Difference between revisions of "Part:BBa K3507002"
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<partinfo>BBa_K3507002 short</partinfo>
 
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YqcG has been characterized as an endonuclease shown to act as a DNase (Elbaz and Ben-Yehuda, 2015). YqcG together with the antitoxin YqcF are part of a toxin-antitoxin system of B. Subtillis. Toxin-antitoxin systems are modules comprised of a component that is toxic for the cell, and its counterpart, the antitoxin that has the ability of blocking the effect of the toxin. The YqcGF module is a type II toxin-antitoxin system characterised by the fact that both the components are proteins. YqcG was identified by Bloom-Ackermann et colleagues through homology search on CDI and Rhs systems and has first been described as a RNase. However, a more recent study that characterised this protein in more depth describes it as having DNase activity. The first study is a more general outlook on toxin antitoxin systems and their discovery through computational methods while the second one focuses mainly on YqcG and goes to the extent of creating DNA-less cells (cells that lost their chromosomal DNA) using this protein. Based on the experimental work of this studies we believe the second one which presents it as being a DNase is more likely the correct one. Regardless, both agree that YqcG has cytotoxic effects and is part of a toxin-antitoxin system.  
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YqcG has been characterized as an endonuclease shown to act as a DNase (Elbaz and Ben-Yehuda, 2015). YqcG together with the antitoxin YqcF are part of a toxin-antitoxin system of B. subtilis. Toxin-antitoxin systems are modules comprised of a component that is toxic for the cell, and its counterpart, the antitoxin that has the ability of blocking the effect of the toxin. The YqcGF module is a type II toxin-antitoxin system characterised by the fact that both the components are proteins. YqcG was identified by Bloom-Ackermann et colleagues through homology search on CDI and Rhs systems and has first been described as a RNase. However, a more recent study that characterised this protein in more depth describes it as having DNase activity. The first study is a more general outlook on toxin antitoxin systems and their discovery through computational methods while the second one focuses mainly on YqcG and goes to the extent of creating DNA-less cells (cells that lost their chromosomal DNA) using this protein. Based on the experimental work of this studies we believe the second one which presents it as being a DNase is more likely the correct one. Regardless, both agree that YqcG has cytotoxic effects and is part of a toxin-antitoxin system.  
 
We intend on using the YqcG protein as part of the kill-switch mechanism that will contain B. mycoides close to the potato roots. To achieve this, we intend on introducing the antitoxin in the bacterial chromosome and maintaining its expression constant under the control of a weak but constitutive promoter. Prior to this, we will also introduce (in the genome or a cytoplasmic plasmid) the antitoxin (YqcF) under the control of a solanine-dependent promoter. Of course, the success of this dependency system is based on a finely tuned expression level between the two components of the toxin-antitoxin system. Unfortunately, we are not able to perform experimental work that would allow us to implement and test the system but we hope that the literature based characterisation of these parts will allow future research in this direction.  
 
We intend on using the YqcG protein as part of the kill-switch mechanism that will contain B. mycoides close to the potato roots. To achieve this, we intend on introducing the antitoxin in the bacterial chromosome and maintaining its expression constant under the control of a weak but constitutive promoter. Prior to this, we will also introduce (in the genome or a cytoplasmic plasmid) the antitoxin (YqcF) under the control of a solanine-dependent promoter. Of course, the success of this dependency system is based on a finely tuned expression level between the two components of the toxin-antitoxin system. Unfortunately, we are not able to perform experimental work that would allow us to implement and test the system but we hope that the literature based characterisation of these parts will allow future research in this direction.  
  
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===Usage and Biology===
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_k3507002 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_k3507002 SequenceAndFeatures</partinfo>
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===Functional Parameters===
 
===Functional Parameters===
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<partinfo>BBa_K3507002 parameters</partinfo>
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<partinfo>BBa_k3507002 parameters</partinfo>
 
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[[File:T--Groningen--yqcgf.png|500px|thumb|centre|Figure 1. The interaction of the two components of the YqcGF system. (Adapted from Brantl et al., 2019)]]
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_k3507002 SequenceAndFeatures</partinfo>
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<h5>Bibliography</h5>
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<p>1.Bloom-Ackermann, Z.; Steinberg, N.; Rosenberg, G.; Oppenheimer-Shaanan, Y.; Pollack, D.; Ely, S.; Storzi, N.; Levy, A.; Kolodkin-Gal, I. Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in Bacillus subtilis biofilms. Environ. Microbiol. 2016, 18, 5032–5047.</p>
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<p>2.Elbaz, M.; Ben-Yehuda, S. Following the fate of bacterial cells experiencing sudden chromosome loss. MBio 2015, 6, e00092-15.</p>

Revision as of 15:24, 27 October 2020


Toxin part of a toxin-antitoxin system of B. subtilis

YqcG has been characterized as an endonuclease shown to act as a DNase (Elbaz and Ben-Yehuda, 2015). YqcG together with the antitoxin YqcF are part of a toxin-antitoxin system of B. subtilis. Toxin-antitoxin systems are modules comprised of a component that is toxic for the cell, and its counterpart, the antitoxin that has the ability of blocking the effect of the toxin. The YqcGF module is a type II toxin-antitoxin system characterised by the fact that both the components are proteins. YqcG was identified by Bloom-Ackermann et colleagues through homology search on CDI and Rhs systems and has first been described as a RNase. However, a more recent study that characterised this protein in more depth describes it as having DNase activity. The first study is a more general outlook on toxin antitoxin systems and their discovery through computational methods while the second one focuses mainly on YqcG and goes to the extent of creating DNA-less cells (cells that lost their chromosomal DNA) using this protein. Based on the experimental work of this studies we believe the second one which presents it as being a DNase is more likely the correct one. Regardless, both agree that YqcG has cytotoxic effects and is part of a toxin-antitoxin system. We intend on using the YqcG protein as part of the kill-switch mechanism that will contain B. mycoides close to the potato roots. To achieve this, we intend on introducing the antitoxin in the bacterial chromosome and maintaining its expression constant under the control of a weak but constitutive promoter. Prior to this, we will also introduce (in the genome or a cytoplasmic plasmid) the antitoxin (YqcF) under the control of a solanine-dependent promoter. Of course, the success of this dependency system is based on a finely tuned expression level between the two components of the toxin-antitoxin system. Unfortunately, we are not able to perform experimental work that would allow us to implement and test the system but we hope that the literature based characterisation of these parts will allow future research in this direction.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 1235
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 801


Figure 1. The interaction of the two components of the YqcGF system. (Adapted from Brantl et al., 2019)
Bibliography

1.Bloom-Ackermann, Z.; Steinberg, N.; Rosenberg, G.; Oppenheimer-Shaanan, Y.; Pollack, D.; Ely, S.; Storzi, N.; Levy, A.; Kolodkin-Gal, I. Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in Bacillus subtilis biofilms. Environ. Microbiol. 2016, 18, 5032–5047.

2.Elbaz, M.; Ben-Yehuda, S. Following the fate of bacterial cells experiencing sudden chromosome loss. MBio 2015, 6, e00092-15.