Difference between revisions of "Part:BBa K5136042"
 
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===Usage and design===
 
===Usage and design===
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To prove the <i>hrp</i> AND gate can work. We used <partinfo>BBa_I0500</partinfo> to construct the regulation system and obtained the composite part <partinfo>BBa_K4907124</partinfo> and <partinfo>BBa_K4907125</partinfo>, which were assembled on the expression vector pSB1C3. And we used the pHrpL and GFP(<partinfo>BBa_K4907036</partinfo>) to construct the reporting system and obtained the composite part <partinfo>BBa_K4907123</partinfo>. Those three composite parts together form the verification system of <i>hrp</i> AND gate (Fig. 1) and corresponding gene circuits were transformed into <i>E. coli</i> DH10β for characterization.
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In the darkness, LexRO dimerizes and binds to the cognate operator sequence to repress the activity of pColE408. Upon blue light exposure, the LexRO dimer dissociates, causing dissociation from the operator sequence, and initiates the expression of ccdB， eventually leading to cell death. We used LexRO, pHybrid 2)-114 version, SD7, ccdA, and ccdB to construct the regulation system and obtained the composite part <partinfo>BBa_K5136231</partinfo>, which was assembled on the expression vector pSB4A5.
  
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<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/and-gate.png" width="700px"></html></center>
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===Characterization===
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<center><b>Fig. 1 Gene circuits of verification system for <i>hrp</i> AND gate. </b></center>
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Facing the threat that the unwanted survival and accumulation of engineered bacteria might happen once they escape to opening environment (1), we designed a light-triggered kill switch for biocontainment of the engineered bacteria. Rather than responding to some chemical inducers, the light-triggered kill switch will be turned to ON state after the engineered bacteria is exposed to the light illumination of specific wavelength. We chose a blue light-inducible optogenetic system, LexRO/pColE408 (2), to control the expression of CcdB toxin, in which an additional expression module of CcdA antitoxin was incorporated as well to neutralize the leaky toxin when the kill switch is in OFF state.
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Here, we firstly characterized the cytotoxicity of CcdB toxin and the blue light-inducible performance of LexRO/pColE408 system respectively, and then tested the killing effect of the blue light-induced kill switch. Further optimization for improving the killing effect of the switch was also tried primarily.
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<center><html><img src=" https://static.igem.wiki/teams/5136/result/32.png" width="400px"></html></center>
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<center><b>Figure 1 Characterization of blue light-induced LexRO/pColE408</b>. (<b>A</b>) The gene circuit to characterize blue light-responding performance of LexRO/pColE408 system (BBa_K5136237) on pSB4A5 vector. (<b>B</b>) Agarose gel electrophoresis of the colony PCR products of BBa_K5136237_pSB4A5 in <i>E. coli</i> BL21(DE3). (<b>C</b>) The relative fluorescence units (RFU) of bacterial culture subtracted the background fluorescence of growth media, resulting in the RFU<sub>mCherry</sub>. p-value: 0.0029 (**).</center>
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We turned to characterize the blue light-responding performance of LexRO/pColE408 optogenetic system used in the kill switch. The photosensor LexRO was controlled by a medium constitutive promoter J23106 and a medium RBS SD7 (3) (<partinfo>BBa_K5136045</partinfo>), while the mCherry fluorescent protein (<partinfo>BBa_J06504</partinfo>) was chosen as the reporter under the control of promoter pColE408 (<partinfo>BBa_K5136044</partinfo>) (Figure 1A), thus generating the composite part <partinfo>BBa_K5136237</partinfo> on the pSB4A5 vector. BL21(DE3) was used to characterize this optogenetic system, and positive transformants were selected and confirmed by colony PCR (Figure 1B) and sequencing.
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Characterization was carried out in a self-made blue light (460 nm) illumination device. After cultured for about 17 hours upon blue light illumination (with a relative light intensity of 250) or kept in dark condition, red fluorescence intensity (<i>λe</i><sub>x</sub> = 585 nm, <i>λ</i><sub>em</sub> = 615 nm) and OD600 were measured. The normalized fluorescence intensity of “Light” group showed a significant higher value than that of “Dark” group (about 2 times), indicating that this <b>optogenetic system could be induced by blue light</b> (Figure 1C) indeed.
  
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<br/>If we use CspA Cold-responsive elements to express proteins at low temperatures, there will be a risk of gene leakage at a higher temperature than we expected because the response temperature has a broad range. To solve this problem, we plan to combine a logic AND gate with the CspA CRE. Based on it, we designed an AND gate to respond to low temperature, namely, <i>hrp</i> AND gate. In this system, the <i>hrpR</i> and <i>hrpS</i> genes are regulated by the CspA CRE (Fig. 2). Under low-temperature conditions, only when both proteins are expressed, can the expression of downstream genes be induced, reducing the leaky expression.
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==<b>Reference</b>==
  
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<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/cspa-and-gate.png" width="700px"></html></center>
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1. H. An et al., TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress. <i>Molecular Cell</i> <b>74</b>, 891-908.e810 (2019).
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<center><b>Fig. 2 Gene circuits of <i>hrp</i> system regulated by the CspA CRE.</b></center>
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<br>2. Li X, Zhang C, Xu X, Miao J, Yao J, Liu R, Zhao Y, Chen X, Yang Y. A Single-component Light Sensor System Allows Highly Tunable and Direct Activation of Gene Expression in Bacterial Cells. Nucleic Acids Res. 2020 Apr 6;48(6):e33
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<br>3. Bernard P, Couturier M. Cell Killing by the F Plasmid CcdB Protein Involves Poisoning of DNA-topoisomerase II complexes. J Mol Biol. 1992 Aug 5;226(3):735-45.
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===Characterization===
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<br>4. Chan CT, Lee JW, Cameron DE, Bashor CJ, Collins JJ. 'Deadman' and 'Passcode' Microbial Kill Switches for Bacterial Containment. Nat. Chem. Biol. 2016 Feb;12(2):82-6. 
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====Agarose gel electrophoresis (AGE)====
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<br>5. Choi J, Ahn J, Bae J, Koh M. Recent Synthetic Biology Approaches for Temperature- and Light-Controlled Gene Expression in Bacterial Hosts. Molecules. 2022 Oct 11;27(20):6798.
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When constructing this circuit of composite part <partinfo>BBa_K4907128</partinfo> which includes the gene of HrpR, colony PCR and gene sequencing were used to verify that the transformants were correct. Target bands (1460 bp) can be observed at the position between 1000 and 1500 bp (Fig. 3).
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<br>6. Lalwani MA, Kawabe H, Mays RL, Hoffman SM, Avalos JL. Optogenetic Control of Microbial Consortia Populations for Chemical Production. ACS Synth Biol. 2021 Aug 20;10(8):2015-2029.
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<br>7. Zhang Y, Xue X, Fang M, Pang G, Xing Y, Zhang X, Li L, Chen Q, Wang Y, Chang J, Zhao P, Wang H. Upconversion Optogenetic Engineered Bacteria System for Time-Resolved Imaging Diagnosis and Light-Controlled Cancer Therapy. ACS Appl Mater Interfaces. 2022 Oct 19;14(41):46351-46361.
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<br>8.  Han C, Zhang X, Pang G, Zhang Y, Pan H, Li L, Cui M, Liu B, Kang R, Xue X, Sun T, Liu J, Chang J, Zhao P, Wang H. Hydrogel Microcapsules Containing Engineered Bacteria for Sustained Production and Release of Protein Drugs. Biomaterials. 2022 Aug;287:121619.
  
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<span class='h3bb'>Sequence and Features</span>
 
  
  

Latest revision as of 10:47, 2 October 2024


LexRO

Biology

LexRO is a synthetic light-switchable repressor, based on a novel LOV light sensor domain, RsLOV. In the darkness, LexRO dimerizes and binds to its cognate operator sequence to repress promoter activity. Upon light exposure, the LexRO dimer dissociates, causing dissociation from the operator sequence, and initiates gene expression.

Usage and design

In the darkness, LexRO dimerizes and binds to the cognate operator sequence to repress the activity of pColE408. Upon blue light exposure, the LexRO dimer dissociates, causing dissociation from the operator sequence, and initiates the expression of ccdB， eventually leading to cell death. We used LexRO, pHybrid 2)-114 version, SD7, ccdA, and ccdB to construct the regulation system and obtained the composite part BBa_K5136231, which was assembled on the expression vector pSB4A5.

Characterization

Facing the threat that the unwanted survival and accumulation of engineered bacteria might happen once they escape to opening environment (1), we designed a light-triggered kill switch for biocontainment of the engineered bacteria. Rather than responding to some chemical inducers, the light-triggered kill switch will be turned to ON state after the engineered bacteria is exposed to the light illumination of specific wavelength. We chose a blue light-inducible optogenetic system, LexRO/pColE408 (2), to control the expression of CcdB toxin, in which an additional expression module of CcdA antitoxin was incorporated as well to neutralize the leaky toxin when the kill switch is in OFF state. Here, we firstly characterized the cytotoxicity of CcdB toxin and the blue light-inducible performance of LexRO/pColE408 system respectively, and then tested the killing effect of the blue light-induced kill switch. Further optimization for improving the killing effect of the switch was also tried primarily.

Figure 1 Characterization of blue light-induced LexRO/pColE408. (A) The gene circuit to characterize blue light-responding performance of LexRO/pColE408 system (BBa_K5136237) on pSB4A5 vector. (B) Agarose gel electrophoresis of the colony PCR products of BBa_K5136237_pSB4A5 in E. coli BL21(DE3). (C) The relative fluorescence units (RFU) of bacterial culture subtracted the background fluorescence of growth media, resulting in the RFUmCherry. p-value: 0.0029 (**).

We turned to characterize the blue light-responding performance of LexRO/pColE408 optogenetic system used in the kill switch. The photosensor LexRO was controlled by a medium constitutive promoter J23106 and a medium RBS SD7 (3) (BBa_K5136045), while the mCherry fluorescent protein (BBa_J06504) was chosen as the reporter under the control of promoter pColE408 (BBa_K5136044) (Figure 1A), thus generating the composite part BBa_K5136237 on the pSB4A5 vector. BL21(DE3) was used to characterize this optogenetic system, and positive transformants were selected and confirmed by colony PCR (Figure 1B) and sequencing. Characterization was carried out in a self-made blue light (460 nm) illumination device. After cultured for about 17 hours upon blue light illumination (with a relative light intensity of 250) or kept in dark condition, red fluorescence intensity (λex = 585 nm, λem = 615 nm) and OD600 were measured. The normalized fluorescence intensity of “Light” group showed a significant higher value than that of “Dark” group (about 2 times), indicating that this optogenetic system could be induced by blue light (Figure 1C) indeed.

Reference

1. H. An et al., TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress. Molecular Cell 74, 891-908.e810 (2019).
2. Li X, Zhang C, Xu X, Miao J, Yao J, Liu R, Zhao Y, Chen X, Yang Y. A Single-component Light Sensor System Allows Highly Tunable and Direct Activation of Gene Expression in Bacterial Cells. Nucleic Acids Res. 2020 Apr 6;48(6):e33
3. Bernard P, Couturier M. Cell Killing by the F Plasmid CcdB Protein Involves Poisoning of DNA-topoisomerase II complexes. J Mol Biol. 1992 Aug 5;226(3):735-45.
4. Chan CT, Lee JW, Cameron DE, Bashor CJ, Collins JJ. 'Deadman' and 'Passcode' Microbial Kill Switches for Bacterial Containment. Nat. Chem. Biol. 2016 Feb;12(2):82-6. 
5. Choi J, Ahn J, Bae J, Koh M. Recent Synthetic Biology Approaches for Temperature- and Light-Controlled Gene Expression in Bacterial Hosts. Molecules. 2022 Oct 11;27(20):6798.
6. Lalwani MA, Kawabe H, Mays RL, Hoffman SM, Avalos JL. Optogenetic Control of Microbial Consortia Populations for Chemical Production. ACS Synth Biol. 2021 Aug 20;10(8):2015-2029.
7. Zhang Y, Xue X, Fang M, Pang G, Xing Y, Zhang X, Li L, Chen Q, Wang Y, Chang J, Zhao P, Wang H. Upconversion Optogenetic Engineered Bacteria System for Time-Resolved Imaging Diagnosis and Light-Controlled Cancer Therapy. ACS Appl Mater Interfaces. 2022 Oct 19;14(41):46351-46361.
8. Han C, Zhang X, Pang G, Zhang Y, Pan H, Li L, Cui M, Liu B, Kang R, Xue X, Sun T, Liu J, Chang J, Zhao P, Wang H. Hydrogel Microcapsules Containing Engineered Bacteria for Sustained Production and Release of Protein Drugs. Biomaterials. 2022 Aug;287:121619.