Difference between revisions of "Part:BBa K1104200"

(→‎Introduction)
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*ahpC ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)] is improved its complex composition and Assembly Compatibility by us. We designed ahpC ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)] improvement into 6 versions:
 
*ahpC ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)] is improved its complex composition and Assembly Compatibility by us. We designed ahpC ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)] improvement into 6 versions:
−
**AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
+
{| border="1" cellpadding="5" cellspacing="0"
−
**AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
+
| AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
−
**AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
+
| The PstI cutting site is mutated.
−
**AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206])
+
|-
−
**AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207])
+
| AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
−
**DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
+
| After mutating the PstI cutting site, the truncated coding sequence from the DsbG promoter sequence is removed.
 +
|-
 +
| AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
 +
| Only one promoter(AhpCp2) and its TFBS.
 +
|-
 +
| 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.
 +
|}
  
 
In order to enhance the strength and sensitivity of ROS-sensing promoters, we make E. coli continuously produce inactivated OxyR transcription factors, so that ROS can affect promoters more easily.  
 
In order to enhance the strength and sensitivity of ROS-sensing promoters, we make E. coli continuously produce inactivated OxyR transcription factors, so that ROS can affect promoters more easily.  
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===Related Parts===
 
===Related Parts===
−
#TrxCp ([https://parts.igem.org/Part:BBa_K1104201 Part:BBa_K1104201])
+
{| border="1" cellpadding="5" cellspacing="0"
−
#[https://parts.igem.org/Part:BBa_K1104241 Part:BBa_K1104241]: TrxCp+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
| colspan=6 align="center"| ahpC([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)]
−
#HemHp ([https://parts.igem.org/Part:BBa_K1104202 Part:BBa_K1104202])
+
|-
−
#[https://parts.igem.org/Part:BBa_K1104242 Part:BBa_K1104242]: HemHp+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
| AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
−
#sufA ([https://parts.igem.org/Part:BBa_K362005 Part:BBa_K362005])
+
| AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
−
*ahpC ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)]
+
| AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
−
**AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
+
| AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206])
−
***[https://parts.igem.org/Part:BBa_K1104242 Part:BBa_K1104243]: AhpCp1000+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
| AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207])
−
**AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
+
| DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
−
***[https://parts.igem.org/Part:BBa_K1104244 Part:BBa_K1104244]: AhpCp2D1+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
|-
−
**AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
+
| AhpCp1000+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104243 Part:BBa_K1104243])
−
***[https://parts.igem.org/Part:BBa_K1104245 Part:BBa_K1104245]: AhpCp2+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
| AhpCp2D1+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104244 Part:BBa_K1104244])  
−
**AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206])
+
| AhpCp2+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104245 Part:BBa_K1104245])  
−
***[https://parts.igem.org/Part:BBa_K1104246 Part:BBa_K1104246]: AhpCpD1+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
| AhpCpD1+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104246 Part:BBa_K1104246])  
−
**AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207])
+
| AhpCp1+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104247 Part:BBa_K1104247])  
−
***[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])
+
|}
−
***[https://parts.igem.org/Part:BBa_K1104248 Part:BBa_K1104248]: DsbGp+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
  
 
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Revision as of 11:18, 27 October 2013

OxyR

Introduction

OxyR is Escherichia coli transcription factor that senses H2O2 to activate transcription, and is activated through the formation of an intramolecular disulfide bond. The OxyR gene, a positive regulatory gene for the oxidative response, then controls proteins which are induced by treatment with H2O2.

OxyR (BBa_K1104200)

Literature Study of OxyR

Illustration of OxyR Activation

OxyR, a positive regulator of hydrogen peroxide-inducible genes in E. coli. The OxyR transcription factor regulates the H2O2 response of E. coli.

Oxidative stress, through the production of Reactive Oxygen Species (ROS) , is a natural consequence of aerobic metabolism. Escherichia coli has several major regulators activated during oxidative stress, including OxyR, SoxRS, and RpoS. OxyR undergo conformation changes when oxidized in the presence of hydrogen peroxide, then positively controls the expression of cognate genes.

Reference: Chiang, S. M., Schellhorn, H. E., & Catalases and Hydrogen Peroxide Metabolism. (September 15, 2012) . Regulators of oxidative stress response genes in Escherichia coli and their functional conservation in bacteria. Archives of Biochemistry and Biophysics, 525, 2, 161-169.

H2O2 oxidizes OxyR Cys199 to an R-SOH that reacts with Cys208 in an intramolecular disulphide bond.

Structure of the OxyR Regulatory Domain
(A) Reduced Form: Inactive
(B) Oxidized Form: Activated by ROS
Reference: D'Autréaux, B., & Toledano, M. B. (October 01, 2007). ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis. Nature Reviews Molecular Cell Biology, 8, 10, 813-824.

Usage and Biology

After Nosema ceranae enter bees' midgut, the natural immune reaction will lead to ROS released by epithelia of bees' midgut. In our project: Bee. coli, we use OxyR-induced promoter as the sensor of Bee. coli to sense Nosema ceranae. We select several promoters that can be induced by OxyR(Part:BBa_K1104200).

There are promoters that can be activated by OxyR: TrxCp(Part:BBa_K1104201), HemHp (Part:BBa_K1104202) , ahpC (Part:BBa_K362001) , sufA (Part:BBa_K362005) , and dps (Part:BBa_K362002) , yiaA (Part:BBa_K362006) .

The OxyR-induced promoters:

  • TrxCp (Part:BBa_K1104201) and HemHp (Part:BBa_K1104202) are parts created by our team [http://2013.igem.org/Team:NYMU-Taipei/Modeling/MainParts NYMU_Taipei]. (Come to the [http://2013.igem.org/Team:NYMU-Taipei/Experiment/Wet_Lab Wet Lab] page to see our part list.)
  • sufA (Part:BBa_K362005) , designed by [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team], is successfully characterized again by us.
AhpCp1000 (Part:BBa_K1104203) 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.
AhpCp2 (Part:BBa_K1104205) Only one promoter(AhpCp2) and its TFBS.
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.

In order to enhance the strength and sensitivity of ROS-sensing promoters, we make E. coli continuously produce inactivated OxyR transcription factors, so that ROS can affect promoters more easily.

We designed a device that is composed of a sensor (OxyR-induced promoter, including TrxCp, HemHp, sufA, AhpCp1000, AhpCp2D1, AhpCp2, AhpCpD1, AhpCp1, DsbGp) plus reporter (Part:BBa_E0840). Device1 in order to enhance the effect of ROS on E. coli is added ahead: a constitutive promoter(Part:BBa_J23102), and OxyR(Part:BBa_K1104200).

Related Parts

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

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]