Team:Bologna

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= Project Summary =
= Project Summary =
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'''Which is our idea?'''
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'''Our idea'''
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The project aims to implement a protein synthesis regulation system in ''Escherichia coli'' that is independent from regulated protein and acts at translational level, to make the control action faster. This "general-purpose" device was named '''T-Rex''' ('''T'''rans '''R'''epressor of '''Ex'''pression). It consists of two new BioBricks: '''Trans-repressor''' and '''Cis-repressing'''.
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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).  
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'''How T-REX works'''
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'''How can we achieve this?'''
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The TRANS-repressor is a non-coding DNA sequence, the transcript of which acts as a silencer of the CIS-repressing RNA target. This target includes a region complementary to the sequence of the TRANS-repressor antisense, ends with a ribosome binding site (RBS), and is assembled upstream of the coding sequence of the gene to be silenced. Upon binding of TRANS-repressor and CIS-repressing RNAs, the access to RBS by ribosomes is hampered, silencing translation from the downstream transcript. Accordingly, the amount of TRANS-repressor controls the translation rate of the regulated gene.
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The device consists of two new BioBricks:
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<li><font color="#000080"><b>CIS-repressing</b></font>, to be assembled upstream of the target coding sequence.
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<li><font color="#000080"><b>TRANS-repressor</b></font>, complementary to the CIS-repressing and placed under the control of a different promoter.  
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The TRANS-repressor sequence was determined by a computational analysis performed to minimize the interference with the genomic mRNAs and to maximize the base-pairing interaction to the CIS-repressing RNA.  
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CIS-repressing and TRANS-repressor sequences were designed by [[Team:Bologna/Software#1|BASER]] software.
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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>)
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[[Image:project3b.png|center|950px|thumb|<center>Figure 1 - T-REX device</center>]]
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'''How we can test the device'''
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'''What can we use it for?'''  
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We developed a circuit in order to test and characterize our T-Rex device:
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In order to test and characterize our T-REX device, we developed the following genetic circuit (Fig 2):
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[[Image:circuit2OK.jpg|center|900px|thumb|<center>Figure 2 - Genetic Circuit to test CIS and TRANS' mRNA affinity</center>]]
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More details about our work are reported in the [[Team:Bologna/Project|Project]] section.
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The T-REX device is proposed as a universal and fast switch in synthetic gene circuits.
 
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More details about our work in the [[Team:Bologna/Project|Project]] section.
 
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= Acknowledgements =
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* ''' [http://www.unibo.it/Portale/default.htm University of Bologna] '''
* ''' [http://www.unibo.it/Portale/default.htm University of Bologna] '''
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* <font color=#0000cd>'''Cultural Association San Sebastiano'''</font>
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Latest revision as of 03:12, 22 October 2009

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HOME TEAM PROJECT SOFTWARE MODELING WET LAB PARTS HUMAN PRACTICE JUDGING CRITERIA




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Project Summary


Our idea

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).


How T-REX works


The device consists of two new BioBricks:

  • CIS-repressing, to be assembled upstream of the target coding sequence.
  • TRANS-repressor, complementary to the CIS-repressing and placed under the control of a different promoter.

CIS-repressing and TRANS-repressor sequences were designed by BASER software.

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



How we can test the device


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

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




More details about our work are reported in the Project section.


Acknowledgements


  • [http://www.unibo.it/Portale/default.htm University of Bologna]


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  • [http://serinar.criad.unibo.it Ser.In.Ar. Cesena]


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  • Cultural Association San Sebastiano
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