Difference between revisions of "Part:BBa K3198001"
 
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<partinfo>BBa_K3198001 short</partinfo>
 
<partinfo>BBa_K3198001 short</partinfo>
  
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This part contains the antitoxin component of a type II toxin-antitoxin (TA) system. It functions as an mRNA interferase antitoxin; overexpression prevents HicA-mediated cessation of cell growth and cell death.
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This part contains the antitoxin component of a type II toxin-antitoxin (TA) system.  
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HicB functions as an mRNA interferase antitoxin. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. HicB neutralizes HicA and therefore functions as an antitoxin. HicB could resuscitate cells inhibited by HicA.
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===Usage===
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<span class='h3bb'>Sequence and Features</span>
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HicB functions as an mRNA interferase antitoxin. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. HicB neutralizes HicA and therefore functions as an antitoxin. HicB could resuscitate cells inhibited by HicA.
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<partinfo>BBa_K3198001 SequenceAndFeatures</partinfo>
  
 +
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===Description===
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This part contains the antitoxin component of a type II toxin-antitoxin (TA) system. It functions as an mRNA interferase antitoxin; overexpression prevents HicA-mediated cessation of cell growth and cell death. Refer to our wiki https://2019.igem.org/Team:NUS_Singapore/Design#Characterization for more details.
 +
 +
===Usage===
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Team NUS Singapore 2019 has added a new biobrick (BBa_K3198001) into the iGEM repository this year. This biobrick was found to possess the ability to neutralize the effect of BBa_K3198000 and therefore functions as an antitoxin. For this reason, team NUS Singapore 2019 used this biobrick as part of their sleep-wake module to control the growth of <i>E. coli</i>. More specifically, to overcome the pre-induced dormant state of these cells.
  
 
===Biology===
 
===Biology===
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HicB is from hicAB locus of Escherichia coli K-12.  
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HicB is from hicAB locus of <i>Escherichia coli</i> K-12. HicB functions as an mRNA interferase antitoxin. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. HicB neutralizes HicA and therefore functions as an antitoxin. HicB could resuscitate cells inhibited by HicA.
  
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===Characterization===
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Since BBa_K3198001 has the ability to neutralize BBa_K3198000 in nature, team NUS Singapore 2019 hypothesized that the induction of both BBa_K3198001 and BBa_K3198000 would result in a growth curve that is comparable to that of control MG1655 which does not possess any plasmid.
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<br><br>To test this hypothesis, BBa_K3198001 was placed under an arabinose-inducible promoter and various arabinose concentrations were used to determine their ability to resume growth in native MG1655.
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<br><br>Characterization of cells transformed with this plasmid was performed at 37°C for 12h continuously. Both toxin and antitoxin inducers were added together at 0h, with IPTG and arabinose concentration fixed at 500μM and 26.6mM respectively.
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<br><br>After the addition of 500μM IPTG into cells co-transformed with BBa_K3198000 and BBa_K3198001 plasmid, it was shown that the cells were able to restore their growth back to the same level as control MG1655 (Figure 2). On the other hand, cells induced with 500μM IPTG only did not manage to show growth resumption in the absence of arabinose (Figure 1).
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<br><br>
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<html>
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<img style="width:400px" src="https://2019.igem.org/wiki/images/b/b2/T--NUS_Singapore--PartsRegistry_HicB1.png">
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</html>
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<br><i>Figure 1: Growth curve of control MG1655 unaffected by the addition of IPTG while MG1655 co-transformed with both plasmids observed a reduction in growth upon the addition of IPTG.</i>
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<br><br>
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<html>
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<img style="width:400px" src="https://2019.igem.org/wiki/images/5/53/T--NUS_Singapore--PartsRegistry_HicB2.png">
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</html>
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<br><i>Figure 2: MG1655 co-transformed with both plasmids demonstrated a normal growth curve which is comparable to control MG1655 when arabinose concentration of 26.6mM was added together with IPTG.</i>
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<br><br>To ensure that the comparison of cell growth between control MG1655 and MG1655 co-transformed with both plasmids is appropriate, the possible effect of IPTG and arabinose on the growth of control MG1655 was investigated. No significant effect was observed in both strains (Figure 3).
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<br><br>
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<html>
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<img style="width:400px" src="https://2019.igem.org/wiki/images/e/e9/T--NUS_Singapore--PartsRegistry_HicB3.png">
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</html>
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<br><i>Figure 3: Growth curve of control MG1655 when treated with various inducers.</i>
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<br><br>Taken together, these results demonstrate that BBa_K3198001 does indeed function as an antitoxin capable of neutralising BBa_K3198000 effect on native MG1655 growth.
  
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===Characterisation===
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===References===
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Team NUS 2019 has added another new biobrick (insert ID) into iGEM repository this year. This biobrick was found to possess the ability to neutralize the effect of HicA( biobrick id) and therefore functions as an antitoxin. For this reason, team NUS 2019 used this biobrick as part of their sleep-wake module to control the growth of E. coli in their project.
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Jorgensen, M. G., Pandey, D. P., Jaskolska, M., & Gerdes, K. (2008). HicA of Escherichia coli Defines a Novel Family of Translation-Independent mRNA Interferases in Bacteria and Archaea. Journal of Bacteriology, 191(4), 1191–1199. doi: 10.1128/jb.01013-08
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<br>(HicB ID) was placed under an arabinose-inducible promoter and various arabinose concentrations were used to determine their ability to resume cell growth native MG1655.
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<br><br>
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<br>Characterization of cells transformed with this plasmid was performed at 37°C for 12h continuously. Both toxin and antitoxin inducers were added together at 0h, with IPTG concentration fixed at 500uM with varying arabinose concentrations of 0M, 0.0266M, 0.133M and 0.266M.  
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Maisonneuve, E., Shakespeare, L. J., Jørgensen, M. G., & Gerdes, K. (2011). Bacterial persistence by RNA endonucleases. Proceedings of the National Academy of Sciences, 108(32), 13206–13211. doi: 10.1073/pnas.1100186108
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<br>After the addition of 500μM IPTG into cells co-transformed with (HicA ID) and (HicB ID) plasmid, it was shown that even at the lowest arabinose concentration of 0.0266M, the growth of the cells was able to restore to the same level as uninduced cells. On the other hand, cells only induced with 500μM IPTG did not managed to show growth resumption in the absence of arabinose. This demonstrated the function of (HicB ID) as an antitoxin capable of neutralising (HicA ID) effect on native MG1655 growth.  
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===Sources===
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BBa_K3198001 originated from E. coli K12 and its sequence was synthesized by IDT.
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===Design Considerations===
  
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<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
  
 
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K3198001 SequenceAndFeatures</partinfo>
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Latest revision as of 07:00, 21 October 2019


HicB

This part contains the antitoxin component of a type II toxin-antitoxin (TA) system.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 48
    Illegal BsaI.rc site found at 88


Description

This part contains the antitoxin component of a type II toxin-antitoxin (TA) system. It functions as an mRNA interferase antitoxin; overexpression prevents HicA-mediated cessation of cell growth and cell death. Refer to our wiki https://2019.igem.org/Team:NUS_Singapore/Design#Characterization for more details.

Usage

Team NUS Singapore 2019 has added a new biobrick (BBa_K3198001) into the iGEM repository this year. This biobrick was found to possess the ability to neutralize the effect of BBa_K3198000 and therefore functions as an antitoxin. For this reason, team NUS Singapore 2019 used this biobrick as part of their sleep-wake module to control the growth of E. coli. More specifically, to overcome the pre-induced dormant state of these cells.

Biology

HicB is from hicAB locus of Escherichia coli K-12. HicB functions as an mRNA interferase antitoxin. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. HicB neutralizes HicA and therefore functions as an antitoxin. HicB could resuscitate cells inhibited by HicA.

Characterization

Since BBa_K3198001 has the ability to neutralize BBa_K3198000 in nature, team NUS Singapore 2019 hypothesized that the induction of both BBa_K3198001 and BBa_K3198000 would result in a growth curve that is comparable to that of control MG1655 which does not possess any plasmid.

To test this hypothesis, BBa_K3198001 was placed under an arabinose-inducible promoter and various arabinose concentrations were used to determine their ability to resume growth in native MG1655.

Characterization of cells transformed with this plasmid was performed at 37°C for 12h continuously. Both toxin and antitoxin inducers were added together at 0h, with IPTG and arabinose concentration fixed at 500μM and 26.6mM respectively.

After the addition of 500μM IPTG into cells co-transformed with BBa_K3198000 and BBa_K3198001 plasmid, it was shown that the cells were able to restore their growth back to the same level as control MG1655 (Figure 2). On the other hand, cells induced with 500μM IPTG only did not manage to show growth resumption in the absence of arabinose (Figure 1).


Figure 1: Growth curve of control MG1655 unaffected by the addition of IPTG while MG1655 co-transformed with both plasmids observed a reduction in growth upon the addition of IPTG.


Figure 2: MG1655 co-transformed with both plasmids demonstrated a normal growth curve which is comparable to control MG1655 when arabinose concentration of 26.6mM was added together with IPTG.

To ensure that the comparison of cell growth between control MG1655 and MG1655 co-transformed with both plasmids is appropriate, the possible effect of IPTG and arabinose on the growth of control MG1655 was investigated. No significant effect was observed in both strains (Figure 3).


Figure 3: Growth curve of control MG1655 when treated with various inducers.

Taken together, these results demonstrate that BBa_K3198001 does indeed function as an antitoxin capable of neutralising BBa_K3198000 effect on native MG1655 growth.

References

Jorgensen, M. G., Pandey, D. P., Jaskolska, M., & Gerdes, K. (2008). HicA of Escherichia coli Defines a Novel Family of Translation-Independent mRNA Interferases in Bacteria and Archaea. Journal of Bacteriology, 191(4), 1191–1199. doi: 10.1128/jb.01013-08

Maisonneuve, E., Shakespeare, L. J., Jørgensen, M. G., & Gerdes, K. (2011). Bacterial persistence by RNA endonucleases. Proceedings of the National Academy of Sciences, 108(32), 13206–13211. doi: 10.1073/pnas.1100186108

Sources

BBa_K3198001 originated from E. coli K12 and its sequence was synthesized by IDT.

Design Considerations