Difference between revisions of "Part:BBa K4579033"
 
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<partinfo>BBa_K4579033 short</partinfo>
 
<partinfo>BBa_K4579033 short</partinfo>
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<h1>Introduction</h1>
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The 2023 UT Austin iGEM Team’s modular microcin expression parts collection includes parts necessary for engineering a bacterial chassis to secrete microcins, a type of small antimicrobial peptide. Our team has specifically designed parts to engineer a modular two-plasmid system that facilitates extracellular secretion of microcins by the chassis. One plasmid contains the microcin with a signal peptide sequence that indicates to the cell that the microcin is to be secreted. The other plasmid (pSK01) is from the literature (Kim et al., 2023) and contains genes for the proteins CvaA and CvaB, which are necessary to secrete small peptides using the <i>E. coli</i> microcin V (MccV) type I secretion system (T1SS) shown in Figure 2 of our <html><a href="https://2023.igem.wiki/austin-utexas/description">Project Description.</a></html>
  
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Following the part type standard of the Bee Toolkit, pBTK1028 is a type 56781 entry vector part that can be used to create assemblies by combining with type 2, 3, and 4 parts according to the BTK standard. This backbone was created for the BTK by Shaunak Kar, with permission for the UT iGEM team to use it as a basis for our composite part assemblies.
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Our parts collection includes a a selection of promoter (Type 2), coding sequence (Type 3), and terminator/regulatory gene (Type 4) parts that can be easily assembled to express microcins either constitutively or under inducible control. This allows for the modular engineering of microcin expression plasmids containing various microcins that can undergo extracellular secretion when used in conjunction with the secretion system plasmid pSK01.
  
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The first four bases of this part correspond to a type 5 part forward prefix, and the last four bases of this part correspond to a type 1 part reverse suffix. https://static.igem.wiki/teams/4579/wiki/btk-overhangs-low-ish-res.png
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<html><center><img src=https://static.igem.wiki/teams/4579/wiki/parts-collection-by-type.jpeg style="width:900px;height:auto;"></center></html>
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<center><b>Figure 1.</b> <i>Basic parts categorized by their BTK/YTK part type. Type 3p and 3q parts assemble as if they were a single Type 3 part.</i> </center>
  
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For additional info on the BTK standard, see: Leonard, S. P., Perutka, J., Powell, J. E., Geng, P., Richhart, D. D., Byrom, M., ... & Barrick, J. E. (2018). Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. <i>ACS Synthetic Biology, 7</i>(5), 1279-1290.
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Our basic and composite parts follow the Bee Toolkit/Yeast Toolkit standard of Golden Gate assembly (Lee et al., 2015; Leonard et al., 2018). Our assembly method involves the use of BsmBI digestion-ligation to create basic parts which can then be further digested with BsaI and ligated to form composite parts. The BTK/YTK standard includes part type-specific prefix and suffix overhangs generated by BsaI for each part, and these overhangs are NOT included in their sequences in the registry. For reference, our standard’s part type-specific overhangs are listed in Figure 2 on our <html><a href=" https://2023.igem.wiki/austin-utexas/parts">Parts page</a></html>.  
  
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<h1>Categorization</h1>
  
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<!-- Add more about the biology of this part here
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===Basic parts===
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===Usage and Biology===
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<ul>
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<li><b>Promoters (Type 2)</b> – Seven inducible promoters selected due to their relatively high dynamic range (Meyer et al., 2019) and apparent functionality in a variety of Proteobacteria (Schuster & Reisch, 2021), and one constitutive CP25 promoter (Leonard et al., 2018).</li>
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<li><b>Coding Sequences (Type 3)</b> – Signal peptide + microcin fusion coding sequences, a green fluorescent protein gene, and secretion system genes <i>cvaA</i> and <i>cvaB</i> which are together referred to as CvaAB.</li>
 +
 
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<li><b>Terminators/Regulatory Genes (Type 4)</b> – An <i>rpoC</i> terminator plus a collection of seven regulatory genes, each associated with one of our seven inducible promoters.</li>
 +
</ul>
 +
 
 +
===Composite parts===
 +
<ul>
 +
<li><b>Constitutive Microcin Expression Assemblies</b> - Assemblies of microcins (some with immunity proteins) with a constitutive CP25 promoter and <i>rpoC</i> terminator. These function alongside pSK01 in a two-plasmid secretion system, and we use these two-plasmid systems to assess if our novel microcins are effective inhibitors of pathogenic targets.</li>
 +
 
 +
<li><b>Inducible GFP Expression Assemblies</b> – Assemblies of GFP under the control of various inducible promoter systems. These were used to assess the dynamic range of our inducible promoter systems.</li>
 +
 
 +
<li><b>Inducible Microcin Expression Assemblies</b> – Assemblies of select microcins under the control of an inducible promoter system.</li>
 +
</ul>
 +
 
 +
 
 +
 
 +
<h1>Usage and Biology</h1>
 +
<html><center><img src=https://static.igem.wiki/teams/4579/wiki/gga-process.jpeg style="width:800px;height:auto;"></center></html>
 +
pBTK1028 is a Type 56781 part from the Bee Toolkit that has been used as the backbone of our team’s composite parts (<html><a href=" https://parts.igem.org/Part:BBa_K4579039">BBa_K4579039</a></html> – <html><a href=" https://parts.igem.org/Part:BBa_K4579061">BBa_K4579061</a></html>), and it contains an mScarlet fluorescent protein as a screening marker for cloning. This backbone can be combined with Type 2, 3, and 4 parts to produce a complete plasmid assembly. pBTK1028 can also be used as a BsmBI dropout vector for second stage assembly of parts beginning with the ConLS overhang and ending with the ConRE overhang. This backbone was created by Shaunak Kar from the Ellington lab at The University of Texas at Austin.
 +
 
 +
<h1>Design Notes</h1>
 +
This part was not designed by the UT Austin iGEM Team. It was designed by Shaunak Kar from the Ellington lab at The University of Texas at Austin.
 +
 
 +
<h1>Characterization</h1>
 +
<b>Disclaimer</b>: This part contains an illegal SapI site and is not meant to be used by others for assembly. This is simply the backbone of the composite parts that we tested for our assays.
 +
 
 +
This part was used as the backbone for all of our composite parts, which assembled correctly and showed expected functionality. Additionally, all composite parts in our registry collection have been sequence confirmed.
 +
 
 +
<h1>Source</h1>
 +
This part was designed for the Bee Toolkit (Leonard et al., 2018) by Shaunak Kar from the Ellington lab at The University of Texas at Austin.
 +
 
 +
<h1>References</h1>
 +
<ol>
 +
<li>Cole, T. J., Parker, J. K., Feller, A. L., Wilke, C. O., & Davies, B. W. (2022). Evidence for widespread class II microcins in Enterobacterales Genomes. <i>Applied and Environmental Microbiology, 88</i>(23), e01486-22.</li>
 +
 
 +
<li>Kim, S. Y., Parker, J. K., Gonzalez-Magaldi, M., Telford, M. S., Leahy, D. J., & Davies, B. W. (2023). Export of Diverse and Bioactive Small Proteins through a Type I Secretion System. <i>Applied and Environmental Microbiology, 89</i>(5), e00335-23.</li>
 +
 
 +
<li>Lee, M. E., DeLoache, W. C., Cervantes, B., & Dueber, J. E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. <i>ACS Synthetic Biology, 4</i>(9), 975-986.</li>
 +
 
 +
<li>Leonard, S. P., Perutka, J., Powell, J. E., Geng, P., Richhart, D. D., Byrom, M., Kar, S., Davies, B. W., Ellington, D. E., Moran, N. A., & Barrick, J. E. (2018). Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. <i>ACS Synthetic Biology, 7</i>(5), 1279-1290.</li>
 +
 
 +
<li>Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J., & Voigt, C. A. (2019). Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. <i>Nature Chemical Biology, 15</i>(2), 196-204.</li>
 +
 
 +
<li>Schuster, L. A., & Reisch, C. R. (2021). A plasmid toolbox for controlled gene expression across the Proteobacteria. <i>Nucleic Acids Research, 49</i>(12), 7189-7202.</li>
 +
</ol>
  
 
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<span class='h3bb'>Sequence and Features</span>
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<h1>Sequence and Features</h1>  
 
<partinfo>BBa_K4579033 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4579033 SequenceAndFeatures</partinfo>
  

Latest revision as of 08:59, 12 October 2023


pBTK1028 assembly backbone

Introduction

The 2023 UT Austin iGEM Team’s modular microcin expression parts collection includes parts necessary for engineering a bacterial chassis to secrete microcins, a type of small antimicrobial peptide. Our team has specifically designed parts to engineer a modular two-plasmid system that facilitates extracellular secretion of microcins by the chassis. One plasmid contains the microcin with a signal peptide sequence that indicates to the cell that the microcin is to be secreted. The other plasmid (pSK01) is from the literature (Kim et al., 2023) and contains genes for the proteins CvaA and CvaB, which are necessary to secrete small peptides using the E. coli microcin V (MccV) type I secretion system (T1SS) shown in Figure 2 of our Project Description.

Our parts collection includes a a selection of promoter (Type 2), coding sequence (Type 3), and terminator/regulatory gene (Type 4) parts that can be easily assembled to express microcins either constitutively or under inducible control. This allows for the modular engineering of microcin expression plasmids containing various microcins that can undergo extracellular secretion when used in conjunction with the secretion system plasmid pSK01.

Figure 1. Basic parts categorized by their BTK/YTK part type. Type 3p and 3q parts assemble as if they were a single Type 3 part.

Our basic and composite parts follow the Bee Toolkit/Yeast Toolkit standard of Golden Gate assembly (Lee et al., 2015; Leonard et al., 2018). Our assembly method involves the use of BsmBI digestion-ligation to create basic parts which can then be further digested with BsaI and ligated to form composite parts. The BTK/YTK standard includes part type-specific prefix and suffix overhangs generated by BsaI for each part, and these overhangs are NOT included in their sequences in the registry. For reference, our standard’s part type-specific overhangs are listed in Figure 2 on our Parts page.

Categorization

Basic parts

  • Promoters (Type 2) – Seven inducible promoters selected due to their relatively high dynamic range (Meyer et al., 2019) and apparent functionality in a variety of Proteobacteria (Schuster & Reisch, 2021), and one constitutive CP25 promoter (Leonard et al., 2018).
  • Coding Sequences (Type 3) – Signal peptide + microcin fusion coding sequences, a green fluorescent protein gene, and secretion system genes cvaA and cvaB which are together referred to as CvaAB.
  • Terminators/Regulatory Genes (Type 4) – An rpoC terminator plus a collection of seven regulatory genes, each associated with one of our seven inducible promoters.

Composite parts

  • Constitutive Microcin Expression Assemblies - Assemblies of microcins (some with immunity proteins) with a constitutive CP25 promoter and rpoC terminator. These function alongside pSK01 in a two-plasmid secretion system, and we use these two-plasmid systems to assess if our novel microcins are effective inhibitors of pathogenic targets.
  • Inducible GFP Expression Assemblies – Assemblies of GFP under the control of various inducible promoter systems. These were used to assess the dynamic range of our inducible promoter systems.
  • Inducible Microcin Expression Assemblies – Assemblies of select microcins under the control of an inducible promoter system.


Usage and Biology

pBTK1028 is a Type 56781 part from the Bee Toolkit that has been used as the backbone of our team’s composite parts (BBa_K4579039 – BBa_K4579061), and it contains an mScarlet fluorescent protein as a screening marker for cloning. This backbone can be combined with Type 2, 3, and 4 parts to produce a complete plasmid assembly. pBTK1028 can also be used as a BsmBI dropout vector for second stage assembly of parts beginning with the ConLS overhang and ending with the ConRE overhang. This backbone was created by Shaunak Kar from the Ellington lab at The University of Texas at Austin.

Design Notes

This part was not designed by the UT Austin iGEM Team. It was designed by Shaunak Kar from the Ellington lab at The University of Texas at Austin.

Characterization

Disclaimer: This part contains an illegal SapI site and is not meant to be used by others for assembly. This is simply the backbone of the composite parts that we tested for our assays.

This part was used as the backbone for all of our composite parts, which assembled correctly and showed expected functionality. Additionally, all composite parts in our registry collection have been sequence confirmed.

Source

This part was designed for the Bee Toolkit (Leonard et al., 2018) by Shaunak Kar from the Ellington lab at The University of Texas at Austin.

References

  1. Cole, T. J., Parker, J. K., Feller, A. L., Wilke, C. O., & Davies, B. W. (2022). Evidence for widespread class II microcins in Enterobacterales Genomes. Applied and Environmental Microbiology, 88(23), e01486-22.
  2. Kim, S. Y., Parker, J. K., Gonzalez-Magaldi, M., Telford, M. S., Leahy, D. J., & Davies, B. W. (2023). Export of Diverse and Bioactive Small Proteins through a Type I Secretion System. Applied and Environmental Microbiology, 89(5), e00335-23.
  3. Lee, M. E., DeLoache, W. C., Cervantes, B., & Dueber, J. E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. ACS Synthetic Biology, 4(9), 975-986.
  4. Leonard, S. P., Perutka, J., Powell, J. E., Geng, P., Richhart, D. D., Byrom, M., Kar, S., Davies, B. W., Ellington, D. E., Moran, N. A., & Barrick, J. E. (2018). Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids. ACS Synthetic Biology, 7(5), 1279-1290.
  5. Meyer, A. J., Segall-Shapiro, T. H., Glassey, E., Zhang, J., & Voigt, C. A. (2019). Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nature Chemical Biology, 15(2), 196-204.
  6. Schuster, L. A., & Reisch, C. R. (2021). A plasmid toolbox for controlled gene expression across the Proteobacteria. Nucleic Acids Research, 49(12), 7189-7202.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Plasmid lacks a prefix.
    Plasmid lacks a suffix.
    Illegal EcoRI site found at 2237
    Illegal XbaI site found at 1229
    Illegal XbaI site found at 2246
  • 12
    INCOMPATIBLE WITH RFC[12]
    Plasmid lacks a prefix.
    Plasmid lacks a suffix.
    Illegal EcoRI site found at 2237
    Illegal NheI site found at 2071
    Illegal NotI site found at 182
    Illegal NotI site found at 2225
  • 21
    INCOMPATIBLE WITH RFC[21]
    Plasmid lacks a prefix.
    Plasmid lacks a suffix.
    Illegal EcoRI site found at 2237
    Illegal BglII site found at 1070
  • 23
    INCOMPATIBLE WITH RFC[23]
    Plasmid lacks a prefix.
    Plasmid lacks a suffix.
    Illegal EcoRI site found at 2237
    Illegal XbaI site found at 1229
    Illegal XbaI site found at 2246
  • 25
    INCOMPATIBLE WITH RFC[25]
    Plasmid lacks a prefix.
    Plasmid lacks a suffix.
    Illegal EcoRI site found at 2237
    Illegal XbaI site found at 1229
    Illegal XbaI site found at 2246
    Illegal NgoMIV site found at 105
    Illegal NgoMIV site found at 406
    Illegal AgeI site found at 1661
    Illegal AgeI site found at 1985
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Plasmid lacks a prefix.
    Plasmid lacks a suffix.
    Illegal SapI site found at 346
    Illegal SapI site found at 556