Difference between revisions of "Part:BBa K2507008"
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<partinfo>BBa_K2507008 short</partinfo>
 
<partinfo>BBa_K2507008 short</partinfo>
  
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== Background ==
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==Usage and Biology==
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<p>
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ThsS (BBa_K2507000) and ThsR (BBa_K2507001), both codon-optimized for <i>E. coli</i>, are two basic parts which belong to the two-component system from the marine bacterium <i>Shewanella halifaxensis</i>. ThsS is the membrane-bound sensor kinase (SK) which can sense thiosulfate outside the cell, and ThsR is the DNA-binding response regulator(RR). PphsA(BBa_K2507018) is a ThsR-activated promoter which is turned on when ThsR is phosphorylated by ThsS after ThsS senses thiosulfate.
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</p>
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<p>
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Because thiosulfate is an indicator of intestinal inflammation (Levitt et al, 1999; Jackson et al, 2012; Vitvitsky et al, 2015), this system can be used as a sensor for intestinal inflammation.
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</p>
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<!-- Add more about the biology of this part here
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===Usage and Biology===
  
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<html>
 
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<body>
 
  
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<p>
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<span class='h3bb'>Sequence and Features</span>
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This part contain a promoter J23105, ThsR coding which can response to the result of BBa_2507012 which contain a ThsS coding, promoter PphsA342 and sfGFP coding.
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<partinfo>BBa_K2507008 SequenceAndFeatures</partinfo>
  
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ThsR (BBa_K2507003) is the report part of the thiosulfate sensor which belong to the ThsS/R two-component system. This system is from S. typhimurium (Hensel et al, 1999; Price-Carter et al, 2001).
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==Characterization==
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After validating the system in the laboratory strains <i>Escherichia coli</i> Top10 and <i>E. coli</i> Nissle 1917, we confirmed that the system indeed works as a thiosulfate sensor, as intended. By linking <i>thsR</i> with <i>sfgfp</i> (BBa_K2507008), chromoprotein genes (BBa_K2507009, BBa_K2507010, BBa_K2507011) or the violacein producing operon vioABDE (BBa_K2507012), this system can respond to thiosulfate by producing a signal visible to the naked eye, either under normal or UV light, such as sfGFP, chromoproteins (spisPink-pink chromoprotein, gfasPurple-purple chromoprotein, amilCP-blue chromoprotein) or a dark-green small-molecule pigment (protoviolaceinic acid).
  
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Combining with BBa_2507012 which contain the ThsS coding, those two part can  produce GFP after they sense the existence of thiosulfate.

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[[File: SHSBNU 17 40a01.png|600px|thumb|center|Figure 1]]
  
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</p>
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Figure 1. Schematic diagram of the ligand-induced signaling through ThsS/R and the plasmid-borne implementation of the sensor components. ThsS/R was tested by introducing BBa_K2507004 into the pSB4K5 backbone and BBa_K2507008 into the pSB1C3 backbone. We submitted all of the parts to the iGEM registry in pSB1C3.
  
  
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</html>
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We first tested whether the system works as intended. Characterization experiments were performed aerobically. Bacteria were cultured overnight in a 96-deep-well-plate, with 1ml LB media + antibiotics + different concentrations of inducer (thiosulfate) in each well.
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<br/><br/>
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<!-- Add more about the biology of this part here
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===Usage and Biology===
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<html>
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<body>
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<!-- -->
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K2507008 SequenceAndFeatures</partinfo>
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<!-- Uncomment this to enable Functional Parameter display
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<b>The conclusion is that while the system (ThsS/ThsR) works, the leaky expression is rather heavy.</b><br/>
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===Functional Parameters===
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<partinfo>BBa_K2507008 parameters</partinfo>
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<html>
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<br/>
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<h2 id="results">Results</h2>
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<p>  </p>
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[[File: SHSBNU 17 40a02.jpg|600px|thumb|center|Figure 2]]
  
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<!--put yout result here-->
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Figure 2. Characterization of the ThsS/R system by observing the sfGFP expression levels. We added 1mM, 0.1mM, 0.01mM and 0 Na2S2O3. The results demonstrate a response with rather heavy leaky expression without inducer.
  
  
 +
Previously, Schmidl et al. have shown that <i>thsR</i> overexpression in the absence of the cognate SK and input can strongly activate the output promoter (Schmidl et al, 2014), possibly due to RR phosphorylation by alternative sources (small molecules, non-cognate SKs), or low-affinity binding by non-phosphorylated RRs.
  
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We realized that our thsR overexpression system is based on pSB4K5 which has several mutations in the pSC101 sequence, which means that pSB4K5 <b>is actually a high-copy plasmid! </b><br/>
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https://parts.igem.org/Part:pSB4K5:Experience
  
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Due to the limited time, we were not able to change the backbone to another low-copy plasmid, but we will certainly do it after the 2017 iGEM Jamboree.
 +
 +
Next, we characterized the system under aerobic and anaerobic conditions. We measured sfGFP intensity by flow cytometry. (http://2017.igem.org/Team:SHSBNU_China/Protocol). The response curves of <i>E. coli</i> Top10 under aerobic and anaerobic conditions seemed almost indistinguishable, while in <i>E. coli</i> Nissle 1917, the GFP expression level was different under aerobic and anaerobic conditions (Figure 5).
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 +
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[[File: SHSBNU 17 40a03.jpg|600px|thumb|center|Figure 3]]
 +
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Figure 3. We characterized the ThsS/R system in <i>E. coli</i> Top10 and <i>E. coli</i> Nissle 1917 by measuring the sfGFP expression levels via flow cytometry.
 +
 +
 +
[[File: SHSBNU 17 40a04.png|600px|thumb|center|Figure 4]]
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Figure 4. We characterized the ThsS/R system by flow cytometry. The response curve seems different.
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[[File: The_last_one.png|600px|thumb|center|Figure 5]]
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Figure5. We cultivated <i>E. coli</i> Nissle 1917 overnight under aerobic or anaerobic condition. Ths/R-sfGFP seems act better under anaerobic condition.
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==Reference==
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<p>
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Daeffler, K. N., Galley, J. D., Sheth, R. U., Ortiz‐Velez, L. C., Bibb, C. O., & Shroyer, N. F., et al. (2017). Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Molecular Systems Biology, 13(4), 923.
 
</p>
 
</p>
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<br/><br/>
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<p>
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</body>
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Jackson MR, Melideo SL, Jorns MS (2012) Human sulfide: quinone oxidoreductase catalyzes the first step in hydrogen sulfide metabolism and produces a sulfane sulfur metabolite. Biochemistry 51: 6804 – 6815
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</html>
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</p>
 +
<p>
 +
Levitt MD, Furne J, Springfield J, Suarez F, DeMaster E (1999) Detoxification of hydrogen sulfide and methanethiol in the cecal mucosa. J Clin Invest 104: 1107 – 1114
 +
</p>
 +
<p>
 +
Schmidl SR, Sheth RU, Wu A, Tabor JJ (2014) Refactoring and optimization of light-switchable Escherichia coli two-component systems. ACS Synth Biol 3: 820 – 831
 +
</p>
 +
<p>
 +
Vitvitsky V, Yadav PK, Kurthen A, Banerjee R (2015) Sulfide oxidation by a noncanonical pathway in red blood cells generates thiosulfate and polysulfides. J Biol Chem 290: 8310 – 8320
 +
</p>
 +
 
 +
<!-- Uncomment this to enable Functional Parameter display
 +
===Functional Parameters===
 +
<partinfo>BBa_K2507008 parameters</partinfo>
 +
<!-- -->

Latest revision as of 13:01, 1 November 2017


J23105-thsR-PphsA342-sfGFP

Usage and Biology

ThsS (BBa_K2507000) and ThsR (BBa_K2507001), both codon-optimized for E. coli, are two basic parts which belong to the two-component system from the marine bacterium Shewanella halifaxensis. ThsS is the membrane-bound sensor kinase (SK) which can sense thiosulfate outside the cell, and ThsR is the DNA-binding response regulator(RR). PphsA(BBa_K2507018) is a ThsR-activated promoter which is turned on when ThsR is phosphorylated by ThsS after ThsS senses thiosulfate.

Because thiosulfate is an indicator of intestinal inflammation (Levitt et al, 1999; Jackson et al, 2012; Vitvitsky et al, 2015), this system can be used as a sensor for intestinal inflammation.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 11
    Illegal NheI site found at 34
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 1313

Characterization

After validating the system in the laboratory strains Escherichia coli Top10 and E. coli Nissle 1917, we confirmed that the system indeed works as a thiosulfate sensor, as intended. By linking thsR with sfgfp (BBa_K2507008), chromoprotein genes (BBa_K2507009, BBa_K2507010, BBa_K2507011) or the violacein producing operon vioABDE (BBa_K2507012), this system can respond to thiosulfate by producing a signal visible to the naked eye, either under normal or UV light, such as sfGFP, chromoproteins (spisPink-pink chromoprotein, gfasPurple-purple chromoprotein, amilCP-blue chromoprotein) or a dark-green small-molecule pigment (protoviolaceinic acid).

Figure 1

Figure 1. Schematic diagram of the ligand-induced signaling through ThsS/R and the plasmid-borne implementation of the sensor components. ThsS/R was tested by introducing BBa_K2507004 into the pSB4K5 backbone and BBa_K2507008 into the pSB1C3 backbone. We submitted all of the parts to the iGEM registry in pSB1C3.


We first tested whether the system works as intended. Characterization experiments were performed aerobically. Bacteria were cultured overnight in a 96-deep-well-plate, with 1ml LB media + antibiotics + different concentrations of inducer (thiosulfate) in each well.


The conclusion is that while the system (ThsS/ThsR) works, the leaky expression is rather heavy.

Figure 2

Figure 2. Characterization of the ThsS/R system by observing the sfGFP expression levels. We added 1mM, 0.1mM, 0.01mM and 0 Na2S2O3. The results demonstrate a response with rather heavy leaky expression without inducer.


Previously, Schmidl et al. have shown that thsR overexpression in the absence of the cognate SK and input can strongly activate the output promoter (Schmidl et al, 2014), possibly due to RR phosphorylation by alternative sources (small molecules, non-cognate SKs), or low-affinity binding by non-phosphorylated RRs.

We realized that our thsR overexpression system is based on pSB4K5 which has several mutations in the pSC101 sequence, which means that pSB4K5 is actually a high-copy plasmid! 

https://parts.igem.org/Part:pSB4K5:Experience

Due to the limited time, we were not able to change the backbone to another low-copy plasmid, but we will certainly do it after the 2017 iGEM Jamboree.

Next, we characterized the system under aerobic and anaerobic conditions. We measured sfGFP intensity by flow cytometry. (http://2017.igem.org/Team:SHSBNU_China/Protocol). The response curves of E. coli Top10 under aerobic and anaerobic conditions seemed almost indistinguishable, while in E. coli Nissle 1917, the GFP expression level was different under aerobic and anaerobic conditions (Figure 5).


Figure 3

Figure 3. We characterized the ThsS/R system in E. coli Top10 and E. coli Nissle 1917 by measuring the sfGFP expression levels via flow cytometry.


Figure 4

Figure 4. We characterized the ThsS/R system by flow cytometry. The response curve seems different.


Figure 5

Figure5. We cultivated E. coli Nissle 1917 overnight under aerobic or anaerobic condition. Ths/R-sfGFP seems act better under anaerobic condition.

Reference

Daeffler, K. N., Galley, J. D., Sheth, R. U., Ortiz‐Velez, L. C., Bibb, C. O., & Shroyer, N. F., et al. (2017). Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Molecular Systems Biology, 13(4), 923.

Jackson MR, Melideo SL, Jorns MS (2012) Human sulfide: quinone oxidoreductase catalyzes the first step in hydrogen sulfide metabolism and produces a sulfane sulfur metabolite. Biochemistry 51: 6804 – 6815

Levitt MD, Furne J, Springfield J, Suarez F, DeMaster E (1999) Detoxification of hydrogen sulfide and methanethiol in the cecal mucosa. J Clin Invest 104: 1107 – 1114

Schmidl SR, Sheth RU, Wu A, Tabor JJ (2014) Refactoring and optimization of light-switchable Escherichia coli two-component systems. ACS Synth Biol 3: 820 – 831

Vitvitsky V, Yadav PK, Kurthen A, Banerjee R (2015) Sulfide oxidation by a noncanonical pathway in red blood cells generates thiosulfate and polysulfides. J Biol Chem 290: 8310 – 8320