Difference between revisions of "Part:BBa K4579044"

 
 
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<partinfo>BBa_K4579044 short</partinfo>
 
<partinfo>BBa_K4579044 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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[long desc]
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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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<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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===Usage and Biology===
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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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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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===Basic parts===
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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>
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</ul>
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===Composite parts===
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<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>
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<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>
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<li><b>Inducible Microcin Expression Assemblies</b> – Assemblies of select microcins under the control of an inducible promoter system.</li>
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</ul>
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 +
 
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<h1>Usage and Biology</h1>
 +
 
 +
 
 +
<h1>Characterization</h1>
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To characterize this composite part, we transformed our chassis with both the microcin expression plasmid and the secretion system plasmid pSK01 (Kim et al., 2023). We then assessed the microcin's effectiveness against its target using Zone of Inhibition assays in which the transformed chassis or 'predator' strain was plated on agar containing the target pathogenic strain—or 'prey' strain. The results of these Zone of Inhibition assays for this microcin are shown below.
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<html><center><img src=https://static.igem.wiki/teams/4579/wiki/mcc06-1600-721-min.jpg style="width:700px;height:auto;"></center></html>
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Zone of inhibition plate with Pantoea ananatis PNA 97-1R lawn as ‘prey’ against E. coli DH5α strain containing Mcc06 expressing plasmid as the ‘predator’. Controls include empty chassis and strain containing microcin expressing plasmid but not secretion system plasmid
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<html><center><img src=https://static.igem.wiki/teams/4579/wiki/mcc06-1599-721-min.jpg style="width:700px;height:auto;"></center></html>
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Zone of inhibition plate with Pantoea allii PNA 200-100 lawn as ‘prey’ against E. coli DH5α strain containing Mcc06 expressing plasmid as the ‘predator’. Controls include empty chassis and strain containing microcin expressing plasmid but not secretion system plasmid.
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<h1>References</h1>
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<ol>
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<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>
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<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>
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 +
<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>
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 +
<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>
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<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>
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</ol>
  
 
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<span class='h3bb'>Sequence and Features</span>
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<h1>Sequence and Features</h1>  
 
<partinfo>BBa_K4579044 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4579044 SequenceAndFeatures</partinfo>
  

Latest revision as of 14:11, 12 October 2023


Constitutive Mcc05 expression plasmid

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


Characterization

To characterize this composite part, we transformed our chassis with both the microcin expression plasmid and the secretion system plasmid pSK01 (Kim et al., 2023). We then assessed the microcin's effectiveness against its target using Zone of Inhibition assays in which the transformed chassis or 'predator' strain was plated on agar containing the target pathogenic strain—or 'prey' strain. The results of these Zone of Inhibition assays for this microcin are shown below.

Zone of inhibition plate with Pantoea ananatis PNA 97-1R lawn as ‘prey’ against E. coli DH5α strain containing Mcc06 expressing plasmid as the ‘predator’. Controls include empty chassis and strain containing microcin expressing plasmid but not secretion system plasmid
Zone of inhibition plate with Pantoea allii PNA 200-100 lawn as ‘prey’ against E. coli DH5α strain containing Mcc06 expressing plasmid as the ‘predator’. Controls include empty chassis and strain containing microcin expressing plasmid but not secretion system plasmid.

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
    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
    COMPATIBLE WITH RFC[1000]