Difference between revisions of "Part:BBa K3606027"

Revision as of 02:54, 25 October 2020

cold triggered RelE/RelB Kill Switch

This composite part is a cold triggered kill switch to deprive of survivability of engineered bacteria in the environment when excreted from the intestine. It consists of a RelE/RelB toxin/antitoxin module and an RNA thermometer NoChill-06 to regulate it.

The antitoxin RelB is liable and expressed at a relatively high level. The RelE toxin is constitutively co-expressed with the antitoxin under the control of an RNA thermometer No-Chill 06. Under the body temperature (37℃)，No-Chill 06 unfolds and exposes its ribosome binding site (RBS) to express. RelE and RelB neutralize each other by protein-protein interaction and form a stable complexity. When the bacteria encounter a cold shock(30℃), RelB is degraded rapidly by an ATP-dependent serine protease Lon and releases RelE. The toxin RelE acts as a global translational inhibitor to cleave mRNAs under translating at the ribosomal A site, therefore resulting in cell growth arrest and finally cell deathCite error: Closing </ref> missing for <ref> tag

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-This composite part is a cold triggered kill switch to deprive of  survivability of engineered Nissle in the environment when excreted with feces, we introduced the first kill switch, consisting a toxin-antitoxin system and an RNA thermometer to regulate it. The toxin RelE has the ability to shut down protein synthesis and cleave mRNA within the ribosomal A site.[1] RelE can result in cell death and is expressed constitutively. The antitoxin RelB is the neutralizer of RelE therefore is able to inhibit the cleavage of mRNA making probiotic survive. [2] RelB is expressed under the control of an RNA thermometer No-Chill 06. Under the body temperature (37&#8451;)&#65292;No-Chill 06 unfolded and expose its ribosome binding site (RBS) starting the expression of RelB. While under 30&#8451;, RelB is not expressed and RelE will kill the probiotic.
+This composite part is a cold triggered kill switch to deprive of survivability of engineered bacteria in the environment when excreted from the intestine. It consists of a RelE/RelB toxin/antitoxin module and an RNA thermometer NoChill-06 to regulate it.
+The antitoxin RelB is liable and expressed at a relatively high level. The RelE toxin is constitutively co-expressed with the antitoxin under the control of an RNA thermometer No-Chill 06. Under the body temperature (37℃)，No-Chill 06 unfolds and exposes its ribosome binding site (RBS) to express. RelE and RelB neutralize each other by protein-protein interaction and form a stable complexity. When the bacteria encounter a cold shock(30℃), RelB is degraded rapidly by an ATP-dependent serine protease Lon and releases RelE. The toxin RelE acts as a global translational inhibitor to cleave mRNAs under translating at the ribosomal A site, therefore resulting in cell growth arrest and finally cell death<ref>Unterholzner, Simon J et al. “Toxin-antitoxin systems: Biology, identification, and application.” Mobile genetic elements vol. 3,5 (2013): e26219. doi:10.4161/mge.26219<ref>.
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-===Usage and Biology===
+===Biology===
+RelE/RelB is one of the best characterized type II toxin/antitoxin systems. The type II toxin/antitoxin system is a mature and stable system that is extensively applied both inside and outside the iGEM competition. In the type II toxin/antitoxin systems, the antitoxin is liable but expressed at a relative high level. And the toxin is constitutively co-expressed with the antitoxin form a stable complexity. When the bacteria encounter special growth conditions, the antitoxin is degraded rapidly by an ATP-dependent serine protease Lon and releases the toxin, therefore resulting cell growth arrest.
+In the context of cold triggered RelE/RelB Kill Switch, the toxin RelE is a global translational inhibitor that cleaves mRNA after the second nucleotide in the empty ribosomal A sites. RelE does not exhibit endoribonuclease activity by itself but act as a ribosome-associated factor tightly interacting with 16S rRNA to executive cleavage function. And RelE shows a modest sequence preference for select codons (CAG, UCG and the stop codon UAG)<ref>Hwang, Jae-Yeon, and Allen R Buskirk. “A ribosome profiling study of mRNA cleavage by the endonuclease RelE.” Nucleic acids research vol. 45,1 (2017): 327-336. doi:10.1093/nar/gkw944<ref>.
+RelB is the antagonist of RelE that can form a stable complexity in a two-to-two or one-to-two ratio with RelE<ref>Hwang, Jae-Yeon, and Allen R Buskirk. “A ribosome profiling study of mRNA cleavage by the endonuclease RelE.” Nucleic acids research vol. 45,1 (2017): 327-336. doi:10.1093/nar/gkw944<ref>.RelB can be degraded rapidly by an ATP-dependent serine protease Lon and releases RelE.
+RNA thermometers are short RNA with special hairpin structure that can response to the temperature change. The hairpin structure occludes the ribosome binding site (RBS) and inhibit the small ribosomal subunit from assembly therefore inhibit the translation. Because of a small number of mismatched base pairs in the complimentary sequence, RNA thermometers unfold easily when encounter a temperature increase then exposes its RBS facilitating protein expression.
+NoChill-06 is a modified RNA thermometer designed by team 19Rice using NUPACK and VSAlgorithm. They mutated the nucleotides by the side of RBS with RBS unchanged obtaining a series of NoChill RNA thermometers that response to temperature change between 25 °C and 37 °C efficiently. NoChill-06 reacts very sensitively when temperature increase from30℃ to 37 °C, so it is appropriate for regulation in human body.
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 <partinfo>BBa_K3606027 parameters</partinfo>
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+===Protocol for characterization===
+Growth Curve Measurement
+.Plasmids construction and transformation: Insert DNA fragments of BBa_K3606027 in to pSB1C3. Transform the two kinds of constructed plasmids into DH5α strain as experimental groups and empty pSB1C plasmids as control group. Culture three groups in 60mL LB medium (with 50 ng/µl ampicillin) at 37℃ overnight.
+.Cold treatment: Divide each group into two test tubes for 30℃-culture groups and 37℃-culture groups. (3 for each temperature).
+.Measure growth situation: Extract 5μl bacteria solution from each test tube every 1h. Diluted each bacteria solution to 10^7 times and culture them on three LB plate (with 50 ng/µl ampicillin) at 37℃ for 24h. Count the number of colonies in 5 cm^2 per plate after cultured for 24h at 37℃.
+.Draw the growth curve.