simulating the whole testing circuit .

Figure 4 - Simulink Model

Characterization of Parts

The Testing Circuit is constituted by intermediate parts that were experimentally characterized to obtain date for the model paramiter identification. Details of this characterization are available in the wet-lab section.

@@ Line 7: / Line 7: @@
 <br><br>
 <font face="Calibri" font size="4" color="#000000">
-The project aims to implement a <b>protein synthesis regulation system</b> in <i>Escherichia coli</i> that acts at translational level, regardless of the target gene. This <b>"general-purpose"</b> device allows a faster control of protein expression.<br><br>
+The aim of our project is the design of a standard device to control the synthesis of any protein of interest. This "general-purpose" device, implemented in <i>E. coli</i>, acts at the translational level to allow silencing of protein expression faster than using regulated promoters. We named this device <b>T-REX</b> (<b>T</b>rans <b>R</b>epressor of <b>Ex</b>pression). <br>T-REX consists of two new BioBricks:
-The device was named <b>T-Rex</b> (<b>T</b>rans <b>R</b>epressor of <b>Ex</b>pression). It consists of two new BioBricks:
 <br><br>
 <ul>
-<li><font color="#000080"><b>CIS-repressing</b></font>, to be assembled upstream of the target protein coding sequence; it contains a ribosomal binding site; <font color="#228b22"><b>(RBS)</b></font>
+<li><font color="#000080"><b>CIS-repressing</b></font>, to be assembled upstream of the target protein coding sequence. It contains a ribosomal binding site <font color="#228b22"><b>(RBS)</b></font>;
 </ul>
-<br>
 <ul>
-<li><font color="#000080"><b>TRANS-repressor</b></font>, to be placed under the control of a different promoter; it is complementary to the CIS-repressing, and contains a <font color="#228b22"><b>RBS cover</b></font> in two versions of different length (4 and 7 nucleotides). <br>The longer version covers also 3 nucleotides of the Shine-Dalgarno sequence.
+<li><font color="#000080"><b>TRANS-repressor</b></font>, complementary to the CIS-repressing and placed under the control of a different promoter.  For a better repressive effectiveness, the TRANS sequence contains also a <font color="#228b22"><b>RBS cover</b></font>, released in two versions of different length (either 4 or 7 nucleotides). <br>The longer version covers also 3 nucleotides of the Shine-Dalgarno sequence.
 </ul>
 <br>
-Transcription of the target gene produces a mRNA strand, starting with the Cis element, which is translated into proteins by ribosome. Trans’ promoter induction produces a transcript that binds with the Cis part. The <b>RNA duplex</b> prevents ribosome from binding to RBS, <b>repressing protein synthesis</b>. Thus, the TRANS-repressor amount regulates the gene mRNA translation rate.
+Transcription of the target gene yields a mRNA strand - containing the CIS-repressing sequence at its 5' end - available for translation into protein by ribosomes (<i>see Fig. 1, left panel</i>). When the promoter controlling the TRANS coding sequence is active, it drives the transcription of an oligoribonucleotide complementary to the CIS mRNA sequence. The TRANS/CIS <b>RNA duplex</b> prevents ribosomes from binding to RBS on target mRNA, thus <b>silencing protein synthesis</b>. The amount of the TRANS-repressor regulates the rate of translation of the target mRNA (<i>see Fig. 1, right panel</i>)
 </html>
-<br><br><br>
-[[Image:project3b.png|center|950px|]]
 <br><br>
+[[Image:project3b.png|center|950px|thumb|<center>Figure 1 - T-REX device</center>]]
+<br><br>
+<font face="Calibri" font size="5" color="#000000"><b>CIS and TRANS Parts Design</b>
+<br><br>
+<font face="Calibri" font size="4" color="#000000">
 <html>
-<font face="Calibri" font size="5" color="#000000"><b>The Parts</b>
+<font face="Calibri" font size="4" color="#000000">
+To identify CIS-repressing and TRANS-repressor DNA sequences, we developed <a href="https://2009.igem.org/Team:Bologna/Software">BASER</a> software. We used it to seek for two complementary 50bp non-coding sequences, whose transcribed RNAs:<br>
+a) feature maximal free energy in the secondary structure (i.e. reducing the probability of its intra-molecular annealing); <br>
+b) have minimal unwanted interactions with genomic mRNA; <br>
+c) present a minimal probability of partial/shifted hybridization with complementary strands. <br><br>
+Here below are the CIS-repressing and TRANS-repressor sequences. More details about BASER and its functioning can be found in the <html><a href="https://2009.igem.org/Team:Bologna/Software">software section</a>.</html>
 <br><br>
-<font face="Calibri" font size="4" color="#000000">
-We choose to use <b>50bp non-coding sequences</b> as CIS-repressing and TRANS-repressor complementary parts, and we developed a bioinformatic tool (<a href="https://2009.igem.org/Team:Bologna/Software">BASER</a>) to design them, in order to minimize <b>unwanted interactions with genomic mRNA</b>, reduce the probability of <b>intra-molecular annealing</b> and of <b>partial/shifted hybridization.</b>
-<br><br><br>
-</html>
 {| align="center"
@@ Line 76: / Line 77: @@
 | <font size="2" color="#228b22">TACTAGTAGCGGCCGCTGCAG
 |}
 <br><br>
 <html>
-<font face="Calibri" font size="5" color="#000000"><b>The Genetic Circuits</b>
+<font face="Calibri" font size="5" color="#000000"><b>Testing Circuit</b>
 <br><br>
 <font face="Calibri" font size="4" color="#000000">
-In order to test and characterize our T-REX device, we developed the following genetic circuit:
+In order to test our T-REX device, we developed the following genetic circuit (Fig. 2):
 </html>
 <br><br>
-[[Image:circuit2.jpg|center|900px]]
+[[Image:circuit2OK.jpg|center|900px|thumb|<center>Figure 2 - Genetic Circuit to test CIS and TRANS' mRNA functionality</center>]]
-<br><br>
-The circuit above represents the ON configuration of our T-Rex device: TRANS-repressor is constitutively expressed and CIS-repressing is assembled upstream the LacI gene (BBa_C0012), while the reporter protein GFP (BBa_J04031) is assembled under the control of another promoter, regulated by LacI natural operator O2.
 <br>
-CIS-repressing and TRANS-repressor mRNAs bind together, preventing LacI translation and allowing GFP production.
+The CIS-repressing sequence is assembled upstream of <i>lac</i> I (BBa_C0012), therefore the synthesis of LacI should be silenced/damped by the constitutively transcribed TRANS-repressor mRNA. To detect silencing of LacI, due to the action of T-REX, we realized a new inverter (BBa_K201001) consisting of  a promoter regulated by LacI (BBa_K201008) and a GFP reporter (BBa_J04031).<br>
-<br>
+We expect that a TRANS-repressor oligoribonucleotide with high affinity to CIS-repressing mRNA, inhibits the translation of LacI and then determines a maximally expressed GFP. Otherwise, in case of low TRANS/CIS affinity one should expect partially (or completely) repressed GFP expression.<br>
-Using some IPTG, the repression action of T-Rex become easily, because the concentration of free LacI in the cells is reduced.
+To maximize the probability to silence the CIS transcript and switch on the GFP, we decided to use a high copy number (HCN) plasmid (pSB1A2) for the TRANS-repressor and a low copy number (LCN) plasmid (pSB3K3) for the LacI generator. <br>If the GFP inverter is unable to reveal the LacI reduction due to T-REX action, because of a high level of the free LacI concentration, IPTG can be supplied to reduce free LacI. In fact, the sensitivity of the GFP inverter to LacI variations depends on free LacI concentration. Using IPTG is thus possible to set actual LacI value in the region where the inverter has the highest sensitivity.
 <br><br>
-To prove T-Rex repression, GFP production level must be compared with the level produced by the OFF configuration of our T-Rex device, that is the same circuit in absence of TRANS-repressor:
+<font face="Calibri" font size="5" color="#000000"><b>Mathematical Model</b>
-<br><br>
-[[Image:OffCircuit_tag.png|center|900px]]
-<br><br>
-In this second case, LacI is regularly translated and, binding with its O2 natural operator, it blocks GFP production.
-<br>
-We choose to use a low copy number plasmid and a weak promoter (J23118) for the CIS-repressing/LacI production, and a high copy number plasmid and a strong promoter (J23100) for the TRANS-repressing, to make reporter production's variations easily to be detected.
-<br>
-<br>
-<br>
-<br>
-Before realizing the whole T-Rex device, we decided to perform some preliminary tests, in order to characterize every single BioBrick involved in it.
-<br>
-<br>
-<html>
-<font face="Calibri" font size="5" color="#000000"><b><i>High</i> vs <i>Low to Medium</i> copy number plasmids </b>
 <br><br>
 <font face="Calibri" font size="4" color="#000000">
-</html>
+To characterize the T-REX device, we developed a [https://2009.igem.org/Team:Bologna/Modeling mathematical model] of the whole testing circuit considering the interaction between all its parts. Model equations were implemented in Simulink (Fig. 4) to simulate the circuit and it intermediate parts. After the identification of model parameters on the data obtained from experiments with the intermediate parts, the GFP level as a function of the TRANS/CIS affinity  was predicted by simulating the whole testing circuit .
-* In order to characterize the difference between the high copy number pSB1A2 and the low to medium copy number pSB3K3, we analyzed production of I13504 (wild type GFP) under J23118 promoter (1429):
+[[Image:ModelSandro.png|center|900px|thumb|<center>Figure 4 - Simulink Model</center>]]
-<br>
-{|align="center"
-|[[Image:1429GFP_openloop_hc.png|center|450 px]]
-|[[Image:1429GFP_openloop_lc.png|center|450 px]]
-|}
-<center>
-Results can be found in the [https://2009.igem.org/Team:Bologna/Characterization#Plasmid_copy_number_characterization wet-lab section] </center>
-<br>
-<br>
-<html>
-<font face="Calibri" font size="5" color="#000000"><b><i>Strong</i> vs <i>Weak</i> promoter </b>
 <br><br>
-<font face="Calibri" font size="4" color="#000000">
+<font face="Calibri" font size="5" color="#000000"><b>Characterization of Parts</b></font>
-</html>
-* In order to characterize the different production of the high copy number pSB1A2 and the low to medium copy number pSB3K3, we analyzed I13504 (wild type GFP) under J23118 promoter (1429):
-<br>
-{|align="center"
-|[[Image:1429GFP_openloop_hc.png|center|450 px]]
-|[[Image:1429GFP_openloop_lc.png|center|450 px]]
-|}
-<center>
-Results can be found in the [https://2009.igem.org/Team:Bologna/Characterization#Plasmid_copy_number_characterization wet-lab section] </center>
 <br><br>
+The Testing Circuit is constituted by intermediate parts that were experimentally characterized to obtain date for the model paramiter identification. Details of this characterization are available in the [https://2009.igem.org/Team:Bologna/Wetlab wet-lab] section.
-<br><br><br><br>
-<br><br><br><br>
-<br><br><br><br>
-every part of the final device in order to obtain some information and values concerning the processes we were analyzing. All studies conducted by us can be found in detail in the [[Team:Bologna/Wetlab|Wetlab]] section.
 <br><br>
-* Then we analyzed the [https://2009.igem.org/Team:Bologna/Characterization#Promoter_characterization difference in strength of the two promoters] J23100 (2547) and J23118 (1429) studying the ratio of fluorescence. To do this we created these two circuits where the only different element was the promoter. Our goal was to find a ratio of fluorescence between the two circuits as close as possible to 1.78 (ratio between 2547 and 1429).
-{|align="center"
-|[[Image:2547GFP_open_tag.png|center|450 px]]
-|[[Image:1429GFP_openloop_hc_tag.png|center|450 px]]
-|}
-<br><br>
-* After that we needed to know if the [https://2009.igem.org/Team:Bologna/Characterization#GFP_production_in_absence_/_presence_of_operator_Ox presence of the Ox operator] could influence or not the production of GFP. We tested two open loop GFP circuits for each promoter, one with the operator Ox and another without. We wanted to obtain the same GFP production in the two circuits built with the promoter 2547 and  in the two circuits built with the 1429 one.
-{|align="center"
-|[[Image:2547GFP_open_tag.png|center|450 px]]
-|[[Image:2547GFPOx_open_tag.png|center|450 px]]
-|}
-{|align="center"
-|[[Image:1429GFP_openloop_hc_tag.png|center|450 px]]
-|[[Image:1429GFP_Ox_tag.png|center|450 px]]
-|}
-<br><br>
-* We started to assemble circuits with the simultaneous presence of GFP and LACI to assess their operation and their interaction with each other. The first one is a closed-loop configuration where GFP expression is auto-regulated by the synthesis of LACI repressor protein; we used different IPTG induction concentration to evaluate the LACI repression strength. The second is an open-loop configuration lacking the operator site, so we can determine if there is repression in absence of Ox operator.
-</font>
-[[Image:LACi_GFP2_tag.png|center|750 px]]
-<br>
-[[Image:openLACi_GFP_tag.png|center|750 px]]