Team:Hong Kong HKUST/pneumosensor/module two

From 2014.igem.org

(Difference between revisions)
Line 113: Line 113:
</div>
</div>
</div>
</div>
-
<p class="first_letter_enhanced">Prof. Donald A. Morrison’s research lab in University of Illinois at Chicago published several papers on  
+
<p class="first_letter_enhanced">Prof. Donald A. Morrison’s research lab in University of Illinois at Chicago published several papers on the competence for genetic transformation in <i>Streptococcus pneumoniae</i> which depends on quorum-sensing system to control many competence-specific genes acting in DNA uptake, processing, and integration. There is a link between this quorum-sensing system and the competence-specific genes, which is an alternative σ<sup>x</sup>. &sigma;<sup>X</sup> (ComX) serve as a competence-specific global transcription modulator. In <i>S. pneumoniae</i>, competence (a state capable of being genetic transformed) happens transiently during the log phase growth, and is regulated by a quorum sensing system utilizing the Competence Signal Peptide (CSP). Upon stimulation by CSP, &sigma;<sup>X</sup> will be expressed and associate with RNA polymerase apoenzyme. The resulting holoenzyme will then be guided by &sigma;<sup>X</sup> to initiate transcription of a set of “late” genes enabling genetic transformation and other unknown functions.
-
the competence for genetic transformation in ''Streptococcus pneumoniae'' which depends on quorum-sensing system to control many competence-specific
+
 
-
genes acting in DNA uptake, processing, and integration. There is a link between this quorum-sensing system and the competence-specific
+
 
-
genes, which is an alternative σ<sup>x</sup>. Expression of σ<sup>x</sup> allows transcription of many genes that are involved in transformation
+
iGEM 2014 Hong_Kong_HKUST Team has cloned &sigma;<sup>X</sup> from <i>S. pneumoniae</i> strain NCTC7465 and characterized its ability to initiate transcription of two downstream promoters: P<sub>chbB</sub> (BBa_K1379000) and P<sub>comFA</sub> (BBa_K1379001).
-
and specifically expressed during competence. These late genes share a conserved 8-bp sequence in their promoter regions, TACGAATA
+
 
-
(combox) which is specifically induced by σ<sup>x</sup>-containing RNA polymerase.  
+
</p>
</p>
<br>
<br>
<p>
<p>
-
Combox promoters can be found on many different regions within the genomic DNA of <i>Streptococcus Pneumoniae</i> strains. The promoters  
+
P<sub>chbB</sub) and P<sub>comFA</sub> promoters can be found on many different regions within the genomic DNA of <i>Streptococcus Pneumoniae</i> strains. These promoters  
-
were reported to have variants with different lengths and consensus sequences, but generally the range of variety has been kept small.  
+
have different lengths and consensus sequences.  
-
Though much information about the combox promoter is readily available nowadays, its characterization of promoter activity, specificity,  
+
Though much information about the the promoters is readily available nowadays, its characterization of promoter activity, specificity,  
sequence, as well as the biomolecular mechanism can be greatly enhanced with further investigations and experiments.<br><br>
sequence, as well as the biomolecular mechanism can be greatly enhanced with further investigations and experiments.<br><br>
Hence, we were interested in reproducing this gene circuit with all the associated genes and promoters to be combined into a single  
Hence, we were interested in reproducing this gene circuit with all the associated genes and promoters to be combined into a single  
Line 131: Line 130:
<br>
<br>
<p>
<p>
-
Combox promoters have high specificity to σ<sup>x</sup> for activation, so genes downstream the combox promoter will be translated only if σx are present. Hence,  
+
P<sub>chbB</sub) and P<sub>comFA</sub> promoters have high specificity to σ<sup>x</sup> for activation, so genes downstream the promoters will be translated only if σ<sup>x</sup> are present. Hence,  
-
by using fluorescence protein as a reporting mechanism, this σ<sup>x</sup>-combox system could be further utilized as a specific reporter device that could be used by iGEM communities.
+
by using fluorescence protein as a reporting mechanism, this σ<sup>x</sup>, P<sub>chbB</sub) and P<sub>comFA</sub> promoters system could be further utilized as a specific reporter device that could be used by iGEM communities.
</p>
</p>
Line 153: Line 152:
<img src= "https://static.igem.org/mediawiki/2014/archive/7/73/20141008143022!Diagram_text_2_edited_without_text.png"/>
<img src= "https://static.igem.org/mediawiki/2014/archive/7/73/20141008143022!Diagram_text_2_edited_without_text.png"/>
<h5>Figure 2. σ<sup>x</sup> - <i>comW</i> Interaction Diagram</h5><br>
<h5>Figure 2. σ<sup>x</sup> - <i>comW</i> Interaction Diagram</h5><br>
-
<h6>σ<sup>x</sup> and ComW are both produced by a constitutive promoter J23100, which continuously expressing σ<sup>x</sup> protein required for combox promoter induction, and ComW protein required for σ<sup>x</sup> stabilization. ComW protein act as a barrier that protect σ<sup>x</sup> from being degraded by ClpXP degradation enzyme, hence it increase the production of σ<sup>x</sup>. The increase in σ<sup>x</sup> production will increase the expression of green fluorescence protein by combox promoter.</h6>
+
<h6>σ<sup>x</sup> and ComW are both produced by a constitutive promoter J23100, which continuously expressing σ<sup>x</sup> protein required for P<sub>chbB</sub) and P<sub>comFA</sub> promotersinduction, and ComW protein required for σ<sup>x</sup> stabilization. ComW protein act as a barrier that protect σ<sup>x</sup> from being degraded by ClpXP degradation enzyme, hence it increase the production of σ<sup>x</sup>. The increase in σ<sup>x</sup> production will increase the expression of green fluorescence protein by P<sub>chbB</sub) and P<sub>comFA</sub> promoters.</h6>
</div>
</div>
</div>
</div>
Line 166: Line 165:
Gram-negative ''Escherichia coli''. We firstly cloned out the σ<sup>x</sup> and <i>comW</i> genes from the genomic DNA of ''S. pneumoniae'' NCTC 7465 strain.  
Gram-negative ''Escherichia coli''. We firstly cloned out the σ<sup>x</sup> and <i>comW</i> genes from the genomic DNA of ''S. pneumoniae'' NCTC 7465 strain.  
We then used BBa_K880005 (consisting of constitutive promoter J23100 and strong RBS B0034) from the BioBricks to express those genes.<br><br>
We then used BBa_K880005 (consisting of constitutive promoter J23100 and strong RBS B0034) from the BioBricks to express those genes.<br><br>
-
Lastly, we combined these constructs with combox promoter and GFP generator to check the functionality of the system, and calculate the  
+
Lastly, we combined these constructs with P<sub>chbB</sub) and P<sub>comFA</sub> promoters and GFP generator to check the functionality of the system, and calculate the  
-
relative promoter unit of combox promoter.
+
relative promoter unit of promoters.
</p>
</p>

Revision as of 15:00, 8 October 2014


S. pneumoniae σx promoters module

Figure 1. σx-Combox promoter mechanism

The reporter system contain a constitutive promoter BBa_J23100, which continuously expressing σx protein required for combox promoter induction. σx protein will then bind to combox promoter and express green fluorescence protein. The whole construct is built in E.Coli DH10B strain.

Prof. Donald A. Morrison’s research lab in University of Illinois at Chicago published several papers on the competence for genetic transformation in Streptococcus pneumoniae which depends on quorum-sensing system to control many competence-specific genes acting in DNA uptake, processing, and integration. There is a link between this quorum-sensing system and the competence-specific genes, which is an alternative σx. σX (ComX) serve as a competence-specific global transcription modulator. In S. pneumoniae, competence (a state capable of being genetic transformed) happens transiently during the log phase growth, and is regulated by a quorum sensing system utilizing the Competence Signal Peptide (CSP). Upon stimulation by CSP, σX will be expressed and associate with RNA polymerase apoenzyme. The resulting holoenzyme will then be guided by σX to initiate transcription of a set of “late” genes enabling genetic transformation and other unknown functions. iGEM 2014 Hong_Kong_HKUST Team has cloned σX from S. pneumoniae strain NCTC7465 and characterized its ability to initiate transcription of two downstream promoters: PchbB (BBa_K1379000) and PcomFA (BBa_K1379001).


PchbBcomFA promoters can be found on many different regions within the genomic DNA of Streptococcus Pneumoniae strains. These promoters have different lengths and consensus sequences. Though much information about the the promoters is readily available nowadays, its characterization of promoter activity, specificity, sequence, as well as the biomolecular mechanism can be greatly enhanced with further investigations and experiments.

Hence, we were interested in reproducing this gene circuit with all the associated genes and promoters to be combined into a single transcriptional unit. Despite the suggested susceptibility to leakage and other factors that may hinder or interrupt the mechanism, researches have reported that the pathway was highly specific to certain environmental conditions and stress, suggesting minimal or no leakage in the entire process.

PchbBcomFA promoters have high specificity to σx for activation, so genes downstream the promoters will be translated only if σx are present. Hence, by using fluorescence protein as a reporting mechanism, this σx, PchbBcomFA promoters system could be further utilized as a specific reporter device that could be used by iGEM communities.

σx and ComW mechanism

Figure 2. σx - comW Interaction Diagram

σx and ComW are both produced by a constitutive promoter J23100, which continuously expressing σx protein required for PchbBcomFA promotersinduction, and ComW protein required for σx stabilization. ComW protein act as a barrier that protect σx from being degraded by ClpXP degradation enzyme, hence it increase the production of σx. The increase in σx production will increase the expression of green fluorescence protein by PchbBcomFA promoters.

Besides σx, another positive factor involved in competence regulation was later found out to be ComW. The gene comW (SP0018) is regulated by the quorum-sensing system and is required for a high-level of competence. Coexpression of ComW with σx restores the accumulation of σx and the expression of late genes as ComW contributes to the stabilization of the alternative sigma factor σx against proteolysis by ClpXP and is required for full activity of σx in directing transcription of late competence genes.


Based on these findings, we integrated this alternative sigma factor system from Gram-positive Streptococcus pneumoniae into Gram-negative ''Escherichia coli''. We firstly cloned out the σx and comW genes from the genomic DNA of ''S. pneumoniae'' NCTC 7465 strain. We then used BBa_K880005 (consisting of constitutive promoter J23100 and strong RBS B0034) from the BioBricks to express those genes.

Lastly, we combined these constructs with PchbBcomFA promoters and GFP generator to check the functionality of the system, and calculate the relative promoter unit of promoters.


References

A. Piotrowski, P. Luo, & D. A. Morrison. (2009). Competence for Genetic Transformation in Streptococcus pneumoniae: Termination of Activity of the Alternative Sigma Factor ComX Is Independent of Proteolysis of ComX and ComW. Journal of Bacteriology, 191(10), 3359-3366. doi:10.1128/JB.01750-08

P. Luo & D. A. Morisson. (2003). Transient Association of an Alternative Sigma Factor, ComX, with RNA Polymerase during the Period of Competence for Genetic Transformation in Streptococcus pneumoniae. Journal of Bacteriology, 185(1), 349-358. doi: 10.1128/JB.185.1.349-358.2003

C. K. Sung & D. A. Morrison. (2005). Two Distinct Functions of ComW in Stabilization and Activation of the Alternative Sigma Factor ComX in Streptococcus pneumoniae. Journal of Bacteriology, 185(9), 3052-3061. doi: 10.1128/JB.187.9.3052-3061.2005

P. Luo, H. Li, & D. A. Morrison. (2004). Identification of ComW as a new component in the regulation of genetic transformation in Streptococcus pneumoniae. Molecular Microbiology, 54(1), 172-183. doi: 10.1111/j.1365-2958.2004.04254.x

M. S. Lee & D. A . Morrison. (1999). Identification of a New Regulator in Streptococcus pneumoniae Linking Quorum Sensing to Competence for Genetic Transformation. Journal of Bacteriology, 181(16), 5004-5016.


Home

Pneumosensor

Riboregulator

Human Practice

Team

WetLab

Achievement