Difference between revisions of "Part:BBa K1405008"
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===Introduction
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<p>Our kill switch is able to be “off” for a certain time for the bacteria to perform its function and then trigger the suicide progress spontaneously at a certain time.</p>
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<p>In the medium, the bacteria are easily controlled by adding or removing regulatory factors. However, when the bacteria perform its function in an unregulated environment, the suicide progress needs to be activated spontaneously. Moreover, the kill switch is supposed to be “off” for a certain time, so the bacteria will gain enough time to perform its function.</p>
  
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<p>Toxin protein MazF is the best candidate for us.</p><p></p>
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    <p>MazEF is a toxin-antitoxin module composed of mazE and mazF locating on the chromosome of E. Coli and other pathogens (Hanna et al, 2005). The expression product of mazF is a stable toxin, while that of mazE is a labile antitoxin of MazF (Hazan et al, 2004; Schusteret al., 2013). MazF is a sequence-specific mRNA endoribonuclease that initiates a programmed cell death pathway in response to various stresses. The mazEF-mediated death pathway can act as a defense mechanism that prevents the spread of bacterial phage infection, allowing bacterial populations to behave like multicellular organisms.</p>
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===Usage and Biology===
 
===Usage and Biology===

Revision as of 01:51, 18 October 2014

===Introduction

Our kill switch is able to be “off” for a certain time for the bacteria to perform its function and then trigger the suicide progress spontaneously at a certain time.

In the medium, the bacteria are easily controlled by adding or removing regulatory factors. However, when the bacteria perform its function in an unregulated environment, the suicide progress needs to be activated spontaneously. Moreover, the kill switch is supposed to be “off” for a certain time, so the bacteria will gain enough time to perform its function.

Toxin protein MazF is the best candidate for us.

MazEF is a toxin-antitoxin module composed of mazE and mazF locating on the chromosome of E. Coli and other pathogens (Hanna et al, 2005). The expression product of mazF is a stable toxin, while that of mazE is a labile antitoxin of MazF (Hazan et al, 2004; Schusteret al., 2013). MazF is a sequence-specific mRNA endoribonuclease that initiates a programmed cell death pathway in response to various stresses. The mazEF-mediated death pathway can act as a defense mechanism that prevents the spread of bacterial phage infection, allowing bacterial populations to behave like multicellular organisms.



Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]



Fig 1. Stable State

Fig 2. Killing State

Fig 3. Node Figure

Fig 4. Truth Table

We plan to establish a new E.Coli strain without lacI and MazEF system gene to avoid the inference of background expression. We will test cI background expression level to see if we need to knock out cI.

As is shown in Fig.1, Fig.2, Fig.3 and Fig.4, in the “Stable State”, before poured into the soil, the E. Coli fertilizer is cultured in the medium with IPTG. Promoter 1 is a weak constitutive promoter, so lacI is transcribed and translated at a considerate low level. Therefore, high concentration of IPTG, which binds LacI and changes LacI’s conformation, is able to inactive LacI and open the promoter 2. Then, CI can be highly expressed to repress promoter3. Finally, mazF is inhibited.

After fertilizing, no more IPTG exists in the soil to bind LacI. As a result, LacI with a tag which stabilize the protein takes time to accumulate to a certain high concentration, which is the repression threshold of promoter 2, aiming to represses promoter 2 as well as the expression of cI. The time needed to finish this progress is the designed “memory time”. During this process, E. coli takes its own responsibility to deliver Mo. And after that, it can be killed to reduce the pollution to environment.

As is shown in table 1, all the biobricks in the design are from the top 10 most used parts of iGEM to guarantee the feasibility.

Table 1 Biobricks used in the design

In the future, we plan to model the “memory time” and do more wet-experiments to confirm its feasibility. As for the modeling, we will test the expression level of promoter 1, the minimal stand of LacI to repress promoter 2 and the degradation speed of LacI. On the other hand, we will test the background expression of CI after removing IPTG to check if the CI concentration is low enough to open the promoter 3. Then we will strive to make this system more effective.

For more information, please go to our wiki:

http://2014.igem.org/Team:BNU-China/home.html


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]