Difference between revisions of "Part:BBa K1379006"

(→‎Characterization)
Line 6: Line 6:
 
===Usage and Biology===
 
===Usage and Biology===
  
−
&sigma;<sup>X</sup> (ComX) is an alternative &sigma; factor in <i>Streptococcus pneumoniae</i> which serve 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 (Piotrowski, Luo, & Morrison, 2009).
+
&sigma;<sup>X</sup> (ComX) is an alternative &sigma; factor in <i>Streptococcus pneumoniae</i> which serve 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. (Piotrowski, Luo, & Morrison, 2009)
  
  
Line 12: Line 12:
  
  
−
Following the principle depicted in Rhodius et al., () &sigma;<sup>X</sup> could achieve orthogonal gene expression regulation if used together with other sigma factors / ECFs. 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.
+
Following the principle depicted in Rhodius et al., (Rhodius et al., 2013) &sigma;<sup>X</sup> could achieve orthogonal gene expression regulation if used together with other sigma factors / ECFs. 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.
  
 
===Characterization===
 
===Characterization===
Line 38: Line 38:
  
 
===Reference===
 
===Reference===
 +
 +
BioCyc retrieved from http://www.biocyc.org/SPNE171101/NEW-IMAGE?type=GENE&object=GJC8-2079
 +
<br>
 +
Luo, P., & Morrison, D. A. (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
 +
<br>
 +
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>
 +
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

Revision as of 15:28, 8 October 2014

S. pneumoniae σx Generator

This is a protein generator for σX CDS (BBa_K1379004). The σX transcription is initiated by the strong constitutive promoter BBa_J23100 and the translation is initiated by strong RBS BBa_B0034, and transcription is terminated by BBa_B0015.

Usage and Biology

σX (ComX) is an alternative σ factor in Streptococcus pneumoniae which serve 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 Signal 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. (Piotrowski, Luo, & Morrison, 2009)


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).


Following the principle depicted in Rhodius et al., (Rhodius et al., 2013) σX could achieve orthogonal gene expression regulation if used together with other sigma factors / ECFs. 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.

Characterization

This generator, which expresses σX, was assembled with the promoter measurement kit BBa_E0240 with either promoter PchbB (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 general negative control. for background fluorescence. Measurement kits for PchbB PcomFA without σX Generator were used as negative controls for function of σX.

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

Figure 1. PchbB and PcomFA promoters activated in presence of σX. PchbB 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 (PchbB) 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
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 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 359


Reference

BioCyc retrieved from http://www.biocyc.org/SPNE171101/NEW-IMAGE?type=GENE&object=GJC8-2079
Luo, P., & Morrison, D. A. (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
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
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