Difference between revisions of "Part:BBa K1104208"

Revision as of 21:34, 4 October 2013

DsbGp

DsbGp

DsbGp is a ROS-induced promoter, which is controlled by OxyR (transcription factor) activated by ROS (Reactive Oxygen Species).

DsbGp is composed of DsbGp promoter and a dual-TFBS (Transcription Factor Binding Site) for OxyR binding.

Improvement of ahpC promoter(Part:K362001)

OxyR is activator of DsbGp promoter. More details about OxyR can be found on the PartRegistry page: Part:BBa_K1104200.

Improvement

We improved a BioBrick Part: ahpC promoter (Part:K362001) designed by [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team]. On PartRegistry, the complex part(according to [http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]) composition contains hybrid promoters, shared TFBS (Transcription Factor Binding Site), and reverse promoter DsbG. In this part DsbGp, we succesfully seperated DsbGp(TFBS included) out of ahpC promoter (Part:K362001).

ahpC promoter, as well as its improvement, can be activated by OxyR (Part:BBa_K1104200).

Where DsbGp is improved?

In this part, we succesfully seperated DsbGp (TFBS included) out of ahpC promoter (Part:K362001).

How ahpCp (Part:BBa_K362001) is improved?

We annotated it thouroughly based on data from ([http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]), and found that it contains dsbG coding sequence, AhpCp2 (Part:BBa_K1104205), reverse promoter DsbGp (Part:BBa_K1104208),and AhpCp1 (Part:BBa_K1104207), and a PstI cutting site. Thus we improved the promoter by extracting the AhpCp2(TFBS included).

Here is the overview about the other ahpC promoter (Part:BBa_K362001) improvements:

AhpCp1000 (Part:BBa_K1104204): The PstI cutting site is mutated.
AhpCp2D1 (Part:BBa_K1104204): After mutating the PstI cutting site, the truncated coding sequence from the DsbG promoter sequence is removed.
AhpCpD1 (Part:BBa_K1104206): Bidirectional promoter: AhpCp1 and DsbGp(reverse promoter), and their shared TFBS.
AhpCp1 (Part:BBa_K1104207): Only one promoter(AhpCp1) and its TFBS.
AhpCp2 (Part:BBa_K1104205): Only one promoter(AhpCp2) and its TFBS.

Usage and Biology

We designed circuit fighting against Nosema ceranae. After Nosema ceranae infected midgut cells of bees, and Bee. coli should sense the pathogen first before the following circuit(fighting against Nosema ceranae)is triggered, and substance such as Defensin (Part:BBa_K1104300), Abaesin(Part:BBa_K1104301) (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Killing Killing Nosema] page) in the following circuit will express.

To enhance the strength , we added a device (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Sensor Sensing Nosema] page).

Strenthening device

Related Parts

ahpC(Part:BBa_K362001)
- AhpCp1000(Part:BBa_K1104203)
  - Part:BBa_K1104243: AhpCp1000+E0840
- AhpCp2D1(Part:BBa_K1104204)
  - Part:BBa_K1104244: AhpCp2D1+E0840
- AhpCp2(Part:BBa_K1104205)
  - Part:BBa_K1104245: AhpCp2+E0840
- AhpCpD1(Part:BBa_K1104206)
  - Part:BBa_K1104246: AhpCpD1+E0840
- AhpCp1(Part:BBa_K1104207)
  - Part:BBa_K1104247: AhpCp1+E0840
- DsbGp(Part:BBa_K1104208)
  - Part:BBa_K1104248: DsbGp+E0840

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
COMPATIBLE WITH RFC[1000]

@@ Line 2: / Line 2: @@
 <partinfo>BBa_K1104208 short</partinfo>
 [[File: NYMU_DsbGp.png|frame|center|'''DsbGp''']]
-We improve the function of a BioBrick Part: AhpC promoter([https://parts.igem.org/Part:BBa_K362001 K362001])designed by [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team] into four versions.On PartRegistry, the complex part(according to [http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]) composition contains hybrid promoters(AhpC1, AhpC2, and DsbG promoter), shared TFBS (Transcription Factor Binding Site), and reverse promoter DsbG.
-There is only DsbGp promoter in this part. We designed the new part and test the promoter separately.
+DsbGp is a ROS-induced promoter, which is controlled by OxyR (transcription factor) activated by ROS (Reactive Oxygen Species).
+DsbGp is composed of DsbGp promoter and a dual-TFBS (Transcription Factor Binding Site) for OxyR binding.
 [[File: NYMU_Ax.png|thumb|600px|center|'''Improvement of ahpC promoter([https://parts.igem.org/Part:BBa_K362001 Part:K362001])''']]
-===Related Parts===
+OxyR is activator of DsbGp promoter. More details about OxyR can be found on the PartRegistry page: [https://parts.igem.org/Part:BBa_K1104200 Part:BBa_K1104200].
+==Improvement==
+We improved a BioBrick Part: ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:K362001]) designed by [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team].  On PartRegistry, the complex part(according to [http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]) composition contains hybrid promoters, shared TFBS (Transcription Factor Binding Site), and reverse promoter DsbG. In this part DsbGp, we succesfully seperated DsbGp(TFBS included) out of ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:K362001]).
+ahpC promoter, as well as its improvement, can be activated by OxyR ([https://parts.igem.org/Part:BBa_K1104200 Part:BBa_K1104200]).
+===Where DsbGp is improved?===
+In this part, we succesfully seperated DsbGp (TFBS included) out of ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:K362001]).
+===How ahpCp ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) is improved?===
+We annotated it thouroughly based on data from ([http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]), and found that it contains dsbG coding sequence, AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]), reverse promoter DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]),and AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]), and a PstI cutting site. Thus we improved the promoter by extracting the AhpCp2(TFBS included).
+Here is the overview about the other ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) improvements:
+*AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204]): The PstI cutting site is mutated.
+*AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204]): After mutating the PstI cutting site, the truncated coding sequence from the DsbG promoter sequence is removed.
+*AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206]): Bidirectional promoter: AhpCp1 and DsbGp(reverse promoter), and their shared TFBS.
+*AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]): Only one promoter(AhpCp1) and its TFBS.
+*AhpCp2 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104205]): Only one promoter(AhpCp2) and its TFBS.
+===Usage and Biology===
+We designed circuit fighting against ''Nosema ceranae''. After Nosema ceranae infected midgut cells of bees, and Bee. coli should sense the pathogen first before the following circuit(fighting against Nosema ceranae)is triggered, and substance such as [https://parts.igem.org/Part:BBa_K1104300 Defensin (Part:BBa_K1104300)], [https://parts.igem.org/Part:BBa_K1104301  Abaesin(Part:BBa_K1104301)] (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Killing Killing Nosema] page) in the following circuit will express.
+To enhance the strength , we added a device (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Sensor Sensing Nosema] page).
+[[File: NYMU_O12.png|frame|center|'''Strenthening device''']]
+===Related Parts===
 *ahpC([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)]
 **AhpCp1000([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
@@ Line 21: / Line 49: @@
 **DsbGp([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
 ***[https://parts.igem.org/Part:BBa_K1104248 Part:BBa_K1104248]: DsbGp+[https://parts.igem.org/Part:BBa_E0840 E0840]
 <!-- Add more about the biology of this part here
 ===Usage and Biology===