Difference between revisions of "Part:BBa K1379045"

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===Usage and Biology===
 
===Usage and Biology===
  
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&sigma;<sup>X</sup> (ComX) is an alternative &sigma; factor in <i>Streptococcus pneumoniae</i> which serves as a competence-specific global transcription modulator. (BioCyc) 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). (Luo & Morrison, 2003) 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. Characterized genes regulated by &sigma;<sup>X</sup> were found to contain a 8-bp consensus sequence TACGAATA known as the Cin-Box or the Com-Box. (Piotrowski, Luo, & Morrison, 2009)
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&sigma;<sup>X</sup> (ComX) is an alternative &sigma; factor in <i>Streptococcus pneumoniae</i> which serves as a competence-specific global transcription modulator. (BioCyc) 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 Stimulating Peptide (CSP). (Luo & Morrison, 2003) 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. Characterized genes regulated by &sigma;<sup>X</sup> were found to contain a 8-bp consensus sequence TACGAATA known as the Cin-Box or the Com-Box. (Piotrowski, Luo, & Morrison, 2009)
  
 
Voigt and his colleagues have demonstrated that orthogonal gene expression could be achieved through the use of &sigma;s, anti-&sigma;s and synthetic promoters. (Rhodius et al., 2013). The principle depicted applies to &sigma;<sup>X</sup>, which when paired with the promoters it regulates, achieves orthogonal expression in <i>E. coli</i>. It should be noted that iGEM 2014 Hong_Kong_HKUST Team has compared the amino acid sequences of ECFs described by Rhodius et al. with that of &sigma;<sup>X</sup> from <i>S. pneumoniae</i>, and found no significant similarities, thus &sigma;<sup>X</sup> is a new sigma factor added to the list.
 
Voigt and his colleagues have demonstrated that orthogonal gene expression could be achieved through the use of &sigma;s, anti-&sigma;s and synthetic promoters. (Rhodius et al., 2013). The principle depicted applies to &sigma;<sup>X</sup>, which when paired with the promoters it regulates, achieves orthogonal expression in <i>E. coli</i>. It should be noted that iGEM 2014 Hong_Kong_HKUST Team has compared the amino acid sequences of ECFs described by Rhodius et al. with that of &sigma;<sup>X</sup> from <i>S. pneumoniae</i>, and found no significant similarities, thus &sigma;<sup>X</sup> is a new sigma factor added to the list.
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===Characterization===
 
===Characterization===
  
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This construct is as a sub part of the &sigma;<sup>X</sup> Generator [[Part:BBa_K1379006|BBa_K1379006]] which expresses &sigma;<sup>X</sup>. The generator was assembled with the promoter measurement kit [[Part:BBa_E0240|BBa_E0240]] with either promoter P<sub>celA</sub> (Promoter only: [[Part:BBa_K1379000|BBa_K1379000]], w/ BBa_E0240: [[Part:BBa_K1379002|BBa_K1379002]]) and P<sub>comFA</sub> (Promoter only: [[Part:BBa_K1379001|BBa_K1379001]], w/ BBa_E0240: [[Part:BBa_K1379003|BBa_K1379003]]). <i>E. coli</i> colonies holding the resulting constructs in [[Part:pSB3K3|pSB3K3]] were observed under fluorescent macroscope with UV filter. Measurement kit for standard reference promoter [[Part:BBa_J23101|BBa_J23101]],  [[Part:BBa_I20260|BBa_I20260]] was used as a positive control; [[Part:BBa_E0240|BBa_E0240]] was used as the negative control for background fluorescence. Measurement kits for P<sub>celA</sub> P<sub>comFA</sub> without &sigma;<sup>X</sup> Generator were used as negative controls for function of &sigma;<sup>X</sup>.
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This construct is a sub part of the &sigma;<sup>X</sup> Generator [[Part:BBa_K1379006|BBa_K1379006]] which expresses &sigma;<sup>X</sup>. The generator was assembled with the promoter measurement kit [[Part:BBa_E0240|BBa_E0240]] with either promoter P<sub>celA</sub> (Promoter only: [[Part:BBa_K1379000|BBa_K1379000]], w/ BBa_E0240: [[Part:BBa_K1379002|BBa_K1379002]]) and P<sub>comFA</sub> (Promoter only: [[Part:BBa_K1379001|BBa_K1379001]], w/ BBa_E0240: [[Part:BBa_K1379003|BBa_K1379003]]). <i>E. coli</i> colonies holding the resulting constructs in [[Part:pSB3K3|pSB3K3]] were observed under fluorescent macroscope with UV filter. Measurement kit for standard reference promoter [[Part:BBa_J23101|BBa_J23101]],  [[Part:BBa_I20260|BBa_I20260]] was used as a positive control; [[Part:BBa_E0240|BBa_E0240]] was used as the negative control for background fluorescence. Measurement kits for P<sub>celA</sub> P<sub>comFA</sub> without &sigma;<sup>X</sup> Generator were used as negative controls for function of &sigma;<sup>X</sup>.
 
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Please refer to the pages [[Part:BBa_K1379000|BBa_K1379000]] (P<sub>celA</sub>) and [[Part:BBa_K1379001|BBa_K1379001]] (P<sub>comFA</sub>) for detailed characterization on the promoter activities in presence of &sigma;<sup>X</sup>.
 
Please refer to the pages [[Part:BBa_K1379000|BBa_K1379000]] (P<sub>celA</sub>) and [[Part:BBa_K1379001|BBa_K1379001]] (P<sub>comFA</sub>) for detailed characterization on the promoter activities in presence of &sigma;<sup>X</sup>.
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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===Reference===
 
===Reference===
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BioCyc was retrieved from http://www.biocyc.org/SPNE171101/NEW-IMAGE?type=GENE&object=GJC8-2079
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BioCyc retrieved from http://www.biocyc.org/SPNE171101/NEW-IMAGE?type=GENE&object=GJC8-2079
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<br><br>
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<br>
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Luo P., & Morrison D. (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. doi:10.1128/JB.185.1.349-358.2003
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Ping Luo., & Donald A. Morrison. (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. doi:10.1128/JB.185.1.349-358.2003
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<br><br>
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<br>
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Piotrowski A., Luo P., & Morrison D. (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. doi:10.1128/JB.01750-08
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Andrew Piotrowski., Ping Luo., & Donald 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.'' doi:10.1128/JB.01750-08<br>
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<br><br>
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Virgil A Rhodius., Thomas H Segall-Shapiro., Brian D Sharon., Amar Ghodasara., Ekaterina Orlova., Hannah Tabakh., . . . Christopher A Voigt. (2013). Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. doi:10.1038/msb.2013.58
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Rhodius V., Segall-Shapiro T., Sharon B., Ghodasara A., Orlova E., Tabakh H., . . . Voigt C. (2013). ''Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters.'' Molecular Systhetic Biology .doi:10.1038/msb.2013.58

Latest revision as of 13:46, 17 October 2014

S. pneumoniae σx-B0015

This is σX CDS (BBa_K1379004) followed by double terminator BBa_B0015. iGEM 2014 Hong_Kong_HKUST Team has created this part to facilitate assembly of σX to promoters and RBSs of choice.

Usage and Biology

σX (ComX) is an alternative σ factor in Streptococcus pneumoniae which serves as a competence-specific global transcription modulator. (BioCyc) 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 Stimulating Peptide (CSP). (Luo & Morrison, 2003) 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. Characterized genes regulated by σX were found to contain a 8-bp consensus sequence TACGAATA known as the Cin-Box or the Com-Box. (Piotrowski, Luo, & Morrison, 2009)

Voigt and his colleagues have demonstrated that orthogonal gene expression could be achieved through the use of σs, anti-σs and synthetic promoters. (Rhodius et al., 2013). The principle depicted applies to σX, which when paired with the promoters it regulates, achieves orthogonal expression in E. coli. It should be noted that iGEM 2014 Hong_Kong_HKUST Team has compared the amino acid sequences of ECFs described by Rhodius et al. with that of σX from S. pneumoniae, and found no significant similarities, thus σX is a new sigma factor added to the list.

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: PcelA(BBa_K1379000) and PcomFA (BBa_K1379001).

Characterization

This construct is a sub part of the σX Generator BBa_K1379006 which expresses σX. The generator was assembled with the promoter measurement kit BBa_E0240 with either promoter PcelA (Promoter only: BBa_K1379000, w/ BBa_E0240: BBa_K1379002) and PcomFA (Promoter only: BBa_K1379001, w/ BBa_E0240: BBa_K1379003). E. coli colonies holding the resulting constructs in pSB3K3 were observed under fluorescent macroscope with UV filter. Measurement kit for standard reference promoter BBa_J23101, BBa_I20260 was used as a positive control; BBa_E0240 was used as the negative control for background fluorescence. Measurement kits for PcelA PcomFA without σX Generator were used as negative controls for function of σX.

As shown below, only in the presence of σX would PcelA and PcomFA be turned on, therefore, σX is functional.

Figure 1. PcelA and PcomFA promoters activated in presence of σX. PcelA and PcomFA gave little GFP signal in the absence of σX but has comparable activity as reference promoter BBa_J23101 in presence of σX. Scale bar = 5mm.

Extensive documentation of our characterization can be found at our [http://2014.igem.org/Team:Hong_Kong_HKUST/pneumosensor/characterization characterization page for Pneumosensor].
Please refer to the pages BBa_K1379000 (PcelA) and BBa_K1379001 (PcomFA) for detailed characterization on the promoter activities in presence of σX.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 298


Reference

BioCyc was retrieved from http://www.biocyc.org/SPNE171101/NEW-IMAGE?type=GENE&object=GJC8-2079

Luo P., & Morrison D. (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. doi:10.1128/JB.185.1.349-358.2003

Piotrowski A., Luo P., & Morrison D. (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. doi:10.1128/JB.01750-08

Rhodius V., Segall-Shapiro T., Sharon B., Ghodasara A., Orlova E., Tabakh H., . . . Voigt C. (2013). Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Molecular Systhetic Biology .doi:10.1038/msb.2013.58