Revision as of 10:01, 2 October 2021 (view source) Igkoni (Talk | contribs) (→‎Thessaly 2021 Literature Characterization) ← Older edit		Revision as of 18:48, 6 October 2021 (view source) Igkoni (Talk | contribs) (→‎Thessaly 2021 Literature Characterization) Newer edit →
Line 15:		Line 15:
	[https://2021.igem.org/Team:Thessaly Thessaly 2021]contributed to the characterization of this part by adding new documentation learned from the literature highlighting why CymR is a better repressor for the cumate kill-switch.		[https://2021.igem.org/Team:Thessaly Thessaly 2021]contributed to the characterization of this part by adding new documentation learned from the literature highlighting why CymR is a better repressor for the cumate kill-switch.
		+
		+	<p>CymR repressor belongs to the widespread and poorly characterized Rrf2 family of regulators.
		+	The rrf2-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 130 residues present in transcription regulators of the rrf2 family.("InterPro", 2021) The global regulator CymR represses the transcription of a large set of genes(Shepard, W.(2011)). </p>
		+	<p>So, we chose CymR for our kill-switch because :
		+	*It is characterized by little leakage
		+	*It is sensitive while it is induced by small amounts of cumate
		+	*It has high affinity as there is no other inducer
		+	*Its inducer is non toxic, cheap
		+	*It is reversible because in the absence of cumate it binds again in its CuO operator
		+	*It is orthogonal as its inducer is not naturally found in gut </p>
		+
		+
		+
		+	Kill switches are safety mechanisms needed to secure the desirable function of a biological system.There are many biological kill-switches used daily in synthetic systems in order to ensure the safety of environmental, human and animal health.
		+
		+	In figure 1, we see the cumate gene switch system. It consists of a repressor, the CymR repressor, an operator site and a toxin. In the absence of cumate, CymR binds to the CuO operator and blocks the production of the target gene, a toxin in our case. On the other hand when cumate is present, it binds to the binding domain of CymR, losing its affinity for CuO, and so the target gene- toxin is expressed, killing the bacteria.This system allows for tight control of gene expression over a linear range in a cumate concentration dependent manner, which is particularly important for the expression of toxic proteins(Seo SO, Schmidt-Dannert C.(2019)).
		+
		+
	===Sequence and Features===		===Sequence and Features===
	<partinfo>BBa_K415202 SequenceAndFeatures</partinfo>		<partinfo>BBa_K415202 SequenceAndFeatures</partinfo>

---

Revision as of 18:48, 6 October 2021

cymR Repressor Protein

The cymR repressor tightly and efficiently binds the cmt operator. In conjunction with part BBa_K415200, this repressor may be used to create an inverter or similar logical circuitry. cymR changes conformation upon induction with cumate (isopropylbenozate), and may be used in a manner similar to the lacI/IPTG system.

The cymR repressor appears to bind the complementary cmt operator more efficiently than lac repressor binds the lac operator, according to Choi, et al. in a recent (as of 2010) paper titled, "A novel, versatile, and tightly regulated expression system for E. Coli strains."

Thessaly 2021 Literature Characterization

Thessaly 2021contributed to the characterization of this part by adding new documentation learned from the literature highlighting why CymR is a better repressor for the cumate kill-switch.

CymR repressor belongs to the widespread and poorly characterized Rrf2 family of regulators. The rrf2-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 130 residues present in transcription regulators of the rrf2 family.("InterPro", 2021) The global regulator CymR represses the transcription of a large set of genes(Shepard, W.(2011)).

So, we chose CymR for our kill-switch because :

• It is characterized by little leakage
• It is sensitive while it is induced by small amounts of cumate
• It has high affinity as there is no other inducer
• Its inducer is non toxic, cheap
• It is reversible because in the absence of cumate it binds again in its CuO operator
• It is orthogonal as its inducer is not naturally found in gut

Kill switches are safety mechanisms needed to secure the desirable function of a biological system.There are many biological kill-switches used daily in synthetic systems in order to ensure the safety of environmental, human and animal health. In figure 1, we see the cumate gene switch system. It consists of a repressor, the CymR repressor, an operator site and a toxin. In the absence of cumate, CymR binds to the CuO operator and blocks the production of the target gene, a toxin in our case. On the other hand when cumate is present, it binds to the binding domain of CymR, losing its affinity for CuO, and so the target gene- toxin is expressed, killing the bacteria.This system allows for tight control of gene expression over a linear range in a cumate concentration dependent manner, which is particularly important for the expression of toxic proteins(Seo SO, Schmidt-Dannert C.(2019)).

Sequence and Features