Difference between revisions of "Part:BBa K206010"

Latest revision as of 15:02, 22 October 2009

Jammer proof of concept (J23100)

This is a proof of concept construct for the jammer system, i.e. gene knockdown via reverse promoter transcription. Theoretically, the presence of arabinose induces transcription from the reverse pBAD promoter. We hypothesized that this would knock down gene expression through several possible methods: 1) collision of RNA polymerase on the opposing strands; 2) hybridization of the complementary RNAs, blocking translation; 3) targeting of the hybridized RNAs for degradation by a putative degradosome.

Usage and Biology

What you can do with it:
If you are interested in inducible knockdown of any coding sequence, suffix it with our part BBa_K206008. The promoter of your product should be prefixed with a terminator that is capable of reverse termination, such as BBa_B0014.

Compatibility:
Chassis: Best used in the E. coli strain [http://cgsc.biology.yale.edu/Strain.php?ID=111773 BW27783], which has been modified to permit homogeneous pBAD promoter expression by substituting the chromosomal arabinose-dependent promoter of AraE (arabinose transporter protein) with a constitutive promoter [1].
Backbone: Has been shown to work on plasmid pSB1C3.
Reporter: Has been shown to work with reporter BBa_K145015.
Subparts: Has been shown to work with terminator BBa_B0014 and reverse promoter BBa_J44002.

Characterization

We inoculated 5mL overnight cultures of LB-Chlor with colonies from a streak plate of BBa_K206010-transformed BW27783 cells. In the morning, we diluted the cultures to an OD600 of 0.2 into 15mL LB-Chlor with or without 0.05% arabinose in 25mL flasks (duplicates). 16 hours post-arabinose induction, we measured GFP fluorescence of the cultures using a Becton-Dickinson FACSCalibur flow cytometer.

GFP fluorescence of Jammer with and without arabinose. Positive control is constitutively expressed GFP_LVA (driven by BBa_K206014). Negative control is BW27783 cells without any construct.

Induction with arabinose clearly results in knockdown of reporter expression, almost to negative control levels.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 110
Illegal NheI site found at 133
Illegal NheI site found at 932
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 992
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 808

References

[http://www.ncbi.nlm.nih.gov/pubmed/11739756 [1]] Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, and Keasling JD. (2001). Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology. 147(12):3241-7.

@@ Line 1: / Line 1: @@
 __NOTOC__
 <partinfo>BBa_K206010 short</partinfo>
-This is a proof of concept construct for the jammer system, i.e. gene knockdown via reverse promoter transcription.
+This is a proof of concept construct for the jammer system, i.e. gene knockdown via reverse promoter transcription. Theoretically, the presence of arabinose induces transcription from the reverse pBAD promoter. We hypothesized that this would knock down gene expression through several possible methods: 1) collision of RNA polymerase on the opposing strands; 2) hybridization of the complementary RNAs, blocking translation; 3) targeting of the hybridized RNAs for degradation by a putative degradosome.
-<!-- Add more about the biology of this part here
 ===Usage and Biology===
-<!-- -->
+''What you can do with it:''
+<br>If you are interested in inducible knockdown of any coding sequence, suffix it with our part <partinfo>K206008</partinfo>. The promoter of your product should be prefixed with a terminator that is capable of reverse termination, such as <partinfo>B0014</partinfo>.
+''Compatibility:''
+<br>
+Chassis: Best used in the ''E. coli'' strain [http://cgsc.biology.yale.edu/Strain.php?ID=111773 BW27783], which has been modified to permit homogeneous pBAD promoter expression by substituting the chromosomal arabinose-dependent promoter of AraE (arabinose transporter protein) with a constitutive promoter [[Part:BBa_K206010#References|[1]]].<br>
+Backbone: Has been shown to work on plasmid <partinfo>pSB1C3</partinfo>.
+<br>
+Reporter: Has been shown to work with reporter <partinfo>K145015</partinfo>.
+<br>
+Subparts: Has been shown to work with terminator <partinfo>B0014</partinfo> and reverse promoter <partinfo>J44002</partinfo>.
+===Characterization===
+We inoculated 5mL overnight cultures of LB-Chlor with colonies from a streak plate of <partinfo>K206010</partinfo>-transformed BW27783 cells. In the morning, we diluted the cultures to an OD600 of 0.2 into 15mL LB-Chlor with or without 0.05% arabinose in 25mL flasks (duplicates). 16 hours post-arabinose induction, we measured GFP fluorescence of the cultures using a Becton-Dickinson FACSCalibur flow cytometer.
+[[Image:J23100-Jammer_Complete.png|center|frame|GFP fluorescence of Jammer with and without arabinose. Positive control is constitutively expressed GFP_LVA (driven by <partinfo>K206014</partinfo>). Negative control is BW27783 cells without any construct.]]
+Induction with arabinose clearly results in knockdown of reporter expression, almost to negative control levels.
 <span class='h3bb'>Sequence and Features</span>
 <partinfo>BBa_K206010 SequenceAndFeatures</partinfo>
+===References===
+[http://www.ncbi.nlm.nih.gov/pubmed/11739756 [1]] Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, and Keasling JD. (2001). Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology. '''147'''(12):3241-7.