Difference between revisions of "Part:BBa K1104206"
(→‎How ahpCp (Part:BBa_K362001) is improved?)
 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K1104206 short</partinfo>
 
<partinfo>BBa_K1104206 short</partinfo>
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[[File: NYMU_AhpCpD1.png|frame|center|'''AhpCpD1''']]
 
[[File: NYMU_AhpCpD1.png|frame|center|'''AhpCpD1''']]
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: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, shared TFBS (Transcription Factor Binding Site), and reverse promoter DsbG.
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AhpCpD1 is a ROS-induced promoter controlled by OxyR (transcription factor)which is activated by ROS (Reactive Oxygen Species).  
 
[[File: NYMU_AD1x.png|thumb|600px|center|'''Improvement of ahpC promoter([https://parts.igem.org/Part:BBa_K362001 Part:K362001])''']]
 
[[File: NYMU_AD1x.png|thumb|600px|center|'''Improvement of ahpC promoter([https://parts.igem.org/Part:BBa_K362001 Part:K362001])''']]
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:OxyR binding to the ahpC-proximal site leads to the induction of both dsbG and ahpC transcripts, while OxyR binding to the dsbG-proximal site leads to the induction of a second ahpC transcript. This transcript of ahpC and the transcript of dsbG overlap by over 100 nucleotides.
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AhpCpD1 is composed of 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]). There are also a dual-TFBS (Transcription Factor Binding Site) for OxyR binding between DsbGp and AhpCp1.
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:The intergenic region between dsbG and ahpC carries two binding sites for OxyR, a dsbG-proximal site, located 54 bp upstream of the dsbG start codon; an ahpC-proximal site, located 290 bp upstream of the dsbG start codon.
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==Improvement==
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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 AhpCpD1, we succesfully mutated the PstI cutting site (ctgcag->ctacag) of ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:K362001]), and removed the dsbG coding sequence, then removed the AhpCp2(TFBS included).
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ahpC promoter, as well as its improvement, can be activated by OxyR ([https://parts.igem.org/Part:BBa_K1104200 Part:BBa_K1104200]).
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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 first mutating the PstI cutting site in ahpCp ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) and make dsbG coding removed, then removed the AhpCp2(TFBS included).
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===How ahpCp ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) is improved?===
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'''In this part, AhpCp1 and DsbGp are left, making this part a bidirectional hybrid promoter which has the ability to transcription in both directions.'''
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Here is the overview about the other ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) improvements:
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*AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203]): The PstI cutting site is mutated.
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*AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104204]): After mutating the PstI cutting site, the truncated coding sequence from the DsbG promoter sequence is removed.
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*AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]): Only one promoter(AhpCp2) and its TFBS.
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*AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]): Only one promoter(AhpCp1) and its TFBS.
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*DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]): Only the reverse promoter(DsbGp) and its TFBS.
  
 
===Usage and Biology===
 
===Usage and Biology===
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There are two TFBSs between AhpCp1 and reverse DsbGp. OxyR binding to the ahpC-proximal site leads to the induction of both dsbG and ahpC transcripts.  
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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.
  
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Once ROS(Reactive Oxygen Species) oxidizes OxyR, making OxyR interact with the TFBS between AhpCp1 and DsbGp, dual-directional transcription will occur. It can be take advantages of by certain special circuit design.
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To enhance the strength , we added a device (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Sensor Sensing Nosema] page).
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[[File: NYMU_O12.png|frame|center|'''Strenthening device''']]
  
 
===Related Parts===
 
===Related Parts===
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***[https://parts.igem.org/Part:BBa_K1104247 Part:BBa_K1104247]: AhpCp1+[https://parts.igem.org/Part:BBa_E0840 E0840]
 
***[https://parts.igem.org/Part:BBa_K1104247 Part:BBa_K1104247]: AhpCp1+[https://parts.igem.org/Part:BBa_E0840 E0840]
 
**DsbGp([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
 
**DsbGp([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
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***[https://parts.igem.org/Part:BBa_K1104248 Part:BBa_K1104248]: DsbGp+[https://parts.igem.org/Part:BBa_E0840 E0840]
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 22:22, 4 October 2013

AhpCpD1

AhpCpD1

AhpCpD1 is a ROS-induced promoter controlled by OxyR (transcription factor)which is activated by ROS (Reactive Oxygen Species).

Improvement of ahpC promoter(Part:K362001)

AhpCpD1 is composed of reverse promoter DsbGp (Part:BBa_K1104208)and AhpCp1 (Part:BBa_K1104207). There are also a dual-TFBS (Transcription Factor Binding Site) for OxyR binding between DsbGp and AhpCp1.

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 AhpCpD1, we succesfully mutated the PstI cutting site (ctgcag->ctacag) of ahpC promoter (Part:K362001), and removed the dsbG coding sequence, then removed the AhpCp2(TFBS included).

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

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 first mutating the PstI cutting site in ahpCp (Part:BBa_K362001) and make dsbG coding removed, then removed the AhpCp2(TFBS included).

How ahpCp (Part:BBa_K362001) is improved?

In this part, AhpCp1 and DsbGp are left, making this part a bidirectional hybrid promoter which has the ability to transcription in both directions.

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

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


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]