Difference between revisions of "Part:BBa K3733010"
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Zhangyuanpu (Talk | contribs) (→Test Protocol) |
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<partinfo>BBa_K3733010 short</partinfo> | <partinfo>BBa_K3733010 short</partinfo> | ||
| − | HepT is a toxin | + | HepT is a toxin, a member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) superfamily, strongly inhibiting cell growth in <i>S.oneidensis</i> and <i>Escherichia coli</i>. The HepT toxin (HEPN-domain protein) could function as an RNase with a RX4-6H active motif and cleave mRNA to inhibit cell growth.[1] |
<p> | <p> | ||
HepT/MntA is one kind of Toxin/Antitoxin (TA) systems in which the enzyme antitoxin chemically modifies the toxin to neutralize it. [1] | HepT/MntA is one kind of Toxin/Antitoxin (TA) systems in which the enzyme antitoxin chemically modifies the toxin to neutralize it. [1] | ||
| Line 10: | Line 10: | ||
===Usage and Biology=== | ===Usage and Biology=== | ||
<p> | <p> | ||
| − | + | The mechanism of the HepT toxin is common in bacteria and archaea. Cytotoxicity is based on the fact that HepT can bind to mRNA, and induce degradation of the mRNA. | |
</p> | </p> | ||
<p> | <p> | ||
| Line 18: | Line 18: | ||
===Functional Parameters=== | ===Functional Parameters=== | ||
<p> | <p> | ||
| − | To | + | To verify the cytotoxicity of HepT, we transferred pET-28a(+)-HepT into <i>E.coil</i> BL21(DE3). The <i>E.coil</i> strain was cultured to OD<sub>600</sub> = 0.4 ~ 0.6, induced with or without 0.5 mM IPTG, and was allowed to grow overnight at 37℃. In the 96-well plates, the Synergy H1 microplate reader was used to measure the cytotoxicity by comparing the OD<sub>600</sub> between experimental group and control group. The results obtained from triple independent experiments are shown below (<b>Figure 1</b>). |
</p> | </p> | ||
<html> | <html> | ||
<head> | <head> | ||
| − | < | + | <meta charset="utf-8"> |
<title>无标题文档</title> | <title>无标题文档</title> | ||
</head> | </head> | ||
<body> | <body> | ||
| − | <center>< | + | <center><img src="https://static.igem.org/mediawiki/parts/0/08/T--HZAU-China-HepT-basic-1.png" style="width:793px;height:360px"></center> |
| − | <center><b>Figure | + | <center><b>Figure 1. A.</b> Turbidity change of the experimental group (induced by IPTG) and control group (without IPTG). <b>B.</b> The result of OD<sub>600</sub> (-IPTG and +IPTG) presents the cytotoxicity of HepT. The error bars are obtained from three independent experiments. </center> |
<br> | <br> | ||
</body> | </body> | ||
| Line 39: | Line 39: | ||
===Experience=== | ===Experience=== | ||
<p> | <p> | ||
| − | This part was used | + | This part was used in iGEM21_HZAU-China`s project “<b>P.E.T</b>”. Considering intestinal temperature of dogs is normally higher than room temperature, we decided to enable the bacteria to kill themselves at low temperatures and only survive at intestinal temperature. To achieve such a function, we utilized RNA thermometers and the HepT toxin to build this module. We used HepT as toxin to let the engineered bacteria suicide or lose competitive advantage in the nature environment until they die off. |
</p> | </p> | ||
| Line 51: | Line 51: | ||
<partinfo>BBa_K3733010 parameters</partinfo> | <partinfo>BBa_K3733010 parameters</partinfo> | ||
<!-- --> | <!-- --> | ||
| + | == Characterized by HZAU_China 2023 == | ||
| + | |||
| + | ===Test Design=== | ||
| + | We referred to the method of verifying Hept by iGEM21_HZAU-China BBa_K3733010. To verify the cytotoxicity of HepT, we connected the HepT toxin protein after the lactose promoter and transferred it to E. coli BL21(DE3) using pet28a. E. coli strains were cultured to OD600 = 0.4-0.6 and induced with 0.5mM, 0.75mM IPTG, then allowed to grow continuously for 5 hours at 37°C. In 96-well plates, cytotoxicity was measured by comparing OD600 between the experimental group and control group using Synergy H1 enzyme-labeled detector. | ||
| + | ===Test Protocol=== | ||
| + | <b>Toxin protein HepT OD600 detection</b> | ||
| + | <p> 1) Methods of molecular cloning and transformation are described above. Transform this plasmid into E. coli BL21. Then spread it onto LB medium plates with 50 μg/mL kanamycin and incubate overnight at 37 °C in an incubator. </p> | ||
| + | <p> 2) Pick four colonies from the same plate as parallel repeats. Each colony is inoculated in two identical media with 5 ml LB medium containing 50 μg/mL kanamycin and cultured at temperature (37 °C) respectively while shaking at 200 rpm. </p> | ||
| + | <p> 3) Measure the OD600 value of the resuspension culture media in an automatic microplate reader (SynergyH1 hybrid multimodal reader) until the OD600 of the bacteria solution reaches 0.4-0.6. </p> | ||
| + | <p> 4) Add IPTG to the bacteria solution of the experimental group to induce expression of the toxin proteins.</p> | ||
| + | <p> 5) Plot the OD600 value curves of the resuspension culture media over time in an automatic microplate reader (SynergyH1 hybrid multimodal reader). Incubate the cultures for 4 hours at 37°C while shaking at 200 rpm. Take samples at intervals or continuously measure the OD600 data of the bacteria solution with a UV spectrophotometer. And then convert the raw data into OD600. Compare the data of experimental groups and control group and compare curves in two schemes with each other.</p> | ||
| + | |||
| + | ===Result=== | ||
| + | <html> | ||
| + | <head> | ||
| + | <meta charset="utf-8"> | ||
| + | <title>无标题文档</title> | ||
| + | </head> | ||
| + | <body> | ||
| + | <center><img src="https://static.igem.wiki/teams/4645/wiki/wet-lab/suicide/hept1-1.jpg" style="width:50%; "></center> | ||
| + | <br> | ||
| + | <center><b>Figure 1. Bacterial OD600 over time .</b> </center> | ||
| + | <br> | ||
| + | </body> | ||
| + | </html> | ||
| + | |||
| + | ===Analysis of the experimental results=== | ||
| + | As shown in Figure 1., the toxin protein HepT has a very obvious bactericidal effect, and this effect is dose-dependent, correlating with the induction concentration of IPTG within a certain range. | ||
Latest revision as of 05:34, 11 October 2023
HepT: A toxin can cleave mRNA
HepT is a toxin, a member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) superfamily, strongly inhibiting cell growth in S.oneidensis and Escherichia coli. The HepT toxin (HEPN-domain protein) could function as an RNase with a RX4-6H active motif and cleave mRNA to inhibit cell growth.[1]
HepT/MntA is one kind of Toxin/Antitoxin (TA) systems in which the enzyme antitoxin chemically modifies the toxin to neutralize it. [1]
Usage and Biology
The mechanism of the HepT toxin is common in bacteria and archaea. Cytotoxicity is based on the fact that HepT can bind to mRNA, and induce degradation of the mRNA.
HepT dimerization enables the formation of a deep cleft at the HEPN-domain interface harboring a composite Rx4-6H active site that functions as an RNA-cleaving ribonuclease. [2][3]
Functional Parameters
To verify the cytotoxicity of HepT, we transferred pET-28a(+)-HepT into E.coil BL21(DE3). The E.coil strain was cultured to OD600 = 0.4 ~ 0.6, induced with or without 0.5 mM IPTG, and was allowed to grow overnight at 37℃. In the 96-well plates, the Synergy H1 microplate reader was used to measure the cytotoxicity by comparing the OD600 between experimental group and control group. The results obtained from triple independent experiments are shown below (Figure 1).
Reference
[1] Yao J, Zhen X, Tang K, et al. Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system[J]. Nucleic acids research, 2020, 48(19): 11054-11067.
[2] Yao J, Guo Y, Zeng Z, et al. Identification and characterization of a HEPN‐MNT family type II toxin–antitoxin in S hewanella oneidensis[J]. Microbial biotechnology, 2015, 8(6): 961-973.
[3] Jia X, Yao J, Gao Z, et al. Structure–function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN–MNT toxin–antitoxin system[J]. Journal of Biological Chemistry, 2018, 293(18): 6812-6823.
Experience
This part was used in iGEM21_HZAU-China`s project “P.E.T”. Considering intestinal temperature of dogs is normally higher than room temperature, we decided to enable the bacteria to kill themselves at low temperatures and only survive at intestinal temperature. To achieve such a function, we utilized RNA thermometers and the HepT toxin to build this module. We used HepT as toxin to let the engineered bacteria suicide or lose competitive advantage in the nature environment until they die off.
Sequence and Features
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Characterized by HZAU_China 2023
Test Design
We referred to the method of verifying Hept by iGEM21_HZAU-China BBa_K3733010. To verify the cytotoxicity of HepT, we connected the HepT toxin protein after the lactose promoter and transferred it to E. coli BL21(DE3) using pet28a. E. coli strains were cultured to OD600 = 0.4-0.6 and induced with 0.5mM, 0.75mM IPTG, then allowed to grow continuously for 5 hours at 37°C. In 96-well plates, cytotoxicity was measured by comparing OD600 between the experimental group and control group using Synergy H1 enzyme-labeled detector.
Test Protocol
Toxin protein HepT OD600 detection
1) Methods of molecular cloning and transformation are described above. Transform this plasmid into E. coli BL21. Then spread it onto LB medium plates with 50 μg/mL kanamycin and incubate overnight at 37 °C in an incubator.
2) Pick four colonies from the same plate as parallel repeats. Each colony is inoculated in two identical media with 5 ml LB medium containing 50 μg/mL kanamycin and cultured at temperature (37 °C) respectively while shaking at 200 rpm.
3) Measure the OD600 value of the resuspension culture media in an automatic microplate reader (SynergyH1 hybrid multimodal reader) until the OD600 of the bacteria solution reaches 0.4-0.6.
4) Add IPTG to the bacteria solution of the experimental group to induce expression of the toxin proteins.
5) Plot the OD600 value curves of the resuspension culture media over time in an automatic microplate reader (SynergyH1 hybrid multimodal reader). Incubate the cultures for 4 hours at 37°C while shaking at 200 rpm. Take samples at intervals or continuously measure the OD600 data of the bacteria solution with a UV spectrophotometer. And then convert the raw data into OD600. Compare the data of experimental groups and control group and compare curves in two schemes with each other.
Result
Analysis of the experimental results
As shown in Figure 1., the toxin protein HepT has a very obvious bactericidal effect, and this effect is dose-dependent, correlating with the induction concentration of IPTG within a certain range.