Difference between revisions of "Part:BBa K4579003"
 
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<partinfo>BBa_K4579003 short</partinfo>
 
<partinfo>BBa_K4579003 short</partinfo>
  
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this part has a function of doing things
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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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===Usage and Biology===
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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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this part is used in frogs for mutation things
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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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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>
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<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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<h1>Usage and Biology</h1>
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This part consists of the P<sub>CymRC</sub> promoter upstream of a ribosome binding site, with a hammerhead ribozyme (HHRz) sequence included in the intervening 5' untranslated region to insulate gene expression levels from coding sequence effects on mRNA structure. This promoter can be bound by CymR (<html><a href="https://parts.igem.org/Part:BBa_K4579029">BBa_K4579029</a></html>), a transcriptional repressor that can be removed from the promoter when bound by cuminic acid, allowing for the selective induction of transcription in cells containing both P<sub>CymRC</sub> and the <i>CymR</i> gene. This part can be used as a Type 2 part in the BTK/YTK standard.
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==Composite Parts==
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<html><center><img src=https://static.igem.wiki/teams/4579/wiki/part-inducible-promoter.jpeg style="width:700px;height:auto;"></center></html>
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<center><b>Figure 2.</b> <i>The general schematic for our inducible microcin and GFP expression assemblies with emphasis on the inducible promoter. Although this example contains an immunity protein sequence, not all of our inducible microcin expression parts include an immunity protein.</i></center>
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<h1>Design Notes</h1>
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When creating our inducible promoter parts, we used the YFP-expressing individual sensor plasmids from the <i>E. coli</i> ‘Marionette’ paper as PCR templates (Meyer et al., 2019), as these include inducible promoters and their regulatory transcription factors on a standardized backbone. Due to the homology of the backbone between these plasmids, we created universal primers that allowed us to amplify the promoter from any one of the sensor plasmids. One big design complication in this process was the fact that the YFP-expressing sensor plasmids all contained a BsaI site in the region just upstream of the promoter where one of the universal primers would bind. We designed our primers to create a single point mutation in order to mutate out this illegal BsaI site.
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<h1>Characterization</h1>
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All parts uploaded to the registry by our team, including this one, have been sequence confirmed.
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<h1>Source</h1>
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This promoter part was amplified from <html><a href="http://www.addgene.org/108525/">pAJM.657</a></html> using PCR before being integrated into a basic part plasmid for use in our assemblies. pAJM.657 contains YFP under inducible control by P<sub>CymRC</sub> and CymR.
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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>
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<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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<h1>Sequence and Features</h1>
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===Sequence and Features===
 
===Sequence and Features===
 
<partinfo>BBa_K4579003 SequenceAndFeatures</partinfo>
 
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<partinfo>BBa_K4579003 parameters</partinfo>
 
<partinfo>BBa_K4579003 parameters</partinfo>
 
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===Characterization===

Latest revision as of 09:39, 12 October 2023


PCymRC promoter + RBS

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

This part consists of the PCymRC promoter upstream of a ribosome binding site, with a hammerhead ribozyme (HHRz) sequence included in the intervening 5' untranslated region to insulate gene expression levels from coding sequence effects on mRNA structure. This promoter can be bound by CymR (BBa_K4579029), a transcriptional repressor that can be removed from the promoter when bound by cuminic acid, allowing for the selective induction of transcription in cells containing both PCymRC and the CymR gene. This part can be used as a Type 2 part in the BTK/YTK standard.

Composite Parts

Figure 2. The general schematic for our inducible microcin and GFP expression assemblies with emphasis on the inducible promoter. Although this example contains an immunity protein sequence, not all of our inducible microcin expression parts include an immunity protein.


Design Notes

When creating our inducible promoter parts, we used the YFP-expressing individual sensor plasmids from the E. coli ‘Marionette’ paper as PCR templates (Meyer et al., 2019), as these include inducible promoters and their regulatory transcription factors on a standardized backbone. Due to the homology of the backbone between these plasmids, we created universal primers that allowed us to amplify the promoter from any one of the sensor plasmids. One big design complication in this process was the fact that the YFP-expressing sensor plasmids all contained a BsaI site in the region just upstream of the promoter where one of the universal primers would bind. We designed our primers to create a single point mutation in order to mutate out this illegal BsaI site.

Characterization

All parts uploaded to the registry by our team, including this one, have been sequence confirmed.

Source

This promoter part was amplified from pAJM.657 using PCR before being integrated into a basic part plasmid for use in our assemblies. pAJM.657 contains YFP under inducible control by PCymRC and CymR.

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


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]


Characterization