Team:Hong Kong HKUST/pneumosensor/modules
From 2014.igem.org
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+ | <div class='content_1'><h3><i>S. pneumoniae</i> σ<sup>x</sup> promoters module </h3> | ||
+ | <table class="content_table" align= "center" > | ||
+ | <tr class= "content_row" valign= "top"> | ||
+ | <td class= "content_cell"> | ||
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+ | <img src= "https://static.igem.org/mediawiki/2014/d/d0/Sigmax_combox_final.png"/> | ||
+ | <h6><b>Figure 1. σ<sup>x</sup>-Com-Box promoter mechanism</h6></b><br> | ||
+ | <h7> The reporter system contains a constitutive promoter <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_J23100">BBa_J23100</a>, which continuously expresses σ<sup>x</sup> required for Com-Box promoter induction. σ<sup>x</sup> will then bind to Com-Box promoter and express green fluorescence protein. The whole construct was built in <i>E. coli</i> DH10B strain. </h7> | ||
+ | </div> | ||
+ | </div> | ||
+ | <p class="first_letter_enhanced">In order to achieve the functionality of pneumosensor, we must have a highly specific reporting system which will only give fluorescent signal under the presence of <i>S. pneumoniae</i>. In search for the suitable gene circuit, the discovery by Prof. Morrison on the competence for genetic transformation in <i>S. pneumoniae</i> which depends on quorum-sensing system to control many competence-specific genes acting in DNA uptake, processing, and integration has provided the ideal framework for this module. (Lee and Morrison, 1999) There is a link between this quorum-sensing system and the competence-specific genes, which is an alternative σ<sup>x</sup> (ComX protein) that serves as a competence-specific global transcription modulator. (Luo and Morrison, 2003) 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, σ<sup>x</sup> will be expressed and associated with RNA polymerase apoenzyme. The resulting holoenzyme will then be guided by σ<sup>x</sup> to initiate transcription of a set of “late” genes enabling genetic transformation and other unknown functions. Characterized genes regulated by σ<sup>x</sup> were found to contain an 8 base pairs consensus sequence TACGAATA known as the Cin-Box or the Com-Box. (Piotrowski, Luo, & Morrison, 2009). Taking advantage of this competence-specific mechanism, it is now able to produce the <i>S. pneumoniae</i> sensing device of high specificity by incorporating this system into <i>E. coli</i>. <br> | ||
+ | |||
+ | </p> | ||
+ | <br> | ||
+ | <p> | ||
+ | iGEM 2014 Hong_Kong_HKUST Team has cloned σ<sup>x</sup> from <i>S. pneumoniae</i> strain NCTC7465 and characterized its ability to initiate transcription of two downstream promoters with different lengths: P<sub>celA</sub> (<a href= "http://parts.igem.org/Part:BBa_K1379000">BBa_K1379000</a>) and P<sub>comFA</sub> (<a href= "http://parts.igem.org/Part:BBa_K1379001">BBa_K1379001</a>), which have the consensus Com-Box sequence. Though much information about 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. <br> | ||
+ | <br> | ||
+ | <p> | ||
+ | P<sub>celA</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> is present. Hence, by using fluorescence protein as a reporting mechanism, this σ<sup>x</sup>, P<sub>celA</sub> and P<sub>comFA</sub> promoters system could be further utilized as a specific reporter device in <i>E. coli</i> DH10B strain that could be used by iGEM communities. | ||
+ | </p> | ||
+ | |||
+ | </div> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </div> | ||
+ | </table> | ||
+ | </div> | ||
+ | <!-- one row of content , one column one picture left--> | ||
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+ | <div class='content_1'><h3>σ<sup>x</sup> and ComW mechanism</h3> | ||
+ | <table class="content_table" align= "center" > | ||
+ | <tr class= "content_row" valign= "top"> | ||
+ | <td class= "content_cell"> | ||
+ | <div class= "content_area_one_row"> | ||
+ | <div class= "embedded_image_right"> | ||
+ | <div class="content_image"> | ||
+ | <img src= "https://static.igem.org/mediawiki/2014/archive/7/73/20141008143022!Diagram_text_2_edited_without_text.png"/> | ||
+ | <h6><b>Figure 2. σ<sup>x</sup> - <i>comW</i> Interaction Diagram</h6></b><br> | ||
+ | <h7>σ<sup>x</sup> and ComW protein are both produced by a constitutive promoter <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_J23100">BBa_J23100</a>, which continuously expresses σ<sup>x</sup> required for P<i><sub>celA</sub></i> and P<i><sub>comFA</sub></i> promoters induction, and ComW protein is required for σ<sup>x</sup> stabilization. ComW protein acts as a barrier that protects σ<sup>x</sup> from being degraded by ClpXP degradation enzyme, hence it increases 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<i><sub>celA</sub></i> and P<i><sub>comFA</sub></i> promoters.</h7> | ||
+ | </div> | ||
+ | </div> | ||
+ | <p class="first_letter_enhanced">To complete the story of competence regulation mechanism from <i>S. Pneumoniae</i>, we would also like to integrate another positive factor involved in competence regulation which was later found out to be ComW. Prof. Morrison's lab released another research paper on the identification of a new component in the regulation of genetic transformation in <i>S. Pneumoniae</i>. The gene <i>comW</i> (SP0018) was found to be | ||
+ | regulated by the quorum-sensing system and is required for a high-level of competence (Luo, Li, and Morrison, 2004). Coexpression of ComW with σ<sup>x</sup> restores the accumulation of σ<sup>x</sup> and the expression of late genes as ComW contributes to the stabilization of the alternative sigma factor X against proteolysis by ClpXP and is required for full activity of σ<sup>x</sup> in directing transcription of late competence genes (Piotrowski, Luo, and Morrison, 2009). | ||
+ | </p> | ||
+ | <br> | ||
+ | <p> | ||
+ | Based on these findings, we tried to integrate this ComW into the mechanism to see whether and how the presence of ComW affects σ<sup>x</sup>. We firstly cloned out the <i>comX</i> gene expressing σ<sup>x</sup>, and <i>comW</i> genes from the genomic DNA of <i>S. pneumoniae</i> NCTC 7465 strain. We then used <a href= "http://parts.igem.org/Part:BBa_K880005">BBa_K880005</a> (consisting of constitutive promoter <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_J23100">BBa_J23100</a> and strong RBS <a href= "http://parts.igem.org/wiki/index.php?title=Part:BBa_B0034">BBa_B0034</a>) from the BioBricks to express those genes.<br><br> | ||
+ | </p> | ||
+ | |||
+ | |||
+ | |||
+ | </div> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </div> | ||
+ | </table> | ||
+ | </div> | ||
+ | <!-- one row of content , one column one picture right--> | ||
+ | |||
+ | |||
+ | <div class='content_1'> | ||
+ | <table class="content_table" align= "center" > | ||
+ | <tr class= "content_row" > | ||
+ | <td class= "content_cell" colspan= "2"> | ||
+ | <div class= "content_area_two_row"> | ||
+ | <p> | ||
+ | <br> | ||
+ | <u>References</u> | ||
+ | <br> | ||
+ | <br> | ||
+ | A. Piotrowski, P. Luo, & D. A. Morrison. (2009). Competence for Genetic Transformation in <i>Streptococcus pneumoniae</i>: Termination of Activity of the Alternative Sigma Factor ComX Is Independent of Proteolysis of ComX and ComW. <i>Journal of Bacteriology</i>, 191(10), 3359-3366. doi:10.1128/JB.01750-08 | ||
+ | <br> | ||
+ | <br> | ||
+ | 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 <i>Streptococcus pneumoniae</i>. <i>Journal of Bacteriology</i>, 185(1), 349-358. doi: 10.1128/JB.185.1.349-358.2003 | ||
+ | <br> | ||
+ | <br> | ||
+ | C. K. Sung & D. A. Morrison. (2005). Two Distinct Functions of ComW in Stabilization and Activation of the Alternative Sigma Factor ComX in <i>Streptococcus pneumoniae</i>. <i>Journal of Bacteriology</i>, 185(9), 3052-3061. doi: 10.1128/JB.187.9.3052-3061.2005 | ||
+ | <br> | ||
+ | <br> | ||
+ | P. Luo, H. Li, & D. A. Morrison. (2004). Identification of ComW as a new component in the regulation of genetic transformation in <i>Streptococcus pneumoniae</i>. <i>Molecular Microbiology</i>, 54(1), 172-183. doi: 10.1111/j.1365-2958.2004.04254.x | ||
+ | <br> | ||
+ | <br> | ||
+ | M. S. Lee & D. A . Morrison. (1999). Identification of a New Regulator in <i>Streptococcus pneumoniae</i> Linking Quorum Sensing to Competence for Genetic Transformation. <i>Journal of Bacteriology</i>, 181(16), 5004-5016. | ||
+ | </p> | ||
+ | </div> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | </div> | ||
Revision as of 09:35, 15 October 2014
Overview
Pneumosensor primarily adopts the quorum sensing pathway components in Streptococcus pneumoniae. The autoinducer molecule, competence-stimulating peptide (CSP) is used as a reporter to detect populations of S. pneumoniae. Genes coding for the cognate CSP receptor, ComD and its response regulator ComE are migrated into our Pneumosensor as a detection platform. PcomCDE is induced by phosphorylated ComE and is adopted to express GFP to report the presence of S. pneumoniae.
Detection Module Description
Transformation in Streptococcus pneumoniae, like many other species, depends on specialized state called competence. Competence is achieved during the exponential growth stage of pneumococcal culture by the secretion of competence-stimulating peptide (CSP), which is a 17- residue long pheromone that is species-specific. Competence development controlled by a two-component regulatory system (TCS), which consists of the histidine kinase (HK) ComD and its cognate response regulator (RR) ComE. When CSP binds to it, ComD autophosphorylates to become phospho-ComD, ComD~P; at the expenditure of ATP. The cytosolic protein ComE is then phosphorylated by ComD~P through transphosphorylation reactions, producing ComE~P. These two genes are part of the comCDE operon, which includes the comC gene (Pestova et al., 1996; Cheng et al., 1997) which encodes a prepeptide that is exported and matured by a dedicated ATP-binding cassette (ABC) transport protein, into CSP. The ABC transport protein is encoded by the comAB operon. Interestingly, ComE~P binds to repeat sites adjacent to both comCDE and comAB (Ween et al., 1999), thereby creating a positive feedback loop, producing both pre-CSP and its required machinery for maturation and transport. The signal is thus amplified and competence is coordinated throughout the population. comD and comE genes were cloned out from the genomic DNA of the NCTC strain of S. pneumoniae. They would be contitutively expressed in our Pneumosensor. As mentioned above, ComE~P induces several promoters, one of which is PcomCDE. In part 2 of our detecting circuit design, we make use of the inducible promoter PcomCDE. We obtain the sequence by oligos, and will characterize it with the help of green fluorescence protein (GFP) that we constructed in the downstream of the promoter by BioBrick RFC10. Rather than using ComE~P that has to be phosphorylated by ComD~P, which involves a chain of reactions, we use a phosphorylmimetic ComE mutant, ComED58E, gratefully shared by Bernard Martin et al. After characterization of PcomCDE, we hope to put PcomCDE together with Module 2 of our project, as the ultimate goal of our project is to make a system of automatic detection and lysis of S. pneumoniae. |
S. pneumoniae σx promoters module
In order to achieve the functionality of pneumosensor, we must have a highly specific reporting system which will only give fluorescent signal under the presence of S. pneumoniae. In search for the suitable gene circuit, the discovery by Prof. Morrison on the competence for genetic transformation in S. pneumoniae which depends on quorum-sensing system to control many competence-specific genes acting in DNA uptake, processing, and integration has provided the ideal framework for this module. (Lee and Morrison, 1999) There is a link between this quorum-sensing system and the competence-specific genes, which is an alternative σx (ComX protein) that serves as a competence-specific global transcription modulator. (Luo and Morrison, 2003) 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 associated 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. Characterized genes regulated by σx were found to contain an 8 base pairs consensus sequence TACGAATA known as the Cin-Box or the Com-Box. (Piotrowski, Luo, & Morrison, 2009). Taking advantage of this competence-specific mechanism, it is now able to produce the S. pneumoniae sensing device of high specificity by incorporating this system into E. coli.
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 with different lengths: PcelA (BBa_K1379000) and PcomFA (BBa_K1379001), which have the consensus Com-Box sequence. Though much information about 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. PcelA and PcomFA promoters have high specificity to σx for activation, so genes downstream the promoters will be translated only if σx is present. Hence, by using fluorescence protein as a reporting mechanism, this σx, PcelA and PcomFA promoters system could be further utilized as a specific reporter device in E. coli DH10B strain that could be used by iGEM communities. |
σx and ComW mechanism
To complete the story of competence regulation mechanism from S. Pneumoniae, we would also like to integrate another positive factor involved in competence regulation which was later found out to be ComW. Prof. Morrison's lab released another research paper on the identification of a new component in the regulation of genetic transformation in S. Pneumoniae. The gene comW (SP0018) was found to be regulated by the quorum-sensing system and is required for a high-level of competence (Luo, Li, and Morrison, 2004). 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 X against proteolysis by ClpXP and is required for full activity of σx in directing transcription of late competence genes (Piotrowski, Luo, and Morrison, 2009).
Based on these findings, we tried to integrate this ComW into the mechanism to see whether and how the presence of ComW affects σx. We firstly cloned out the comX gene expressing σx, and comW genes from the genomic DNA of S. pneumoniae NCTC 7465 strain. We then used BBa_K880005 (consisting of constitutive promoter BBa_J23100 and strong RBS BBa_B0034) from the BioBricks to express those genes. |
|
References
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