Difference between revisions of "Part:BBa K2627000"

Latest revision as of 03:58, 18 October 2018

Advanced CcaS with PAS domain knocked out

Usage and Biology

CcaS protein belongs to green/red light sensing two-component system. The two-component system consists of the membrane-associated histidine kinase CcaS and its response regulator CcaR. The activating information stored in light is captured by phytochromes in situ. In phytochromes, a bilin-chromophore (in this case phycocyanobilin) binds at a conserved cysteine within an N-terminal GAF (cyclic GMP phosphodiesterase, adenylyl cyclase, FhlA) domain and imparts reversible photoactivation of signaling activity with maximal responses to 535-nm (green) and 672-nm (red) light. Absorption of green light increases the rate of CcaS autophosphorylation, phosphorylation of CcaR by phosphate transferring, and transcription from the promoter of the phycobilisome linker protein cpcG2, while absorption of red light reverses this process. The lower leakiness is reported to be acquired after removing the second putative promoter in cpcG2, which is thought to be constitutive and contributes to leakiness and low dynamic range.

Part BBa_K2627000 was improved from the original CcaS (BBa_K592001) by deleting about 800 bases corresponding to two PAS domains since we were inspired by Professor Koji’s work. Part BBa_K2627000 (CcaS#4) is a varient of CcaS having an opposite response to green/red light. High intensity of fluorescence can be seen when bacteria are cultured under red light while fluorescence is pretty weak under green light.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 606
21
INCOMPATIBLE WITH RFC[21]
Illegal XhoI site found at 1397
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

Results

Characaterization of BBa_K2627000

Part BBa_K2627000 was characterizaed through measuring relative fluorescence intensity, this measurment was taken place in 24-well plates. Cells were cultured in the seed culture medium for 12 hours before inoculated in 24-well plates in three kinds of culture medium. Then fluorescence intensity of CcaS#4 was measured at 9h in comparison with BBa_K592001.
The following figure shows the relative fluorescence intensity induced by green light and red light.

Figure 1. Characterization of part BBa_K2627000 and BBa_K592001 in M9 medium whose carbon source is glucose. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index. The #4 has the reverse function and the dynamic range is about 2.6.

Figure 2. Characterization of part BBa_K2627000 and BBa_K592001 in M9 medium whose carbon source is glycerol. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index. The #4 has the reverse function and the dynamic range is about 1.5.

Figure 3. Characterization of part BBa_K2627000 and BBa_K592001 in M9 medium whose nitrogen source is yeast extract. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index. The #4 has the reverse function and the dynamic range is about 1.2.

@@ Line 2: / Line 2: @@
 __NOTOC__
 <partinfo>BBa_K2627000 short</partinfo>
+===Usage and Biology===
+CcaS protein belongs to green/red light sensing two-component system. The two-component system consists of the membrane-associated histidine kinase CcaS and its response regulator CcaR. The activating information stored in light is captured by phytochromes in situ. In phytochromes, a bilin-chromophore (in this case phycocyanobilin) binds at a conserved cysteine within an N-terminal GAF (cyclic GMP phosphodiesterase, adenylyl cyclase, FhlA) domain and imparts reversible photoactivation of signaling activity with maximal responses to 535-nm (green) and 672-nm (red) light. Absorption of green light increases the rate of CcaS autophosphorylation, phosphorylation of CcaR by phosphate transferring, and transcription from the promoter of the phycobilisome linker protein cpcG2, while absorption of red light reverses this process. The lower leakiness is reported to be acquired after removing the second putative promoter in cpcG2, which is thought to be constitutive and contributes to leakiness and low dynamic range.
-CcaS is a protein in CcaS-CcaR two-component system, which is sensitive to green light and red light. CcaS is located on the cell membrane and when it senses the existence of green light or red light, it will experience autophosphorylation and thus phosphorylate the downstream CcaR, and CcaR will bind to specific promoter to activate gene transcription. Typically, gene will be activated under green light and repressed under red light, but this advanced CcaS with PAS domain knocked out has reverse effect, gene will be repressed under green light and activated under red light. In our project, this advanced two-component system is used as a switch to sense different light and turn on the gene to produce PHB.
+[[File:T--SDU-China--3410.png|600px|center]]
-[[File:T--SDU-China--3410.png|800px|center]]
+<p>Part BBa_K2627000 was improved from the original CcaS (<partinfo>BBa_K592001</partinfo>) by deleting about 800 bases corresponding to two PAS domains since we were inspired by Professor Koji’s work. Part BBa_K2627000 (CcaS#4) is a varient of CcaS having an opposite response to green/red light. High intensity of fluorescence can be seen when bacteria are cultured under red light while fluorescence is pretty weak under green light.</p><br>
 <!-- Add more about the biology of this part here
-==Usage and Biology==
-Usage and biology
-CcaS protein belongs to green/red light sensing two-component system. The two-component system consists of the membrane-associated histidine kinase CcaS and its response regulator CcaR. The activating information stored in light is captured by phytochromes in situ. In phytochromes, a bilin-chromophore (in this case phycocyanobilin) binds at a conserved cysteine within an N-terminal GAF (cyclic GMP phosphodiesterase, adenylyl cyclase, FhlA) domain and imparts reversible photoactivation of signaling activity with maximal responses to 535-nm (green) and 672-nm (red) light. Absorption of green light increases the rate of CcaS autophosphorylation, phosphorylation of CcaR by phosphate transferring, and transcription from the promoter of the phycobilisome linker protein cpcG2, while absorption of red light reverses this process. The lower leakiness is reported to be acquired after removing the second putative promoter in cpcG2, which is thought to be constitutive and contributes to leakiness and low dynamic range.
 <!-- -->
@@ Line 20: / Line 20: @@
 <partinfo>BBa_K2627000 parameters</partinfo>
 <!-- -->
 ==Results==
-[[File:T--SDU-China--4.png|800px|center]]
+===Characaterization of BBa_K2627000===
-Figure 1: Characterization of part BBa_K2627000 and BBa_K592001. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. The Fluorescence intensity is about 1207.4 under green light while it is about 3146.3 under red light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index.
+<p>Part BBa_K2627000 was characterizaed through measuring relative fluorescence intensity, this measurment was taken place in 24-well plates. Cells were cultured in the seed culture medium for 12 hours before inoculated in 24-well plates in three kinds of culture medium. Then fluorescence intensity of CcaS#4 was measured at 9h in comparison with BBa_K592001.<br>
+The following figure shows the relative fluorescence intensity induced by green light and red light.</p>
+[[File:T--SDU-China--4.png|600px|center|thumb|
+<p align="justify">'''Figure 1. Characterization of part BBa_K2627000 and BBa_K592001 in M9 medium whose carbon source is glucose. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index. The #4 has the reverse function and the dynamic range is about 2.6.'''</p>]]<br>
+[[File:T--SDU-China--42.png|600px|center|thumb|
+<p align="justify">'''Figure 2. Characterization of part BBa_K2627000 and BBa_K592001 in M9 medium whose carbon source is glycerol. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index. The #4 has the reverse function and the dynamic range is about 1.5.'''</p>]]
+[[File:T--SDU-China--43.png|600px|center|thumb|
+<p align="justify">'''Figure 3. Characterization of part BBa_K2627000 and BBa_K592001 in M9 medium whose nitrogen source is yeast extract. Part BBa_K2627000 shows a different effect that the index under red light is higher than the index under green light. For this reason, we can treat the index under red light as expression index and treat the index under green light as leak index. The #4 has the reverse function and the dynamic range is about 1.2.'''</p>]]